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Experiment: Auxin induced in-vitro cambium initiation in Atrabidopsis thaliana

Experiment Description

NASCArrays Experiment Reference Number: NASCARRAYS-503

An in-vitro system has been used to induce Cambium initiation in Arabidopsis thaliana stems via Auxin treatments. A time course experiment has been performed and LCM harvested samples from different tissue types have been hybridized. The aim of the project is to isolate and characterize important regulators for cambium initiation.

About the Experimenter

Name:Dr Javier Agusti
Head of Lab Name:Dr Thomas Greb
Lab:
Address:Gregor Mendel Institute of Plant Molecular Biology, Austrian Academy of Sciences, Dr. Bohr-Gasse 3
Postcode: 1030
Country: Austria
 
Telephone Number: +43-(0)1-79044-9871
Fax Number: +43-(0)1-79044-23-9870

All of the data available in this website/database is free, and you are free to do whatever you please with it. If you intend to publish work based on any of this data, please acknowledge us, contact the experimenter above, and either acknowledge them or use them as co-authors in the work.

About this Experiment

Experiment Type: compound_treatment_design; time_series_design; strain_or_line_design
Number of Slides:24
 
Experimental Parameters:
parameterhormones
parametertimepoint
parametercell_type
Quality Control Measures Taken:
References:
 
Other Information:
titleAuxin induced in-vitro cambium initiation in Atrabidopsis thaliana

Slides in this Experiment

Hybridisation Set: Agusti: Auxin induced in-vitro cambium initiation in Atrabidopsis thaliana_genome

Slide: Agusti_0dSS1_SLD

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Summary BioSource 1 Information Extraction / Labelling Protocol for Source 1 Information Slide Information Hybridisation Analysis Information for "Affymetrix MAS 5.0 Scaling Protocol" normalised data.

Summary Information

This slide has had 1 extract(s) hybridised to it (1-colour).

  • Extract 1 ("Agusti_0dSS1_SRC") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

The slide used was "Affymetrix ATH1 Arabidopsis Genome Array".

Click on the options above for more information about this slide and its preparation.

Hybridisation Protocol Information

Name of Protocol: Affymetrix Antibody Amplification Protocol
Solution:
BufferEDTA, NaCl, Tween20 according to Affymetrix protocol
Water
Blocking Agent:
Herring Sperm DNA(Source: Promega)100pg/ml
Acetylated BSA(Source: Sigma-Aldrich)0.1mg/ml
Wash Procedure:
Step 1(Source: Affymetrix)10 cycles of 2 mixes/cycle with Non-Stringent buffer
Step 2(Source: Affymetrix)4 cycles of 15 mixes/cycle with Stringent buffer
Step 3(Source: Affymetrix)Stain the probe array for 10 minutes in Streptavaidin Phycoerythrin (SAPE) solution at 25 C
Step 4(Source: Affymetrix)10 cycles of 4 mixes/cycle with Non-Stringent buffer
Step 5(Source: Affymetrix)Stain the probe array for 10 minutes in antibody solution
Step 6(Source: Affymetrix)Stain the probe array for 10 minutes in SAPE solution at 25 C
Step 7(Source: Affymetrix)15 cycles of 4mixes/cycle with Non-Stringent buffer at 30 C
Step 8(Source: Affymetrix)Hold at 25 C
Quantity Used:
Amount15 microgram Fragmented cRNA
Time: 16 hours
Concentration: 50 pg/ml
Volume: 200 microlitres
Temperature: 45 C
Other Information:
Spike(Source: Affymetrix)Control Oligo B2 to 50pM for landing lights
Spike(Source: Affymetrix)20X Eukaryotic Hybridisation Controls (bioB (1.5pM, bioC 5pM, bioD 25pM, cre 100pM)
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

BioSource 1 Information

BioSource Name: Agusti_0dSS1_SRC
Organism: Arabidopsis thaliana
Alias: Columbia
Stock Code:
Growth Conditions:
ProtocolLayed out seeds were kept at 4°C for two days. Then, plants were grown for 3 weeks in short day conditions (8h light, 16h darkness) and then shifted into long day conditions (16h light, 8h darkness) to induce flowering.
Soil ConstituentsManufacturer: Frux. Composition: Standard.
Temperature22 °C average, 22.5 °C day, 21.5 °C night
Humidity61 % average, 63 % day, 59 % night
Medium
Lighting(Source: Cool white fluorescent manufactured by Philips. Intensity: 25µEinsteins. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)6.10
Tissue: Stem starch sheath layer + interfascicular fibers
in vivo Treatment: Stems from 15cm plants were harvested. Only plants which first internode was at least 5cm long were selected. Stems were surface sterylised and a 1.5cm sample located 2cm away from the rosette was separated for our experiments. The samples were rapidly embedded in OCT and frozen until used.
Additional Organism Information:
Sample Description15cm plants with a first internode at least 5cm long.
Other Information:
ecotype_habitat
Timecourse start procedureStart point was set when plant were collected.

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:4.227886
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
Spike_AFFX-r2-P1-cre_3-5-ratio1.277613
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.688355
Spike_AFFX-r2-Bs-dap_5_signal91.639282
NoiseAvg:2.57,Std:0.09,Min:2.3,Max:2.9
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal84.177589
#P7581
Spike_AFFX-r2-Bs-phe_M_signal73.457741
Corner-Avg:19925,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal1122.919678
Spike_AFFX-r2-Ec-bioB_3_signal1260.869141
Spike_AFFX-r2-Bs-lys_M_signal21.384819
Spike_AFFX-r2-P1-cre_3_signal40654.656250
Spike_AFFX-r2-Bs-lys_3-5-ratio2.725279
Spike_AFFX-r2-Bs-dap_M_signal244.556641
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.212141
Spike_AFFX-r2-Ec-bioB_avg-signal1043.530640
Spike_AFFX-r2-Bs-thr_avg-signal140.352829
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal12042.375977
Spike_AFFX-r2-Bs-phe_5_signal70.499969
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal14762.709961
RawQ2.667259
Spike_AFFX-r2-Bs-lys_5_signal23.335482
Signal(A)28.952093
%A63.279263
Signal(All)162.679398
Corner+Avg:173,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal3009.575195
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal93.326340
Spike_AFFX-r2-Ec-bioD_avg-signal13402.542969
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P33.235424
Spike_AFFX-r2-Bs-lys_avg-signal36.105331
Spike_AFFX-r2-P1-cre_avg-signal36237.726563
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionA
#Probe Sets Exceeding Probe Pair Threshold22810
%M3.485313
Spike_AFFX-r2-Bs-thr_3_signal186.212662
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal79.094688
Spike_AFFX-r2-Bs-dap_3_signal549.042297
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.225897
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal2446.666748
#M795
Spike_AFFX-r2-Bs-lys_5_detectionA
Spike_AFFX-r2-Bs-lys_3_signal63.595695
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.230072
Spike_AFFX-r2-Bs-thr_M_signal150.668228
Signal(P)423.759033
Spike_AFFX-r2-Bs-phe_3-5-ratio1.323778
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:17716,Count:9
Spike_AFFX-r2-P1-cre_5_signal31820.792969
Spike_AFFX-r2-Bs-phe_M_detectionM
#A14434
Signal(M)101.013176
BackgroundAvg:63.31,Std:0.87,Min:61.6,Max:65.9
Spike_AFFX-r2-Ec-bioC_avg-signal2728.121094
Spike_AFFX-r2-Bs-dap_avg-signal295.079407
Spike_AFFX-r2-Bs-dap_3-5-ratio5.991342
Spike_AFFX-r2-Ec-bioB_5_signal746.803223
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF4.227886
NF1.000000
HZ4
Tau0.015000

Slide: Agusti_0dSS2_SLD

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Summary BioSource 1 Information Extraction / Labelling Protocol for Source 1 Information Slide Information Hybridisation Analysis Information for "Affymetrix MAS 5.0 Scaling Protocol" normalised data.

Summary Information

This slide has had 1 extract(s) hybridised to it (1-colour).

  • Extract 1 ("Agusti_0dSS2_SRC") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

The slide used was "Affymetrix ATH1 Arabidopsis Genome Array".

Click on the options above for more information about this slide and its preparation.

Hybridisation Protocol Information

Name of Protocol: Affymetrix Antibody Amplification Protocol
Solution:
BufferEDTA, NaCl, Tween20 according to Affymetrix protocol
Water
Blocking Agent:
Herring Sperm DNA(Source: Promega)100pg/ml
Acetylated BSA(Source: Sigma-Aldrich)0.1mg/ml
Wash Procedure:
Step 1(Source: Affymetrix)10 cycles of 2 mixes/cycle with Non-Stringent buffer
Step 2(Source: Affymetrix)4 cycles of 15 mixes/cycle with Stringent buffer
Step 3(Source: Affymetrix)Stain the probe array for 10 minutes in Streptavaidin Phycoerythrin (SAPE) solution at 25 C
Step 4(Source: Affymetrix)10 cycles of 4 mixes/cycle with Non-Stringent buffer
Step 5(Source: Affymetrix)Stain the probe array for 10 minutes in antibody solution
Step 6(Source: Affymetrix)Stain the probe array for 10 minutes in SAPE solution at 25 C
Step 7(Source: Affymetrix)15 cycles of 4mixes/cycle with Non-Stringent buffer at 30 C
Step 8(Source: Affymetrix)Hold at 25 C
Quantity Used:
Amount15 microgram Fragmented cRNA
Time: 16 hours
Concentration: 50 pg/ml
Volume: 200 microlitres
Temperature: 45 C
Other Information:
Spike(Source: Affymetrix)Control Oligo B2 to 50pM for landing lights
Spike(Source: Affymetrix)20X Eukaryotic Hybridisation Controls (bioB (1.5pM, bioC 5pM, bioD 25pM, cre 100pM)
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

BioSource 1 Information

BioSource Name: Agusti_0dSS2_SRC
Organism: Arabidopsis thaliana
Alias: Columbia
Stock Code:
Growth Conditions:
ProtocolLayed out seeds were kept at 4°C for two days. Then, plants were grown for 3 weeks in short day conditions (8h light, 16h darkness) and then shifted into long day conditions (16h light, 8h darkness) to induce flowering.
Soil ConstituentsManufacturer: Frux. Composition: Standard.
Temperature22 °C average, 22.5 °C day, 21.5 °C night
Humidity61 % average, 63 % day, 59 % night
Medium
Lighting(Source: Cool white fluorescent manufactured by Philips. Intensity: 25µEinsteins. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)6.10
Tissue: Stem starch sheath layer + interfascicular fibers
in vivo Treatment: Stems from 15cm plants were harvested. Only plants which first internode was at least 5cm long were selected. Stems were surface sterylised and a 1.5cm sample located 2cm away from the rosette was separated for our experiments. The samples were rapidly embedded in OCT and frozen until used.
Additional Organism Information:
Sample Description15cm plants with a first internode at least 5cm long.
Other Information:
ecotype_habitat
Timecourse start procedureStart point was set when plant were collected.

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:16.556236
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
Spike_AFFX-r2-P1-cre_3-5-ratio1.126136
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.367496
Spike_AFFX-r2-Bs-dap_5_signal111.028534
NoiseAvg:2.69,Std:0.10,Min:2.5,Max:3.1
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal319.361755
#P1656
Spike_AFFX-r2-Bs-phe_M_signal172.653976
Corner-Avg:17579,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal5833.094727
Spike_AFFX-r2-Ec-bioB_3_signal5945.475586
Spike_AFFX-r2-Bs-lys_M_signal37.536942
Spike_AFFX-r2-P1-cre_3_signal157999.718750
Spike_AFFX-r2-Bs-lys_3-5-ratio34.846180
Spike_AFFX-r2-Bs-dap_M_signal390.113647
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio1.018895
Spike_AFFX-r2-Ec-bioB_avg-signal5375.427246
Spike_AFFX-r2-Bs-thr_avg-signal333.631409
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal53864.871094
Spike_AFFX-r2-Bs-phe_5_signal205.244064
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal69767.656250
RawQ2.828387
Spike_AFFX-r2-Bs-lys_5_signal5.431584
Signal(A)82.614525
%A90.863655
Signal(All)154.443039
Corner+Avg:154,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal13522.878906
Spike_AFFX-r2-Bs-lys_3_detectionA
Spike_AFFX-r2-Bs-phe_3_signal67.581192
Spike_AFFX-r2-Ec-bioD_avg-signal61816.265625
Spike_AFFX-r2-Bs-dap_5_detectionA
Spike_AFFX-r2-Bs-phe_5_detectionP
%P7.259974
Spike_AFFX-r2-Bs-lys_avg-signal77.412819
Spike_AFFX-r2-P1-cre_avg-signal149151.125000
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionA
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.876370
Spike_AFFX-r2-Bs-thr_3_signal325.395935
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionA
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal148.493088
Spike_AFFX-r2-Bs-dap_3_signal779.299500
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.295235
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal13633.052734
#M428
Spike_AFFX-r2-Bs-lys_5_detectionA
Spike_AFFX-r2-Bs-lys_3_signal189.269943
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.991919
Spike_AFFX-r2-Bs-thr_M_signal356.136566
Signal(P)1015.261902
Spike_AFFX-r2-Bs-phe_3-5-ratio0.329272
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:15065,Count:9
Spike_AFFX-r2-P1-cre_5_signal140302.531250
Spike_AFFX-r2-Bs-phe_M_detectionA
#A20726
Signal(M)302.110748
BackgroundAvg:68.44,Std:1.11,Min:66.1,Max:72.3
Spike_AFFX-r2-Ec-bioC_avg-signal13577.965820
Spike_AFFX-r2-Bs-dap_avg-signal426.813873
Spike_AFFX-r2-Bs-dap_3-5-ratio7.018912
Spike_AFFX-r2-Ec-bioB_5_signal4347.710449
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF16.556236
NF1.000000
HZ4
Tau0.015000

Slide: Agusti_0dSS3_SLD

Add to Slide Selection

Get the data!

Summary BioSource 1 Information Extraction / Labelling Protocol for Source 1 Information Slide Information Hybridisation Analysis Information for "Affymetrix MAS 5.0 Scaling Protocol" normalised data.

Summary Information

This slide has had 1 extract(s) hybridised to it (1-colour).

  • Extract 1 ("Agusti_0dSS3_SRC") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

The slide used was "Affymetrix ATH1 Arabidopsis Genome Array".

Click on the options above for more information about this slide and its preparation.

Hybridisation Protocol Information

Name of Protocol: Affymetrix Antibody Amplification Protocol
Solution:
BufferEDTA, NaCl, Tween20 according to Affymetrix protocol
Water
Blocking Agent:
Herring Sperm DNA(Source: Promega)100pg/ml
Acetylated BSA(Source: Sigma-Aldrich)0.1mg/ml
Wash Procedure:
Step 1(Source: Affymetrix)10 cycles of 2 mixes/cycle with Non-Stringent buffer
Step 2(Source: Affymetrix)4 cycles of 15 mixes/cycle with Stringent buffer
Step 3(Source: Affymetrix)Stain the probe array for 10 minutes in Streptavaidin Phycoerythrin (SAPE) solution at 25 C
Step 4(Source: Affymetrix)10 cycles of 4 mixes/cycle with Non-Stringent buffer
Step 5(Source: Affymetrix)Stain the probe array for 10 minutes in antibody solution
Step 6(Source: Affymetrix)Stain the probe array for 10 minutes in SAPE solution at 25 C
Step 7(Source: Affymetrix)15 cycles of 4mixes/cycle with Non-Stringent buffer at 30 C
Step 8(Source: Affymetrix)Hold at 25 C
Quantity Used:
Amount15 microgram Fragmented cRNA
Time: 16 hours
Concentration: 50 pg/ml
Volume: 200 microlitres
Temperature: 45 C
Other Information:
Spike(Source: Affymetrix)Control Oligo B2 to 50pM for landing lights
Spike(Source: Affymetrix)20X Eukaryotic Hybridisation Controls (bioB (1.5pM, bioC 5pM, bioD 25pM, cre 100pM)
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

BioSource 1 Information

BioSource Name: Agusti_0dSS3_SRC
Organism: Arabidopsis thaliana
Alias: Columbia
Stock Code:
Growth Conditions:
ProtocolLayed out seeds were kept at 4°C for two days. Then, plants were grown for 3 weeks in short day conditions (8h light, 16h darkness) and then shifted into long day conditions (16h light, 8h darkness) to induce flowering.
Soil ConstituentsManufacturer: Frux. Composition: Standard.
Temperature22 °C average, 22.5 °C day, 21.5 °C night
Humidity61 % average, 63 % day, 59 % night
Medium
Lighting(Source: Cool white fluorescent manufactured by Philips. Intensity: 25µEinsteins. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)6.10
Tissue: Stem starch sheath layer + interfascicular fibers
in vivo Treatment: Stems from 15cm plants were harvested. Only plants which first internode was at least 5cm long were selected. Stems were surface sterylised and a 1.5cm sample located 2cm away from the rosette was separated for our experiments. The samples were rapidly embedded in OCT and frozen until used.
Additional Organism Information:
Sample Description15cm plants with a first internode at least 5cm long.
Other Information:
ecotype_habitat
Timecourse start procedureStart point was set when plant were collected.

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:22.627508
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
Spike_AFFX-r2-P1-cre_3-5-ratio1.171960
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.788158
Spike_AFFX-r2-Bs-dap_5_signal333.142029
NoiseAvg:2.26,Std:0.26,Min:1.9,Max:3.7
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal159.786545
#P1242
Spike_AFFX-r2-Bs-phe_M_signal148.082245
Corner-Avg:17521,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal7001.203125
Spike_AFFX-r2-Ec-bioB_3_signal9120.503906
Spike_AFFX-r2-Bs-lys_M_signal9.595059
Spike_AFFX-r2-P1-cre_3_signal197406.359375
Spike_AFFX-r2-Bs-lys_3-5-ratio1.321058
Spike_AFFX-r2-Bs-dap_M_signal466.282013
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.138061
Spike_AFFX-r2-Ec-bioB_avg-signal7074.070313
Spike_AFFX-r2-Bs-thr_avg-signal373.790497
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal60634.121094
Spike_AFFX-r2-Bs-phe_5_signal242.213364
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal94050.859375
RawQ2.397511
Spike_AFFX-r2-Bs-lys_5_signal116.410492
Signal(A)88.816780
%A92.880318
Signal(All)157.125046
Corner+Avg:138,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal16714.917969
Spike_AFFX-r2-Bs-lys_3_detectionA
Spike_AFFX-r2-Bs-phe_3_signal190.682831
Spike_AFFX-r2-Ec-bioD_avg-signal77342.492188
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P5.444980
Spike_AFFX-r2-Bs-lys_avg-signal93.263527
Spike_AFFX-r2-P1-cre_avg-signal182923.750000
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionA
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.674704
Spike_AFFX-r2-Bs-thr_3_signal501.419891
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionA
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal193.659485
Spike_AFFX-r2-Bs-dap_3_signal887.204468
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.551121
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal17734.140625
#M382
Spike_AFFX-r2-Bs-lys_5_detectionA
Spike_AFFX-r2-Bs-lys_3_signal153.785034
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.942528
Spike_AFFX-r2-Bs-thr_M_signal460.165009
Signal(P)1280.011475
Spike_AFFX-r2-Bs-phe_3-5-ratio0.787251
Spike_AFFX-r2-Bs-thr_3_detectionA
Central-Avg:14855,Count:9
Spike_AFFX-r2-P1-cre_5_signal168441.156250
Spike_AFFX-r2-Bs-phe_M_detectionA
#A21186
Signal(M)294.700623
BackgroundAvg:55.60,Std:0.63,Min:54.2,Max:57.5
Spike_AFFX-r2-Ec-bioC_avg-signal17224.529297
Spike_AFFX-r2-Bs-dap_avg-signal562.209473
Spike_AFFX-r2-Bs-dap_3-5-ratio2.663142
Spike_AFFX-r2-Ec-bioB_5_signal5100.503418
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF22.627508
NF1.000000
HZ4
Tau0.015000

Slide: Agusti_0dC1_SLD

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Summary BioSource 1 Information Extraction / Labelling Protocol for Source 1 Information Slide Information Hybridisation Analysis Information for "Affymetrix MAS 5.0 Scaling Protocol" normalised data.

Summary Information

This slide has had 1 extract(s) hybridised to it (1-colour).

  • Extract 1 ("Agusti_0dC1_SRC") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

The slide used was "Affymetrix ATH1 Arabidopsis Genome Array".

Click on the options above for more information about this slide and its preparation.

Hybridisation Protocol Information

Name of Protocol: Affymetrix Antibody Amplification Protocol
Solution:
BufferEDTA, NaCl, Tween20 according to Affymetrix protocol
Water
Blocking Agent:
Herring Sperm DNA(Source: Promega)100pg/ml
Acetylated BSA(Source: Sigma-Aldrich)0.1mg/ml
Wash Procedure:
Step 1(Source: Affymetrix)10 cycles of 2 mixes/cycle with Non-Stringent buffer
Step 2(Source: Affymetrix)4 cycles of 15 mixes/cycle with Stringent buffer
Step 3(Source: Affymetrix)Stain the probe array for 10 minutes in Streptavaidin Phycoerythrin (SAPE) solution at 25 C
Step 4(Source: Affymetrix)10 cycles of 4 mixes/cycle with Non-Stringent buffer
Step 5(Source: Affymetrix)Stain the probe array for 10 minutes in antibody solution
Step 6(Source: Affymetrix)Stain the probe array for 10 minutes in SAPE solution at 25 C
Step 7(Source: Affymetrix)15 cycles of 4mixes/cycle with Non-Stringent buffer at 30 C
Step 8(Source: Affymetrix)Hold at 25 C
Quantity Used:
Amount15 microgram Fragmented cRNA
Time: 16 hours
Concentration: 50 pg/ml
Volume: 200 microlitres
Temperature: 45 C
Other Information:
Spike(Source: Affymetrix)Control Oligo B2 to 50pM for landing lights
Spike(Source: Affymetrix)20X Eukaryotic Hybridisation Controls (bioB (1.5pM, bioC 5pM, bioD 25pM, cre 100pM)
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

BioSource 1 Information

BioSource Name: Agusti_0dC1_SRC
Organism: Arabidopsis thaliana
Alias: Columbia
Stock Code:
Growth Conditions:
ProtocolLayed out seeds were kept at 4°C for two days. Then, plants were grown for 3 weeks in short day conditions (8h light, 16h darkness) and then shifted into long day conditions (16h light, 8h darkness) to induce flowering.
Soil ConstituentsManufacturer: Frux. Composition: Standard.
Temperature22 °C average, 22.5 °C day, 21.5 °C night
Humidity61 % average, 63 % day, 59 % night
Medium
Lighting(Source: Cool white fluorescent manufactured by Philips. Intensity: 25µEinsteins. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)6.10
Tissue: Stem except starch sheath layer and vascular bundles.
in vivo Treatment: Stems from 15cm plants were harvested. Only plants which first internode was at least 5cm long were selected. Stems were surface sterylised and a 1.5cm sample located 2cm away from the rosette was separated for our experiments. The samples were rapidly embedded in OCT and frozen until used.
Additional Organism Information:
Sample Description15cm plants with a first internode at least 5cm long.
Other Information:
ecotype_habitat
Timecourse start procedureStart point was set when plant were collected.

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:4.314348
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
Spike_AFFX-r2-P1-cre_3-5-ratio1.112705
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.525105
Spike_AFFX-r2-Bs-dap_5_signal87.728928
NoiseAvg:2.11,Std:0.05,Min:2.0,Max:2.2
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal49.770020
#P8906
Spike_AFFX-r2-Bs-phe_M_signal36.820072
Corner-Avg:17584,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal1104.222412
Spike_AFFX-r2-Ec-bioB_3_signal1180.026489
Spike_AFFX-r2-Bs-lys_M_signal31.196133
Spike_AFFX-r2-P1-cre_3_signal38907.406250
Spike_AFFX-r2-Bs-lys_3-5-ratio3.871189
Spike_AFFX-r2-Bs-dap_M_signal201.614075
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.888854
Spike_AFFX-r2-Ec-bioB_avg-signal1019.327942
Spike_AFFX-r2-Bs-thr_avg-signal118.649567
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal11854.013672
Spike_AFFX-r2-Bs-phe_5_signal53.522385
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal14041.365234
RawQ2.232263
Spike_AFFX-r2-Bs-lys_5_signal16.214472
Signal(A)22.743773
%A57.619465
Signal(All)159.098785
Corner+Avg:136,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal3059.133545
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal96.454468
Spike_AFFX-r2-Ec-bioD_avg-signal12947.689453
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P39.044277
Spike_AFFX-r2-Bs-lys_avg-signal36.726627
Spike_AFFX-r2-P1-cre_avg-signal36936.960938
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionA
#Probe Sets Exceeding Probe Pair Threshold22810
%M3.336256
Spike_AFFX-r2-Bs-thr_3_signal193.548355
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionA
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal62.265640
Spike_AFFX-r2-Bs-dap_3_signal598.479370
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.184524
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal2512.631104
#M761
Spike_AFFX-r2-Bs-lys_5_detectionM
Spike_AFFX-r2-Bs-lys_3_signal62.769283
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.217502
Spike_AFFX-r2-Bs-thr_M_signal112.630318
Signal(P)367.605194
Spike_AFFX-r2-Bs-phe_3-5-ratio1.802133
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:16088,Count:9
Spike_AFFX-r2-P1-cre_5_signal34966.515625
Spike_AFFX-r2-Bs-phe_M_detectionP
#A13143
Signal(M)73.889832
BackgroundAvg:52.56,Std:0.52,Min:51.6,Max:54.3
Spike_AFFX-r2-Ec-bioC_avg-signal2785.882324
Spike_AFFX-r2-Bs-dap_avg-signal295.940796
Spike_AFFX-r2-Bs-dap_3-5-ratio6.821916
Spike_AFFX-r2-Ec-bioB_5_signal773.734802
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF4.314348
NF1.000000
HZ4
Tau0.015000

Slide: Agusti_0dC2_SLD

Add to Slide Selection

Get the data!

Summary BioSource 1 Information Extraction / Labelling Protocol for Source 1 Information Slide Information Hybridisation Analysis Information for "Affymetrix MAS 5.0 Scaling Protocol" normalised data.

Summary Information

This slide has had 1 extract(s) hybridised to it (1-colour).

  • Extract 1 ("Agusti_0dC2_SRC") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

The slide used was "Affymetrix ATH1 Arabidopsis Genome Array".

Click on the options above for more information about this slide and its preparation.

Hybridisation Protocol Information

Name of Protocol: Affymetrix Antibody Amplification Protocol
Solution:
BufferEDTA, NaCl, Tween20 according to Affymetrix protocol
Water
Blocking Agent:
Herring Sperm DNA(Source: Promega)100pg/ml
Acetylated BSA(Source: Sigma-Aldrich)0.1mg/ml
Wash Procedure:
Step 1(Source: Affymetrix)10 cycles of 2 mixes/cycle with Non-Stringent buffer
Step 2(Source: Affymetrix)4 cycles of 15 mixes/cycle with Stringent buffer
Step 3(Source: Affymetrix)Stain the probe array for 10 minutes in Streptavaidin Phycoerythrin (SAPE) solution at 25 C
Step 4(Source: Affymetrix)10 cycles of 4 mixes/cycle with Non-Stringent buffer
Step 5(Source: Affymetrix)Stain the probe array for 10 minutes in antibody solution
Step 6(Source: Affymetrix)Stain the probe array for 10 minutes in SAPE solution at 25 C
Step 7(Source: Affymetrix)15 cycles of 4mixes/cycle with Non-Stringent buffer at 30 C
Step 8(Source: Affymetrix)Hold at 25 C
Quantity Used:
Amount15 microgram Fragmented cRNA
Time: 16 hours
Concentration: 50 pg/ml
Volume: 200 microlitres
Temperature: 45 C
Other Information:
Spike(Source: Affymetrix)Control Oligo B2 to 50pM for landing lights
Spike(Source: Affymetrix)20X Eukaryotic Hybridisation Controls (bioB (1.5pM, bioC 5pM, bioD 25pM, cre 100pM)
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

BioSource 1 Information

BioSource Name: Agusti_0dC2_SRC
Organism: Arabidopsis thaliana
Alias: Columbia
Stock Code:
Growth Conditions:
ProtocolLayed out seeds were kept at 4°C for two days. Then, plants were grown for 3 weeks in short day conditions (8h light, 16h darkness) and then shifted into long day conditions (16h light, 8h darkness) to induce flowering.
Soil ConstituentsManufacturer: Frux. Composition: Standard.
Temperature22 °C average, 22.5 °C day, 21.5 °C night
Humidity61 % average, 63 % day, 59 % night
Medium
Lighting(Source: Cool white fluorescent manufactured by Philips. Intensity: 25µEinsteins. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)6.10
Tissue: Stem except starch sheath layer and vascular bundles.
in vivo Treatment: Stems from 15cm plants were harvested. Only plants which first internode was at least 5cm long were selected. Stems were surface sterylised and a 1.5cm sample located 2cm away from the rosette was separated for our experiments. The samples were rapidly embedded in OCT and frozen until used.
Additional Organism Information:
Sample Description15cm plants with a first internode at least 5cm long.
Other Information:
ecotype_habitat
Timecourse start procedureStart point was set when plant were collected.

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:5.625166
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
Spike_AFFX-r2-P1-cre_3-5-ratio1.233182
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.416001
Spike_AFFX-r2-Bs-dap_5_signal70.280930
NoiseAvg:2.61,Std:0.10,Min:2.3,Max:2.9
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal44.705677
#P6351
Spike_AFFX-r2-Bs-phe_M_signal32.327190
Corner-Avg:18831,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal1770.204956
Spike_AFFX-r2-Ec-bioB_3_signal1795.832886
Spike_AFFX-r2-Bs-lys_M_signal79.822975
Spike_AFFX-r2-P1-cre_3_signal54566.804688
Spike_AFFX-r2-Bs-lys_3-5-ratio14.566704
Spike_AFFX-r2-Bs-dap_M_signal190.049438
Spike_AFFX-r2-Bs-thr_M_detectionM
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.886408
Spike_AFFX-r2-Ec-bioB_avg-signal1611.426880
Spike_AFFX-r2-Bs-thr_avg-signal94.483948
Spike_AFFX-r2-Bs-thr_5_detectionM
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal16043.761719
Spike_AFFX-r2-Bs-phe_5_signal31.248045
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal20520.763672
RawQ2.635026
Spike_AFFX-r2-Bs-lys_5_signal4.716101
Signal(A)37.951180
%A68.807541
Signal(All)155.950867
Corner+Avg:170,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal4344.712402
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal17.395382
Spike_AFFX-r2-Ec-bioD_avg-signal18282.261719
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionA
%P27.843052
Spike_AFFX-r2-Bs-lys_avg-signal51.079041
Spike_AFFX-r2-P1-cre_avg-signal49407.800781
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionA
#Probe Sets Exceeding Probe Pair Threshold22810
%M3.349408
Spike_AFFX-r2-Bs-thr_3_signal129.038803
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionA
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal26.990206
Spike_AFFX-r2-Bs-dap_3_signal436.392578
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.279049
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal3973.521973
#M764
Spike_AFFX-r2-Bs-lys_5_detectionA
Spike_AFFX-r2-Bs-lys_3_signal68.698044
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.093416
Spike_AFFX-r2-Bs-thr_M_signal109.707352
Signal(P)450.542480
Spike_AFFX-r2-Bs-phe_3-5-ratio0.556687
Spike_AFFX-r2-Bs-thr_3_detectionA
Central-Avg:14439,Count:9
Spike_AFFX-r2-P1-cre_5_signal44248.796875
Spike_AFFX-r2-Bs-phe_M_detectionA
#A15695
Signal(M)131.152176
BackgroundAvg:66.48,Std:1.91,Min:62.4,Max:72.4
Spike_AFFX-r2-Ec-bioC_avg-signal4159.117188
Spike_AFFX-r2-Bs-dap_avg-signal232.240982
Spike_AFFX-r2-Bs-dap_3-5-ratio6.209260
Spike_AFFX-r2-Ec-bioB_5_signal1268.242798
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF5.625166
NF1.000000
HZ4
Tau0.015000

Slide: Agusti_0dC3_SLD

Add to Slide Selection

Get the data!

Summary BioSource 1 Information Extraction / Labelling Protocol for Source 1 Information Slide Information Hybridisation Analysis Information for "Affymetrix MAS 5.0 Scaling Protocol" normalised data.

Summary Information

This slide has had 1 extract(s) hybridised to it (1-colour).

  • Extract 1 ("Agusti_0dC3_SRC") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

The slide used was "Affymetrix ATH1 Arabidopsis Genome Array".

Click on the options above for more information about this slide and its preparation.

Hybridisation Protocol Information

Name of Protocol: Affymetrix Antibody Amplification Protocol
Solution:
BufferEDTA, NaCl, Tween20 according to Affymetrix protocol
Water
Blocking Agent:
Herring Sperm DNA(Source: Promega)100pg/ml
Acetylated BSA(Source: Sigma-Aldrich)0.1mg/ml
Wash Procedure:
Step 1(Source: Affymetrix)10 cycles of 2 mixes/cycle with Non-Stringent buffer
Step 2(Source: Affymetrix)4 cycles of 15 mixes/cycle with Stringent buffer
Step 3(Source: Affymetrix)Stain the probe array for 10 minutes in Streptavaidin Phycoerythrin (SAPE) solution at 25 C
Step 4(Source: Affymetrix)10 cycles of 4 mixes/cycle with Non-Stringent buffer
Step 5(Source: Affymetrix)Stain the probe array for 10 minutes in antibody solution
Step 6(Source: Affymetrix)Stain the probe array for 10 minutes in SAPE solution at 25 C
Step 7(Source: Affymetrix)15 cycles of 4mixes/cycle with Non-Stringent buffer at 30 C
Step 8(Source: Affymetrix)Hold at 25 C
Quantity Used:
Amount15 microgram Fragmented cRNA
Time: 16 hours
Concentration: 50 pg/ml
Volume: 200 microlitres
Temperature: 45 C
Other Information:
Spike(Source: Affymetrix)Control Oligo B2 to 50pM for landing lights
Spike(Source: Affymetrix)20X Eukaryotic Hybridisation Controls (bioB (1.5pM, bioC 5pM, bioD 25pM, cre 100pM)
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

BioSource 1 Information

BioSource Name: Agusti_0dC3_SRC
Organism: Arabidopsis thaliana
Alias: Columbia
Stock Code:
Growth Conditions:
ProtocolLayed out seeds were kept at 4°C for two days. Then, plants were grown for 3 weeks in short day conditions (8h light, 16h darkness) and then shifted into long day conditions (16h light, 8h darkness) to induce flowering.
Soil ConstituentsManufacturer: Frux. Composition: Standard.
Temperature22 °C average, 22.5 °C day, 21.5 °C night
Humidity61 % average, 63 % day, 59 % night
Medium
Lighting(Source: Cool white fluorescent manufactured by Philips. Intensity: 25µEinsteins. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)6.10
Tissue: Stem except starch sheath layer and vascular bundles.
in vivo Treatment: Stems from 15cm plants were harvested. Only plants which first internode was at least 5cm long were selected. Stems were surface sterylised and a 1.5cm sample located 2cm away from the rosette was separated for our experiments. The samples were rapidly embedded in OCT and frozen until used.
Additional Organism Information:
Sample Description15cm plants with a first internode at least 5cm long.
Other Information:
ecotype_habitat
Timecourse start procedureStart point was set when plant were collected.

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:12.360315
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
Spike_AFFX-r2-P1-cre_3-5-ratio1.211602
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.613591
Spike_AFFX-r2-Bs-dap_5_signal222.166870
NoiseAvg:2.63,Std:0.13,Min:2.3,Max:3.0
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal202.334488
#P2637
Spike_AFFX-r2-Bs-phe_M_signal163.594940
Corner-Avg:9221,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal3573.522705
Spike_AFFX-r2-Ec-bioB_3_signal4498.481934
Spike_AFFX-r2-Bs-lys_M_signal14.052785
Spike_AFFX-r2-P1-cre_3_signal140188.625000
Spike_AFFX-r2-Bs-lys_3-5-ratio1.285966
Spike_AFFX-r2-Bs-dap_M_signal309.958618
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio1.641814
Spike_AFFX-r2-Ec-bioB_avg-signal3619.958252
Spike_AFFX-r2-Bs-thr_avg-signal314.779938
Spike_AFFX-r2-Bs-thr_5_detectionM
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal33426.078125
Spike_AFFX-r2-Bs-phe_5_signal31.059839
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal44449.761719
RawQ2.756773
Spike_AFFX-r2-Bs-lys_5_signal90.933479
Signal(A)72.312645
%A85.615959
Signal(All)153.067108
Corner+Avg:101,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal13453.291992
Spike_AFFX-r2-Bs-lys_3_detectionA
Spike_AFFX-r2-Bs-phe_3_signal172.612274
Spike_AFFX-r2-Ec-bioD_avg-signal38937.921875
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionA
%P11.560719
Spike_AFFX-r2-Bs-lys_avg-signal73.974525
Spike_AFFX-r2-P1-cre_avg-signal127946.914063
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionA
#Probe Sets Exceeding Probe Pair Threshold22810
%M2.823323
Spike_AFFX-r2-Bs-thr_3_signal332.195648
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionA
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal122.422356
Spike_AFFX-r2-Bs-dap_3_signal733.210266
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.329793
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal12463.041992
#M644
Spike_AFFX-r2-Bs-lys_5_detectionA
Spike_AFFX-r2-Bs-lys_3_signal116.937332
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.079455
Spike_AFFX-r2-Bs-thr_M_signal409.809692
Signal(P)726.166199
Spike_AFFX-r2-Bs-phe_3-5-ratio5.557410
Spike_AFFX-r2-Bs-thr_3_detectionM
Central-Avg:6328,Count:9
Spike_AFFX-r2-P1-cre_5_signal115705.203125
Spike_AFFX-r2-Bs-phe_M_detectionA
#A19529
Signal(M)255.228287
BackgroundAvg:67.91,Std:1.43,Min:64.4,Max:71.8
Spike_AFFX-r2-Ec-bioC_avg-signal12958.166992
Spike_AFFX-r2-Bs-dap_avg-signal421.778595
Spike_AFFX-r2-Bs-dap_3-5-ratio3.300268
Spike_AFFX-r2-Ec-bioB_5_signal2787.869629
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF12.360315
NF1.000000
HZ4
Tau0.015000

Slide: Agusti_2dNAA_SS1_SLD

Add to Slide Selection

Get the data!

Summary BioSource 1 Information Extraction / Labelling Protocol for Source 1 Information Slide Information Hybridisation Analysis Information for "Affymetrix MAS 5.0 Scaling Protocol" normalised data.

Summary Information

This slide has had 1 extract(s) hybridised to it (1-colour).

  • Extract 1 ("Agusti_2dNAA_SS1_SRC") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

The slide used was "Affymetrix ATH1 Arabidopsis Genome Array".

Click on the options above for more information about this slide and its preparation.

Hybridisation Protocol Information

Name of Protocol: Affymetrix Antibody Amplification Protocol
Solution:
BufferEDTA, NaCl, Tween20 according to Affymetrix protocol
Water
Blocking Agent:
Herring Sperm DNA(Source: Promega)100pg/ml
Acetylated BSA(Source: Sigma-Aldrich)0.1mg/ml
Wash Procedure:
Step 1(Source: Affymetrix)10 cycles of 2 mixes/cycle with Non-Stringent buffer
Step 2(Source: Affymetrix)4 cycles of 15 mixes/cycle with Stringent buffer
Step 3(Source: Affymetrix)Stain the probe array for 10 minutes in Streptavaidin Phycoerythrin (SAPE) solution at 25 C
Step 4(Source: Affymetrix)10 cycles of 4 mixes/cycle with Non-Stringent buffer
Step 5(Source: Affymetrix)Stain the probe array for 10 minutes in antibody solution
Step 6(Source: Affymetrix)Stain the probe array for 10 minutes in SAPE solution at 25 C
Step 7(Source: Affymetrix)15 cycles of 4mixes/cycle with Non-Stringent buffer at 30 C
Step 8(Source: Affymetrix)Hold at 25 C
Quantity Used:
Amount15 microgram Fragmented cRNA
Time: 16 hours
Concentration: 50 pg/ml
Volume: 200 microlitres
Temperature: 45 C
Other Information:
Spike(Source: Affymetrix)Control Oligo B2 to 50pM for landing lights
Spike(Source: Affymetrix)20X Eukaryotic Hybridisation Controls (bioB (1.5pM, bioC 5pM, bioD 25pM, cre 100pM)
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

BioSource 1 Information

BioSource Name: Agusti_2dNAA_SS1_SRC
Organism: Arabidopsis thaliana
Alias: Columbia
Stock Code:
Growth Conditions:
ProtocolLayed out seeds were kept at 4°C for two days. Then, plants were grown for 3 weeks in short day conditions (8h light, 16h darkness) and then shifted into long day conditions (16h light, 8h darkness) to induce flowering.
Soil ConstituentsManufacturer: Frux. Composition: Standard.
Temperature22 °C average, 22.5 °C day, 21.5 °C night
Humidity61 % average, 63 % day, 59 % night
Medium
Lighting(Source: Cool white fluorescent manufactured by Philips. Intensity: 25µEinsteins. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)6.10
Tissue: Stem starch sheath + interfascicular fibers.
in vivo Treatment: Stems from 15cm plants were harvested. Only plants which first internode was at least 5cm long were selected. Stems were surface sterylised and a 1.5cm sample located 2cm away from the rosette was separated for our experiments. The samples were then incubated with NAA in a MS split-plate. The samples were then rapidly embedded in OCT and frozen until used.
Additional Organism Information:
Sample Description15cm plants with a first internode at least 5cm long.
Other Information:
ecotype_habitat
Timecourse start procedureStart point was set when plant were collected.

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:5.153924
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
Spike_AFFX-r2-P1-cre_3-5-ratio1.194523
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.396847
Spike_AFFX-r2-Bs-dap_5_signal19.084408
NoiseAvg:2.77,Std:0.09,Min:2.5,Max:3.1
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal55.197151
#P6489
Spike_AFFX-r2-Bs-phe_M_signal52.084888
Corner-Avg:18227,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal1318.699219
Spike_AFFX-r2-Ec-bioB_3_signal1233.993530
Spike_AFFX-r2-Bs-lys_M_signal16.975618
Spike_AFFX-r2-P1-cre_3_signal47176.191406
Spike_AFFX-r2-Bs-lys_3-5-ratio2.236751
Spike_AFFX-r2-Bs-dap_M_signal142.226410
Spike_AFFX-r2-Bs-thr_M_detectionM
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.313586
Spike_AFFX-r2-Ec-bioB_avg-signal1145.368774
Spike_AFFX-r2-Bs-thr_avg-signal92.582588
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal13857.499023
Spike_AFFX-r2-Bs-phe_5_signal53.936920
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal16616.585938
RawQ2.903248
Spike_AFFX-r2-Bs-lys_5_signal19.911018
Signal(A)36.559872
%A68.009644
Signal(All)157.743210
Corner+Avg:161,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal3398.298096
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal63.617943
Spike_AFFX-r2-Ec-bioD_avg-signal15237.042969
Spike_AFFX-r2-Bs-dap_5_detectionA
Spike_AFFX-r2-Bs-phe_5_detectionA
%P28.448050
Spike_AFFX-r2-Bs-lys_avg-signal27.140871
Spike_AFFX-r2-P1-cre_avg-signal43334.972656
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionA
#Probe Sets Exceeding Probe Pair Threshold22810
%M3.542306
Spike_AFFX-r2-Bs-thr_3_signal127.703331
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionM
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal56.546585
Spike_AFFX-r2-Bs-dap_3_signal341.749847
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.199104
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal3088.726807
#M808
Spike_AFFX-r2-Bs-lys_5_detectionA
Spike_AFFX-r2-Bs-lys_3_signal44.535980
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.100226
Spike_AFFX-r2-Bs-thr_M_signal94.847290
Signal(P)451.669952
Spike_AFFX-r2-Bs-phe_3-5-ratio1.179488
Spike_AFFX-r2-Bs-thr_3_detectionA
Central-Avg:15326,Count:9
Spike_AFFX-r2-P1-cre_5_signal39493.753906
Spike_AFFX-r2-Bs-phe_M_detectionA
#A15513
Signal(M)123.865166
BackgroundAvg:70.31,Std:1.17,Min:68.1,Max:73.9
Spike_AFFX-r2-Ec-bioC_avg-signal3243.512451
Spike_AFFX-r2-Bs-dap_avg-signal167.686890
Spike_AFFX-r2-Bs-dap_3-5-ratio17.907280
Spike_AFFX-r2-Ec-bioB_5_signal883.413513
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF5.153924
NF1.000000
HZ4
Tau0.015000

Slide: Agusti_2dNAA_SS2_SLD

Add to Slide Selection

Get the data!

Summary BioSource 1 Information Extraction / Labelling Protocol for Source 1 Information Slide Information Hybridisation Analysis Information for "Affymetrix MAS 5.0 Scaling Protocol" normalised data.

Summary Information

This slide has had 1 extract(s) hybridised to it (1-colour).

  • Extract 1 ("Agusti_2dNAA_SS2_SRC") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

The slide used was "Affymetrix ATH1 Arabidopsis Genome Array".

Click on the options above for more information about this slide and its preparation.

Hybridisation Protocol Information

Name of Protocol: Affymetrix Antibody Amplification Protocol
Solution:
BufferEDTA, NaCl, Tween20 according to Affymetrix protocol
Water
Blocking Agent:
Herring Sperm DNA(Source: Promega)100pg/ml
Acetylated BSA(Source: Sigma-Aldrich)0.1mg/ml
Wash Procedure:
Step 1(Source: Affymetrix)10 cycles of 2 mixes/cycle with Non-Stringent buffer
Step 2(Source: Affymetrix)4 cycles of 15 mixes/cycle with Stringent buffer
Step 3(Source: Affymetrix)Stain the probe array for 10 minutes in Streptavaidin Phycoerythrin (SAPE) solution at 25 C
Step 4(Source: Affymetrix)10 cycles of 4 mixes/cycle with Non-Stringent buffer
Step 5(Source: Affymetrix)Stain the probe array for 10 minutes in antibody solution
Step 6(Source: Affymetrix)Stain the probe array for 10 minutes in SAPE solution at 25 C
Step 7(Source: Affymetrix)15 cycles of 4mixes/cycle with Non-Stringent buffer at 30 C
Step 8(Source: Affymetrix)Hold at 25 C
Quantity Used:
Amount15 microgram Fragmented cRNA
Time: 16 hours
Concentration: 50 pg/ml
Volume: 200 microlitres
Temperature: 45 C
Other Information:
Spike(Source: Affymetrix)Control Oligo B2 to 50pM for landing lights
Spike(Source: Affymetrix)20X Eukaryotic Hybridisation Controls (bioB (1.5pM, bioC 5pM, bioD 25pM, cre 100pM)
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

BioSource 1 Information

BioSource Name: Agusti_2dNAA_SS2_SRC
Organism: Arabidopsis thaliana
Alias: Columbia
Stock Code:
Growth Conditions:
ProtocolLayed out seeds were kept at 4°C for two days. Then, plants were grown for 3 weeks in short day conditions (8h light, 16h darkness) and then shifted into long day conditions (16h light, 8h darkness) to induce flowering.
Soil ConstituentsManufacturer: Frux. Composition: Standard.
Temperature22 °C average, 22.5 °C day, 21.5 °C night
Humidity61 % average, 63 % day, 59 % night
Medium
Lighting(Source: Cool white fluorescent manufactured by Philips. Intensity: 25µEinsteins. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)6.10
Tissue: Stem starch sheath + interfascicular fibers.
in vivo Treatment: Stems from 15cm plants were harvested. Only plants which first internode was at least 5cm long were selected. Stems were surface sterylised and a 1.5cm sample located 2cm away from the rosette was separated for our experiments. The samples were then incubated with NAA in a MS split-plate. The samples were then rapidly embedded in OCT and frozen until used.
Additional Organism Information:
Sample Description15cm plants with a first internode at least 5cm long.
Other Information:
ecotype_habitat
Timecourse start procedureStart point was set when plant were collected.

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:3.510536
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
Spike_AFFX-r2-P1-cre_3-5-ratio1.224098
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.545429
Spike_AFFX-r2-Bs-dap_5_signal82.132118
NoiseAvg:2.38,Std:0.06,Min:2.3,Max:2.6
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal26.042187
#P9122
Spike_AFFX-r2-Bs-phe_M_signal5.138700
Corner-Avg:18277,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal922.953857
Spike_AFFX-r2-Ec-bioB_3_signal975.061768
Spike_AFFX-r2-Bs-lys_M_signal15.177579
Spike_AFFX-r2-P1-cre_3_signal33741.964844
Spike_AFFX-r2-Bs-lys_3-5-ratio3.054280
Spike_AFFX-r2-Bs-dap_M_signal119.397865
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.805078
Spike_AFFX-r2-Ec-bioB_avg-signal842.982849
Spike_AFFX-r2-Bs-thr_avg-signal66.298393
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal9590.391602
Spike_AFFX-r2-Bs-phe_5_signal39.107368
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal11451.875977
RawQ2.441157
Spike_AFFX-r2-Bs-lys_5_signal15.532956
Signal(A)22.459595
%A56.729504
Signal(All)152.571640
Corner+Avg:143,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal2473.615479
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal32.977589
Spike_AFFX-r2-Ec-bioD_avg-signal10521.133789
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionA
%P39.991230
Spike_AFFX-r2-Bs-lys_avg-signal26.050844
Spike_AFFX-r2-P1-cre_avg-signal30653.367188
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionA
#Probe Sets Exceeding Probe Pair Threshold22810
%M3.279263
Spike_AFFX-r2-Bs-thr_3_signal99.092560
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionA
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal25.741219
Spike_AFFX-r2-Bs-dap_3_signal296.822876
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.194099
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal2263.652588
#M748
Spike_AFFX-r2-Bs-lys_5_detectionA
Spike_AFFX-r2-Bs-lys_3_signal47.442001
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.092754
Spike_AFFX-r2-Bs-thr_M_signal73.760437
Signal(P)343.352417
Spike_AFFX-r2-Bs-phe_3-5-ratio0.843258
Spike_AFFX-r2-Bs-thr_3_detectionA
Central-Avg:15888,Count:9
Spike_AFFX-r2-P1-cre_5_signal27564.767578
Spike_AFFX-r2-Bs-phe_M_detectionA
#A12940
Signal(M)76.833054
BackgroundAvg:58.37,Std:0.68,Min:57.4,Max:61.3
Spike_AFFX-r2-Ec-bioC_avg-signal2368.634033
Spike_AFFX-r2-Bs-dap_avg-signal166.117615
Spike_AFFX-r2-Bs-dap_3-5-ratio3.613968
Spike_AFFX-r2-Ec-bioB_5_signal630.932922
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF3.510536
NF1.000000
HZ4
Tau0.015000

Slide: Agusti_2dNAA_SS3_SLD

Add to Slide Selection

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Summary BioSource 1 Information Extraction / Labelling Protocol for Source 1 Information Slide Information Hybridisation Analysis Information for "Affymetrix MAS 5.0 Scaling Protocol" normalised data.

Summary Information

This slide has had 1 extract(s) hybridised to it (1-colour).

  • Extract 1 ("Agusti_2dNAA_SS3_SRC") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

The slide used was "Affymetrix ATH1 Arabidopsis Genome Array".

Click on the options above for more information about this slide and its preparation.

Hybridisation Protocol Information

Name of Protocol: Affymetrix Antibody Amplification Protocol
Solution:
BufferEDTA, NaCl, Tween20 according to Affymetrix protocol
Water
Blocking Agent:
Herring Sperm DNA(Source: Promega)100pg/ml
Acetylated BSA(Source: Sigma-Aldrich)0.1mg/ml
Wash Procedure:
Step 1(Source: Affymetrix)10 cycles of 2 mixes/cycle with Non-Stringent buffer
Step 2(Source: Affymetrix)4 cycles of 15 mixes/cycle with Stringent buffer
Step 3(Source: Affymetrix)Stain the probe array for 10 minutes in Streptavaidin Phycoerythrin (SAPE) solution at 25 C
Step 4(Source: Affymetrix)10 cycles of 4 mixes/cycle with Non-Stringent buffer
Step 5(Source: Affymetrix)Stain the probe array for 10 minutes in antibody solution
Step 6(Source: Affymetrix)Stain the probe array for 10 minutes in SAPE solution at 25 C
Step 7(Source: Affymetrix)15 cycles of 4mixes/cycle with Non-Stringent buffer at 30 C
Step 8(Source: Affymetrix)Hold at 25 C
Quantity Used:
Amount15 microgram Fragmented cRNA
Time: 16 hours
Concentration: 50 pg/ml
Volume: 200 microlitres
Temperature: 45 C
Other Information:
Spike(Source: Affymetrix)Control Oligo B2 to 50pM for landing lights
Spike(Source: Affymetrix)20X Eukaryotic Hybridisation Controls (bioB (1.5pM, bioC 5pM, bioD 25pM, cre 100pM)
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

BioSource 1 Information

BioSource Name: Agusti_2dNAA_SS3_SRC
Organism: Arabidopsis thaliana
Alias: Columbia
Stock Code:
Growth Conditions:
ProtocolLayed out seeds were kept at 4°C for two days. Then, plants were grown for 3 weeks in short day conditions (8h light, 16h darkness) and then shifted into long day conditions (16h light, 8h darkness) to induce flowering.
Soil ConstituentsManufacturer: Frux. Composition: Standard.
Temperature22 °C average, 22.5 °C day, 21.5 °C night
Humidity61 % average, 63 % day, 59 % night
Medium
Lighting(Source: Cool white fluorescent manufactured by Philips. Intensity: 25µEinsteins. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)6.10
Tissue: Stem starch sheath + interfascicular fibers.
in vivo Treatment: Stems from 15cm plants were harvested. Only plants which first internode was at least 5cm long were selected. Stems were surface sterylised and a 1.5cm sample located 2cm away from the rosette was separated for our experiments. The samples were then incubated with NAA in a MS split-plate. The samples were then rapidly embedded in OCT and frozen until used.
Additional Organism Information:
Sample Description15cm plants with a first internode at least 5cm long.
Other Information:
ecotype_habitat
Timecourse start procedureStart point was set when plant were collected.

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:3.902302
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
Spike_AFFX-r2-P1-cre_3-5-ratio1.176306
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.521546
Spike_AFFX-r2-Bs-dap_5_signal63.390598
NoiseAvg:2.50,Std:0.16,Min:2.1,Max:3.0
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal5.577913
#P8084
Spike_AFFX-r2-Bs-phe_M_signal15.097836
Corner-Avg:20631,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal1206.352905
Spike_AFFX-r2-Ec-bioB_3_signal1251.242798
Spike_AFFX-r2-Bs-lys_M_signal1.773976
Spike_AFFX-r2-P1-cre_3_signal38812.339844
Spike_AFFX-r2-Bs-lys_3-5-ratio5.554086
Spike_AFFX-r2-Bs-dap_M_signal118.071686
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio20.193228
Spike_AFFX-r2-Ec-bioB_avg-signal1093.315063
Spike_AFFX-r2-Bs-thr_avg-signal74.964424
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal11425.226563
Spike_AFFX-r2-Bs-phe_5_signal15.295177
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal14412.771484
RawQ2.556952
Spike_AFFX-r2-Bs-lys_5_signal12.978849
Signal(A)25.807030
%A61.266987
Signal(All)154.735703
Corner+Avg:167,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal2849.752930
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal67.874825
Spike_AFFX-r2-Ec-bioD_avg-signal12918.999023
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionA
%P35.440598
Spike_AFFX-r2-Bs-lys_avg-signal28.946157
Spike_AFFX-r2-P1-cre_avg-signal35903.722656
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionA
#Probe Sets Exceeding Probe Pair Threshold22810
%M3.292416
Spike_AFFX-r2-Bs-thr_3_signal112.636070
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionM
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal32.755947
Spike_AFFX-r2-Bs-dap_3_signal325.529175
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.261487
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal2892.479980
#M751
Spike_AFFX-r2-Bs-lys_5_detectionA
Spike_AFFX-r2-Bs-lys_3_signal72.085640
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.985228
Spike_AFFX-r2-Bs-thr_M_signal106.679291
Signal(P)383.108124
Spike_AFFX-r2-Bs-phe_3-5-ratio4.437662
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:16941,Count:9
Spike_AFFX-r2-P1-cre_5_signal32995.105469
Spike_AFFX-r2-Bs-phe_M_detectionA
#A13975
Signal(M)95.635391
BackgroundAvg:83.09,Std:1.41,Min:81.0,Max:86.9
Spike_AFFX-r2-Ec-bioC_avg-signal2871.116455
Spike_AFFX-r2-Bs-dap_avg-signal168.997147
Spike_AFFX-r2-Bs-dap_3-5-ratio5.135291
Spike_AFFX-r2-Ec-bioB_5_signal822.349365
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF3.902302
NF1.000000
HZ4
Tau0.015000

Slide: Agusti_2dNAA_C1_SLD

Add to Slide Selection

Get the data!

Summary BioSource 1 Information Extraction / Labelling Protocol for Source 1 Information Slide Information Hybridisation Analysis Information for "Affymetrix MAS 5.0 Scaling Protocol" normalised data.

Summary Information

This slide has had 1 extract(s) hybridised to it (1-colour).

  • Extract 1 ("Agusti_2dNAA_C1_SRC") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

The slide used was "Affymetrix ATH1 Arabidopsis Genome Array".

Click on the options above for more information about this slide and its preparation.

Hybridisation Protocol Information

Name of Protocol: Affymetrix Antibody Amplification Protocol
Solution:
BufferEDTA, NaCl, Tween20 according to Affymetrix protocol
Water
Blocking Agent:
Herring Sperm DNA(Source: Promega)100pg/ml
Acetylated BSA(Source: Sigma-Aldrich)0.1mg/ml
Wash Procedure:
Step 1(Source: Affymetrix)10 cycles of 2 mixes/cycle with Non-Stringent buffer
Step 2(Source: Affymetrix)4 cycles of 15 mixes/cycle with Stringent buffer
Step 3(Source: Affymetrix)Stain the probe array for 10 minutes in Streptavaidin Phycoerythrin (SAPE) solution at 25 C
Step 4(Source: Affymetrix)10 cycles of 4 mixes/cycle with Non-Stringent buffer
Step 5(Source: Affymetrix)Stain the probe array for 10 minutes in antibody solution
Step 6(Source: Affymetrix)Stain the probe array for 10 minutes in SAPE solution at 25 C
Step 7(Source: Affymetrix)15 cycles of 4mixes/cycle with Non-Stringent buffer at 30 C
Step 8(Source: Affymetrix)Hold at 25 C
Quantity Used:
Amount15 microgram Fragmented cRNA
Time: 16 hours
Concentration: 50 pg/ml
Volume: 200 microlitres
Temperature: 45 C
Other Information:
Spike(Source: Affymetrix)Control Oligo B2 to 50pM for landing lights
Spike(Source: Affymetrix)20X Eukaryotic Hybridisation Controls (bioB (1.5pM, bioC 5pM, bioD 25pM, cre 100pM)
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

BioSource 1 Information

BioSource Name: Agusti_2dNAA_C1_SRC
Organism: Arabidopsis thaliana
Alias: Columbia
Stock Code:
Growth Conditions:
ProtocolLayed out seeds were kept at 4°C for two days. Then, plants were grown for 3 weeks in short day conditions (8h light, 16h darkness) and then shifted into long day conditions (16h light, 8h darkness) to induce flowering.
Soil ConstituentsManufacturer: Frux. Composition: Standard.
Temperature22 °C average, 22.5 °C day, 21.5 °C night
Humidity61 % average, 63 % day, 59 % night
Medium
Lighting(Source: Cool white fluorescent manufactured by Philips. Intensity: 25µEinsteins. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)6.10
Tissue: Stem except stach sheath layer and vascular bundles.
in vivo Treatment: Stems from 15cm plants were harvested. Only plants which first internode was at least 5cm long were selected. Stems were surface sterylised and a 1.5cm sample located 2cm away from the rosette was separated for our experiments. The samples were then incubated with NAA in a MS split-plate. The samples were then rapidly embedded in OCT and frozen until used.
Additional Organism Information:
Sample Description15cm plants with a first internode at least 5cm long.
Other Information:
ecotype_habitat
Timecourse start procedureStart point was set when plant were collected.

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:4.570395
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
Spike_AFFX-r2-P1-cre_3-5-ratio1.178002
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.297812
Spike_AFFX-r2-Bs-dap_5_signal105.217567
NoiseAvg:2.51,Std:0.10,Min:2.3,Max:2.8
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal35.034653
#P7266
Spike_AFFX-r2-Bs-phe_M_signal50.690926
Corner-Avg:19558,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal1211.007568
Spike_AFFX-r2-Ec-bioB_3_signal1088.813477
Spike_AFFX-r2-Bs-lys_M_signal37.523861
Spike_AFFX-r2-P1-cre_3_signal44261.140625
Spike_AFFX-r2-Bs-lys_3-5-ratio1.150466
Spike_AFFX-r2-Bs-dap_M_signal256.613861
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio4.367930
Spike_AFFX-r2-Ec-bioB_avg-signal1046.260620
Spike_AFFX-r2-Bs-thr_avg-signal105.269798
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal12030.994141
Spike_AFFX-r2-Bs-phe_5_signal67.013496
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal17342.619141
RawQ2.612601
Spike_AFFX-r2-Bs-lys_5_signal68.509781
Signal(A)30.576321
%A65.037262
Signal(All)158.043060
Corner+Avg:162,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal2989.047852
Spike_AFFX-r2-Bs-lys_3_detectionM
Spike_AFFX-r2-Bs-phe_3_signal83.553307
Spike_AFFX-r2-Ec-bioD_avg-signal14686.806641
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P31.854450
Spike_AFFX-r2-Bs-lys_avg-signal61.617275
Spike_AFFX-r2-P1-cre_avg-signal40917.093750
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionM
#Probe Sets Exceeding Probe Pair Threshold22810
%M3.108286
Spike_AFFX-r2-Bs-thr_3_signal153.028915
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionM
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal67.085907
Spike_AFFX-r2-Bs-dap_3_signal433.663971
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.441495
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal3286.418945
#M709
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal78.818184
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.909515
Spike_AFFX-r2-Bs-thr_M_signal127.745789
Signal(P)423.722931
Spike_AFFX-r2-Bs-phe_3-5-ratio1.246813
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:15858,Count:9
Spike_AFFX-r2-P1-cre_5_signal37573.050781
Spike_AFFX-r2-Bs-phe_M_detectionP
#A14835
Signal(M)102.385880
BackgroundAvg:85.83,Std:1.27,Min:83.4,Max:89.2
Spike_AFFX-r2-Ec-bioC_avg-signal3137.733398
Spike_AFFX-r2-Bs-dap_avg-signal265.165131
Spike_AFFX-r2-Bs-dap_3-5-ratio4.121593
Spike_AFFX-r2-Ec-bioB_5_signal838.960815
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF4.570395
NF1.000000
HZ4
Tau0.015000

Slide: Agusti_2dNAA_C2_SLD

Add to Slide Selection

Get the data!

Summary BioSource 1 Information Extraction / Labelling Protocol for Source 1 Information Slide Information Hybridisation Analysis Information for "Affymetrix MAS 5.0 Scaling Protocol" normalised data.

Summary Information

This slide has had 1 extract(s) hybridised to it (1-colour).

  • Extract 1 ("Agusti_2dNAA_C2_SRC") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

The slide used was "Affymetrix ATH1 Arabidopsis Genome Array".

Click on the options above for more information about this slide and its preparation.

Hybridisation Protocol Information

Name of Protocol: Affymetrix Antibody Amplification Protocol
Solution:
BufferEDTA, NaCl, Tween20 according to Affymetrix protocol
Water
Blocking Agent:
Herring Sperm DNA(Source: Promega)100pg/ml
Acetylated BSA(Source: Sigma-Aldrich)0.1mg/ml
Wash Procedure:
Step 1(Source: Affymetrix)10 cycles of 2 mixes/cycle with Non-Stringent buffer
Step 2(Source: Affymetrix)4 cycles of 15 mixes/cycle with Stringent buffer
Step 3(Source: Affymetrix)Stain the probe array for 10 minutes in Streptavaidin Phycoerythrin (SAPE) solution at 25 C
Step 4(Source: Affymetrix)10 cycles of 4 mixes/cycle with Non-Stringent buffer
Step 5(Source: Affymetrix)Stain the probe array for 10 minutes in antibody solution
Step 6(Source: Affymetrix)Stain the probe array for 10 minutes in SAPE solution at 25 C
Step 7(Source: Affymetrix)15 cycles of 4mixes/cycle with Non-Stringent buffer at 30 C
Step 8(Source: Affymetrix)Hold at 25 C
Quantity Used:
Amount15 microgram Fragmented cRNA
Time: 16 hours
Concentration: 50 pg/ml
Volume: 200 microlitres
Temperature: 45 C
Other Information:
Spike(Source: Affymetrix)Control Oligo B2 to 50pM for landing lights
Spike(Source: Affymetrix)20X Eukaryotic Hybridisation Controls (bioB (1.5pM, bioC 5pM, bioD 25pM, cre 100pM)
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

BioSource 1 Information

BioSource Name: Agusti_2dNAA_C2_SRC
Organism: Arabidopsis thaliana
Alias: Columbia
Stock Code:
Growth Conditions:
ProtocolLayed out seeds were kept at 4°C for two days. Then, plants were grown for 3 weeks in short day conditions (8h light, 16h darkness) and then shifted into long day conditions (16h light, 8h darkness) to induce flowering.
Soil ConstituentsManufacturer: Frux. Composition: Standard.
Temperature22 °C average, 22.5 °C day, 21.5 °C night
Humidity61 % average, 63 % day, 59 % night
Medium
Lighting(Source: Cool white fluorescent manufactured by Philips. Intensity: 25µEinsteins. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)6.10
Tissue: Stem except stach sheath layer and vascular bundles.
in vivo Treatment: Stems from 15cm plants were harvested. Only plants which first internode was at least 5cm long were selected. Stems were surface sterylised and a 1.5cm sample located 2cm away from the rosette was separated for our experiments. The samples were then incubated with NAA in a MS split-plate. The samples were then rapidly embedded in OCT and frozen until used.
Additional Organism Information:
Sample Description15cm plants with a first internode at least 5cm long.
Other Information:
ecotype_habitat
Timecourse start procedureStart point was set when plant were collected.

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:4.699398
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
Spike_AFFX-r2-P1-cre_3-5-ratio1.186030
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.395571
Spike_AFFX-r2-Bs-dap_5_signal71.878075
NoiseAvg:2.54,Std:0.07,Min:2.4,Max:2.8
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal59.061073
#P7607
Spike_AFFX-r2-Bs-phe_M_signal18.266691
Corner-Avg:15073,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal952.816711
Spike_AFFX-r2-Ec-bioB_3_signal866.788391
Spike_AFFX-r2-Bs-lys_M_signal29.404657
Spike_AFFX-r2-P1-cre_3_signal34438.078125
Spike_AFFX-r2-Bs-lys_3-5-ratio0.513089
Spike_AFFX-r2-Bs-dap_M_signal143.262833
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.664791
Spike_AFFX-r2-Ec-bioB_avg-signal813.568176
Spike_AFFX-r2-Bs-thr_avg-signal121.911888
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal8629.992188
Spike_AFFX-r2-Bs-phe_5_signal23.331635
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal12606.458984
RawQ2.537683
Spike_AFFX-r2-Bs-lys_5_signal43.129433
Signal(A)29.750984
%A63.358177
Signal(All)149.356171
Corner+Avg:128,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal2445.824463
Spike_AFFX-r2-Bs-lys_3_detectionA
Spike_AFFX-r2-Bs-phe_3_signal50.914074
Spike_AFFX-r2-Ec-bioD_avg-signal10618.225586
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionA
%P33.349407
Spike_AFFX-r2-Bs-lys_avg-signal31.554438
Spike_AFFX-r2-P1-cre_avg-signal31737.253906
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionA
#Probe Sets Exceeding Probe Pair Threshold22810
%M3.292416
Spike_AFFX-r2-Bs-thr_3_signal157.385391
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionA
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal30.837465
Spike_AFFX-r2-Bs-dap_3_signal257.472626
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.460773
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal2374.935059
#M751
Spike_AFFX-r2-Bs-lys_5_detectionA
Spike_AFFX-r2-Bs-lys_3_signal22.129229
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.029849
Spike_AFFX-r2-Bs-thr_M_signal149.289200
Signal(P)381.967987
Spike_AFFX-r2-Bs-phe_3-5-ratio2.182191
Spike_AFFX-r2-Bs-thr_3_detectionA
Central-Avg:13901,Count:9
Spike_AFFX-r2-P1-cre_5_signal29036.431641
Spike_AFFX-r2-Bs-phe_M_detectionA
#A14452
Signal(M)94.837090
BackgroundAvg:86.94,Std:1.02,Min:85.2,Max:90.2
Spike_AFFX-r2-Ec-bioC_avg-signal2410.379883
Spike_AFFX-r2-Bs-dap_avg-signal157.537857
Spike_AFFX-r2-Bs-dap_3-5-ratio3.582075
Spike_AFFX-r2-Ec-bioB_5_signal621.099487
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF4.699398
NF1.000000
HZ4
Tau0.015000

Slide: Agusti_2dNAA_C3_SLD

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Summary BioSource 1 Information Extraction / Labelling Protocol for Source 1 Information Slide Information Hybridisation Analysis Information for "Affymetrix MAS 5.0 Scaling Protocol" normalised data.

Summary Information

This slide has had 1 extract(s) hybridised to it (1-colour).

  • Extract 1 ("Agusti_2dNAA_C3_SRC") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

The slide used was "Affymetrix ATH1 Arabidopsis Genome Array".

Click on the options above for more information about this slide and its preparation.

Hybridisation Protocol Information

Name of Protocol: Affymetrix Antibody Amplification Protocol
Solution:
BufferEDTA, NaCl, Tween20 according to Affymetrix protocol
Water
Blocking Agent:
Herring Sperm DNA(Source: Promega)100pg/ml
Acetylated BSA(Source: Sigma-Aldrich)0.1mg/ml
Wash Procedure:
Step 1(Source: Affymetrix)10 cycles of 2 mixes/cycle with Non-Stringent buffer
Step 2(Source: Affymetrix)4 cycles of 15 mixes/cycle with Stringent buffer
Step 3(Source: Affymetrix)Stain the probe array for 10 minutes in Streptavaidin Phycoerythrin (SAPE) solution at 25 C
Step 4(Source: Affymetrix)10 cycles of 4 mixes/cycle with Non-Stringent buffer
Step 5(Source: Affymetrix)Stain the probe array for 10 minutes in antibody solution
Step 6(Source: Affymetrix)Stain the probe array for 10 minutes in SAPE solution at 25 C
Step 7(Source: Affymetrix)15 cycles of 4mixes/cycle with Non-Stringent buffer at 30 C
Step 8(Source: Affymetrix)Hold at 25 C
Quantity Used:
Amount15 microgram Fragmented cRNA
Time: 16 hours
Concentration: 50 pg/ml
Volume: 200 microlitres
Temperature: 45 C
Other Information:
Spike(Source: Affymetrix)Control Oligo B2 to 50pM for landing lights
Spike(Source: Affymetrix)20X Eukaryotic Hybridisation Controls (bioB (1.5pM, bioC 5pM, bioD 25pM, cre 100pM)
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

BioSource 1 Information

BioSource Name: Agusti_2dNAA_C3_SRC
Organism: Arabidopsis thaliana
Alias: Columbia
Stock Code:
Growth Conditions:
ProtocolLayed out seeds were kept at 4°C for two days. Then, plants were grown for 3 weeks in short day conditions (8h light, 16h darkness) and then shifted into long day conditions (16h light, 8h darkness) to induce flowering.
Soil ConstituentsManufacturer: Frux. Composition: Standard.
Temperature22 °C average, 22.5 °C day, 21.5 °C night
Humidity61 % average, 63 % day, 59 % night
Medium
Lighting(Source: Cool white fluorescent manufactured by Philips. Intensity: 25µEinsteins. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)6.10
Tissue: Stem except stach sheath layer and vascular bundles.
in vivo Treatment: Stems from 15cm plants were harvested. Only plants which first internode was at least 5cm long were selected. Stems were surface sterylised and a 1.5cm sample located 2cm away from the rosette was separated for our experiments. The samples were then incubated with NAA in a MS split-plate. The samples were then rapidly embedded in OCT and frozen until used.
Additional Organism Information:
Sample Description15cm plants with a first internode at least 5cm long.
Other Information:
ecotype_habitat
Timecourse start procedureStart point was set when plant were collected.

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:3.903882
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
Spike_AFFX-r2-P1-cre_3-5-ratio1.187062
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.412111
Spike_AFFX-r2-Bs-dap_5_signal76.282135
NoiseAvg:2.22,Std:0.04,Min:2.1,Max:2.4
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal46.587425
#P8155
Spike_AFFX-r2-Bs-phe_M_signal37.041828
Corner-Avg:9731,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal981.256409
Spike_AFFX-r2-Ec-bioB_3_signal847.204895
Spike_AFFX-r2-Bs-lys_M_signal7.914635
Spike_AFFX-r2-P1-cre_3_signal37148.753906
Spike_AFFX-r2-Bs-lys_3-5-ratio1.502119
Spike_AFFX-r2-Bs-dap_M_signal126.200104
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.308108
Spike_AFFX-r2-Ec-bioB_avg-signal809.472473
Spike_AFFX-r2-Bs-thr_avg-signal111.365692
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal7874.647461
Spike_AFFX-r2-Bs-phe_5_signal25.366394
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal10761.130859
RawQ2.254125
Spike_AFFX-r2-Bs-lys_5_signal20.448477
Signal(A)27.300705
%A60.762825
Signal(All)155.119019
Corner+Avg:85,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal3985.595703
Spike_AFFX-r2-Bs-lys_3_detectionA
Spike_AFFX-r2-Bs-phe_3_signal77.118607
Spike_AFFX-r2-Ec-bioD_avg-signal9317.888672
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P35.751862
Spike_AFFX-r2-Bs-lys_avg-signal19.693054
Spike_AFFX-r2-P1-cre_avg-signal34221.726563
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionA
#Probe Sets Exceeding Probe Pair Threshold22810
%M3.485313
Spike_AFFX-r2-Bs-thr_3_signal154.116226
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionA
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal46.508942
Spike_AFFX-r2-Bs-dap_3_signal435.102325
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.366554
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal2373.359619
#M795
Spike_AFFX-r2-Bs-lys_5_detectionA
Spike_AFFX-r2-Bs-lys_3_signal30.716047
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.679305
Spike_AFFX-r2-Bs-thr_M_signal133.393402
Signal(P)378.931091
Spike_AFFX-r2-Bs-phe_3-5-ratio3.040188
Spike_AFFX-r2-Bs-thr_3_detectionM
Central-Avg:7572,Count:9
Spike_AFFX-r2-P1-cre_5_signal31294.699219
Spike_AFFX-r2-Bs-phe_M_detectionM
#A13860
Signal(M)87.665619
BackgroundAvg:75.62,Std:0.44,Min:74.1,Max:76.5
Spike_AFFX-r2-Ec-bioC_avg-signal3179.477539
Spike_AFFX-r2-Bs-dap_avg-signal212.528198
Spike_AFFX-r2-Bs-dap_3-5-ratio5.703856
Spike_AFFX-r2-Ec-bioB_5_signal599.956238
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF3.903882
NF1.000000
HZ4
Tau0.015000

Slide: Agusti_2dMS_SS1_SLD

Add to Slide Selection

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Summary BioSource 1 Information Extraction / Labelling Protocol for Source 1 Information Slide Information Hybridisation Analysis Information for "Affymetrix MAS 5.0 Scaling Protocol" normalised data.

Summary Information

This slide has had 1 extract(s) hybridised to it (1-colour).

  • Extract 1 ("Agusti_2dMS_SS1_SRC") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

The slide used was "Affymetrix ATH1 Arabidopsis Genome Array".

Click on the options above for more information about this slide and its preparation.

Hybridisation Protocol Information

Name of Protocol: Affymetrix Antibody Amplification Protocol
Solution:
BufferEDTA, NaCl, Tween20 according to Affymetrix protocol
Water
Blocking Agent:
Herring Sperm DNA(Source: Promega)100pg/ml
Acetylated BSA(Source: Sigma-Aldrich)0.1mg/ml
Wash Procedure:
Step 1(Source: Affymetrix)10 cycles of 2 mixes/cycle with Non-Stringent buffer
Step 2(Source: Affymetrix)4 cycles of 15 mixes/cycle with Stringent buffer
Step 3(Source: Affymetrix)Stain the probe array for 10 minutes in Streptavaidin Phycoerythrin (SAPE) solution at 25 C
Step 4(Source: Affymetrix)10 cycles of 4 mixes/cycle with Non-Stringent buffer
Step 5(Source: Affymetrix)Stain the probe array for 10 minutes in antibody solution
Step 6(Source: Affymetrix)Stain the probe array for 10 minutes in SAPE solution at 25 C
Step 7(Source: Affymetrix)15 cycles of 4mixes/cycle with Non-Stringent buffer at 30 C
Step 8(Source: Affymetrix)Hold at 25 C
Quantity Used:
Amount15 microgram Fragmented cRNA
Time: 16 hours
Concentration: 50 pg/ml
Volume: 200 microlitres
Temperature: 45 C
Other Information:
Spike(Source: Affymetrix)Control Oligo B2 to 50pM for landing lights
Spike(Source: Affymetrix)20X Eukaryotic Hybridisation Controls (bioB (1.5pM, bioC 5pM, bioD 25pM, cre 100pM)
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

BioSource 1 Information

BioSource Name: Agusti_2dMS_SS1_SRC
Organism: Arabidopsis thaliana
Alias: Columbia
Stock Code:
Growth Conditions:
ProtocolLayed out seeds were kept at 4°C for two days. Then, plants were grown for 3 weeks in short day conditions (8h light, 16h darkness) and then shifted into long day conditions (16h light, 8h darkness) to induce flowering.
Soil ConstituentsManufacturer: Frux. Composition: Standard.
Temperature22 °C average, 22.5 °C day, 21.5 °C night
Humidity61 % average, 63 % day, 59 % night
Medium
Lighting(Source: Cool white fluorescent manufactured by Philips. Intensity: 25µEinsteins. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)6.10
Tissue: Starch sheath + interfascicular fibers
in vivo Treatment: Stems from 15cm plants were harvested. Only plants which first internode was at least 5cm long were selected. Stems were surface sterylised and a 1.5cm sample located 2cm away from the rosette was separated for our experiments. The samples were then incubated in a MS split-plate. The samples were then rapidly embedded in OCT and frozen until used.
Additional Organism Information:
Sample Description15cm plants with a first internode at least 5cm long.
Other Information:
ecotype_habitat
Timecourse start procedureStart point was set when plant were collected.

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:5.379141
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
Spike_AFFX-r2-P1-cre_3-5-ratio1.183516
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.496648
Spike_AFFX-r2-Bs-dap_5_signal84.504730
NoiseAvg:2.68,Std:0.17,Min:2.4,Max:3.5
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal85.598007
#P6376
Spike_AFFX-r2-Bs-phe_M_signal67.395844
Corner-Avg:20465,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal1322.261353
Spike_AFFX-r2-Ec-bioB_3_signal1369.022095
Spike_AFFX-r2-Bs-lys_M_signal25.076107
Spike_AFFX-r2-P1-cre_3_signal47078.304688
Spike_AFFX-r2-Bs-lys_3-5-ratio1.338391
Spike_AFFX-r2-Bs-dap_M_signal214.730835
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.227428
Spike_AFFX-r2-Ec-bioB_avg-signal1202.002930
Spike_AFFX-r2-Bs-thr_avg-signal145.791626
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal18818.703125
Spike_AFFX-r2-Bs-phe_5_signal66.871559
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal24041.285156
RawQ2.703525
Spike_AFFX-r2-Bs-lys_5_signal51.231903
Signal(A)38.124943
%A68.877686
Signal(All)151.797821
Corner+Avg:161,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal4027.353516
Spike_AFFX-r2-Bs-lys_3_detectionA
Spike_AFFX-r2-Bs-phe_3_signal83.434532
Spike_AFFX-r2-Ec-bioD_avg-signal21429.994141
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P27.952652
Spike_AFFX-r2-Bs-lys_avg-signal48.292110
Spike_AFFX-r2-P1-cre_avg-signal43428.324219
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionA
#Probe Sets Exceeding Probe Pair Threshold22810
%M3.169662
Spike_AFFX-r2-Bs-thr_3_signal190.663437
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionA
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal72.567314
Spike_AFFX-r2-Bs-dap_3_signal527.721863
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.277521
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal3964.978271
#M723
Spike_AFFX-r2-Bs-lys_5_detectionA
Spike_AFFX-r2-Bs-lys_3_signal68.568321
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.015732
Spike_AFFX-r2-Bs-thr_M_signal161.113434
Signal(P)435.449890
Spike_AFFX-r2-Bs-phe_3-5-ratio1.247683
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:17852,Count:9
Spike_AFFX-r2-P1-cre_5_signal39778.343750
Spike_AFFX-r2-Bs-phe_M_detectionA
#A15711
Signal(M)120.468613
BackgroundAvg:66.65,Std:0.60,Min:65.2,Max:68.6
Spike_AFFX-r2-Ec-bioC_avg-signal3996.166016
Spike_AFFX-r2-Bs-dap_avg-signal275.652466
Spike_AFFX-r2-Bs-dap_3-5-ratio6.244880
Spike_AFFX-r2-Ec-bioB_5_signal914.725403
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF5.379141
NF1.000000
HZ4
Tau0.015000

Slide: Agusti_2dMS_SS2_SLD

Add to Slide Selection

Get the data!

Summary BioSource 1 Information Extraction / Labelling Protocol for Source 1 Information Slide Information Hybridisation Analysis Information for "Affymetrix MAS 5.0 Scaling Protocol" normalised data.

Summary Information

This slide has had 1 extract(s) hybridised to it (1-colour).

  • Extract 1 ("Agusti_2dMS_SS2_SRC") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

The slide used was "Affymetrix ATH1 Arabidopsis Genome Array".

Click on the options above for more information about this slide and its preparation.

Hybridisation Protocol Information

Name of Protocol: Affymetrix Antibody Amplification Protocol
Solution:
BufferEDTA, NaCl, Tween20 according to Affymetrix protocol
Water
Blocking Agent:
Herring Sperm DNA(Source: Promega)100pg/ml
Acetylated BSA(Source: Sigma-Aldrich)0.1mg/ml
Wash Procedure:
Step 1(Source: Affymetrix)10 cycles of 2 mixes/cycle with Non-Stringent buffer
Step 2(Source: Affymetrix)4 cycles of 15 mixes/cycle with Stringent buffer
Step 3(Source: Affymetrix)Stain the probe array for 10 minutes in Streptavaidin Phycoerythrin (SAPE) solution at 25 C
Step 4(Source: Affymetrix)10 cycles of 4 mixes/cycle with Non-Stringent buffer
Step 5(Source: Affymetrix)Stain the probe array for 10 minutes in antibody solution
Step 6(Source: Affymetrix)Stain the probe array for 10 minutes in SAPE solution at 25 C
Step 7(Source: Affymetrix)15 cycles of 4mixes/cycle with Non-Stringent buffer at 30 C
Step 8(Source: Affymetrix)Hold at 25 C
Quantity Used:
Amount15 microgram Fragmented cRNA
Time: 16 hours
Concentration: 50 pg/ml
Volume: 200 microlitres
Temperature: 45 C
Other Information:
Spike(Source: Affymetrix)Control Oligo B2 to 50pM for landing lights
Spike(Source: Affymetrix)20X Eukaryotic Hybridisation Controls (bioB (1.5pM, bioC 5pM, bioD 25pM, cre 100pM)
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

BioSource 1 Information

BioSource Name: Agusti_2dMS_SS2_SRC
Organism: Arabidopsis thaliana
Alias: Columbia
Stock Code:
Growth Conditions:
ProtocolLayed out seeds were kept at 4°C for two days. Then, plants were grown for 3 weeks in short day conditions (8h light, 16h darkness) and then shifted into long day conditions (16h light, 8h darkness) to induce flowering.
Soil ConstituentsManufacturer: Frux. Composition: Standard.
Temperature22 °C average, 22.5 °C day, 21.5 °C night
Humidity61 % average, 63 % day, 59 % night
Medium
Lighting(Source: Cool white fluorescent manufactured by Philips. Intensity: 25µEinsteins. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)6.10
Tissue: Starch sheath + interfascicular fibers
in vivo Treatment: Stems from 15cm plants were harvested. Only plants which first internode was at least 5cm long were selected. Stems were surface sterylised and a 1.5cm sample located 2cm away from the rosette was separated for our experiments. The samples were then incubated in a MS split-plate. The samples were then rapidly embedded in OCT and frozen until used.
Additional Organism Information:
Sample Description15cm plants with a first internode at least 5cm long.
Other Information:
ecotype_habitat
Timecourse start procedureStart point was set when plant were collected.

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:7.48915
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
Spike_AFFX-r2-P1-cre_3-5-ratio0.933781
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.513304
Spike_AFFX-r2-Bs-dap_5_signal207.701767
NoiseAvg:2.92,Std:0.13,Min:2.6,Max:3.3
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal15.521801
#P4853
Spike_AFFX-r2-Bs-phe_M_signal60.225895
Corner-Avg:17171,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal2204.280518
Spike_AFFX-r2-Ec-bioB_3_signal1935.620972
Spike_AFFX-r2-Bs-lys_M_signal3.027935
Spike_AFFX-r2-P1-cre_3_signal49386.003906
Spike_AFFX-r2-Bs-lys_3-5-ratio15.807755
Spike_AFFX-r2-Bs-dap_M_signal271.905640
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio10.836814
Spike_AFFX-r2-Ec-bioB_avg-signal1806.323730
Spike_AFFX-r2-Bs-thr_avg-signal152.140991
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal23868.695313
Spike_AFFX-r2-Bs-phe_5_signal34.882118
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal33908.671875
RawQ3.020419
Spike_AFFX-r2-Bs-lys_5_signal8.898486
Signal(A)50.118259
%A74.962738
Signal(All)149.512909
Corner+Avg:150,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal4740.309082
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal80.817703
Spike_AFFX-r2-Ec-bioD_avg-signal28888.683594
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionA
%P21.275757
Spike_AFFX-r2-Bs-lys_avg-signal50.863834
Spike_AFFX-r2-P1-cre_avg-signal51137.117188
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionA
#Probe Sets Exceeding Probe Pair Threshold22810
%M3.761508
Spike_AFFX-r2-Bs-thr_3_signal168.206863
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionA
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal58.641907
Spike_AFFX-r2-Bs-dap_3_signal526.786255
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.420634
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal5372.788574
#M858
Spike_AFFX-r2-Bs-lys_5_detectionA
Spike_AFFX-r2-Bs-lys_3_signal140.665085
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.882281
Spike_AFFX-r2-Bs-thr_M_signal272.694336
Signal(P)497.103180
Spike_AFFX-r2-Bs-phe_3-5-ratio2.316881
Spike_AFFX-r2-Bs-thr_3_detectionM
Central-Avg:13296,Count:9
Spike_AFFX-r2-P1-cre_5_signal52888.234375
Spike_AFFX-r2-Bs-phe_M_detectionA
#A17099
Signal(M)164.307297
BackgroundAvg:76.15,Std:1.20,Min:73.0,Max:79.3
Spike_AFFX-r2-Ec-bioC_avg-signal5056.548828
Spike_AFFX-r2-Bs-dap_avg-signal335.464569
Spike_AFFX-r2-Bs-dap_3-5-ratio2.536263
Spike_AFFX-r2-Ec-bioB_5_signal1279.069702
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF7.489150
NF1.000000
HZ4
Tau0.015000

Slide: Agusti_2dMS_SS3_SLD

Add to Slide Selection

Get the data!

Summary BioSource 1 Information Extraction / Labelling Protocol for Source 1 Information Slide Information Hybridisation Analysis Information for "Affymetrix MAS 5.0 Scaling Protocol" normalised data.

Summary Information

This slide has had 1 extract(s) hybridised to it (1-colour).

  • Extract 1 ("Agusti_2dMS_SS3_SRC") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

The slide used was "Affymetrix ATH1 Arabidopsis Genome Array".

Click on the options above for more information about this slide and its preparation.

Hybridisation Protocol Information

Name of Protocol: Affymetrix Antibody Amplification Protocol
Solution:
BufferEDTA, NaCl, Tween20 according to Affymetrix protocol
Water
Blocking Agent:
Herring Sperm DNA(Source: Promega)100pg/ml
Acetylated BSA(Source: Sigma-Aldrich)0.1mg/ml
Wash Procedure:
Step 1(Source: Affymetrix)10 cycles of 2 mixes/cycle with Non-Stringent buffer
Step 2(Source: Affymetrix)4 cycles of 15 mixes/cycle with Stringent buffer
Step 3(Source: Affymetrix)Stain the probe array for 10 minutes in Streptavaidin Phycoerythrin (SAPE) solution at 25 C
Step 4(Source: Affymetrix)10 cycles of 4 mixes/cycle with Non-Stringent buffer
Step 5(Source: Affymetrix)Stain the probe array for 10 minutes in antibody solution
Step 6(Source: Affymetrix)Stain the probe array for 10 minutes in SAPE solution at 25 C
Step 7(Source: Affymetrix)15 cycles of 4mixes/cycle with Non-Stringent buffer at 30 C
Step 8(Source: Affymetrix)Hold at 25 C
Quantity Used:
Amount15 microgram Fragmented cRNA
Time: 16 hours
Concentration: 50 pg/ml
Volume: 200 microlitres
Temperature: 45 C
Other Information:
Spike(Source: Affymetrix)Control Oligo B2 to 50pM for landing lights
Spike(Source: Affymetrix)20X Eukaryotic Hybridisation Controls (bioB (1.5pM, bioC 5pM, bioD 25pM, cre 100pM)
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

BioSource 1 Information

BioSource Name: Agusti_2dMS_SS3_SRC
Organism: Arabidopsis thaliana
Alias: Columbia
Stock Code:
Growth Conditions:
ProtocolLayed out seeds were kept at 4°C for two days. Then, plants were grown for 3 weeks in short day conditions (8h light, 16h darkness) and then shifted into long day conditions (16h light, 8h darkness) to induce flowering.
Soil ConstituentsManufacturer: Frux. Composition: Standard.
Temperature22 °C average, 22.5 °C day, 21.5 °C night
Humidity61 % average, 63 % day, 59 % night
Medium
Lighting(Source: Cool white fluorescent manufactured by Philips. Intensity: 25µEinsteins. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)6.10
Tissue: Starch sheath + interfascicular fibers
in vivo Treatment: Stems from 15cm plants were harvested. Only plants which first internode was at least 5cm long were selected. Stems were surface sterylised and a 1.5cm sample located 2cm away from the rosette was separated for our experiments. The samples were then incubated in a MS split-plate. The samples were then rapidly embedded in OCT and frozen until used.
Additional Organism Information:
Sample Description15cm plants with a first internode at least 5cm long.
Other Information:
ecotype_habitat
Timecourse start procedureStart point was set when plant were collected.

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:6.075945
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
Spike_AFFX-r2-P1-cre_3-5-ratio1.198112
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.936361
Spike_AFFX-r2-Bs-dap_5_signal7.974338
NoiseAvg:2.65,Std:0.07,Min:2.5,Max:2.9
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal81.089516
#P6407
Spike_AFFX-r2-Bs-phe_M_signal6.612871
Corner-Avg:17022,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal1494.371216
Spike_AFFX-r2-Ec-bioB_3_signal1505.871216
Spike_AFFX-r2-Bs-lys_M_signal61.836300
Spike_AFFX-r2-P1-cre_3_signal47412.425781
Spike_AFFX-r2-Bs-lys_3-5-ratio0.793872
Spike_AFFX-r2-Bs-dap_M_signal167.417679
Spike_AFFX-r2-Bs-thr_M_detectionM
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio1.593001
Spike_AFFX-r2-Ec-bioB_avg-signal1259.307739
Spike_AFFX-r2-Bs-thr_avg-signal105.394684
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal17950.876953
Spike_AFFX-r2-Bs-phe_5_signal43.935284
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal27036.726563
RawQ2.710541
Spike_AFFX-r2-Bs-lys_5_signal75.979034
Signal(A)39.654793
%A68.342834
Signal(All)150.393021
Corner+Avg:150,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal3762.588135
Spike_AFFX-r2-Bs-lys_3_detectionA
Spike_AFFX-r2-Bs-phe_3_signal87.373489
Spike_AFFX-r2-Ec-bioD_avg-signal22493.800781
Spike_AFFX-r2-Bs-dap_5_detectionA
Spike_AFFX-r2-Bs-phe_5_detectionA
%P28.088558
Spike_AFFX-r2-Bs-lys_avg-signal66.044334
Spike_AFFX-r2-P1-cre_avg-signal43492.531250
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionA
#Probe Sets Exceeding Probe Pair Threshold22810
%M3.568610
Spike_AFFX-r2-Bs-thr_3_signal129.175690
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionA
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal45.973881
Spike_AFFX-r2-Bs-dap_3_signal364.106415
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.506151
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal3745.604004
#M814
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal60.317661
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.004534
Spike_AFFX-r2-Bs-thr_M_signal105.918861
Signal(P)421.783142
Spike_AFFX-r2-Bs-phe_3-5-ratio1.988686
Spike_AFFX-r2-Bs-thr_3_detectionA
Central-Avg:15021,Count:9
Spike_AFFX-r2-P1-cre_5_signal39572.632813
Spike_AFFX-r2-Bs-phe_M_detectionA
#A15589
Signal(M)135.039047
BackgroundAvg:68.46,Std:1.03,Min:66.3,Max:71.9
Spike_AFFX-r2-Ec-bioC_avg-signal3754.096191
Spike_AFFX-r2-Bs-dap_avg-signal179.832825
Spike_AFFX-r2-Bs-dap_3-5-ratio45.659767
Spike_AFFX-r2-Ec-bioB_5_signal777.680908
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF6.075945
NF1.000000
HZ4
Tau0.015000

Slide: Agusti_5dNAA_CAM1_SLD

Add to Slide Selection

Get the data!

Summary BioSource 1 Information Extraction / Labelling Protocol for Source 1 Information Slide Information Hybridisation Analysis Information for "Affymetrix MAS 5.0 Scaling Protocol" normalised data.

Summary Information

This slide has had 1 extract(s) hybridised to it (1-colour).

  • Extract 1 ("Agusti_5dNAA_CAM1_SRC") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

The slide used was "Affymetrix ATH1 Arabidopsis Genome Array".

Click on the options above for more information about this slide and its preparation.

Hybridisation Protocol Information

Name of Protocol: Affymetrix Antibody Amplification Protocol
Solution:
BufferEDTA, NaCl, Tween20 according to Affymetrix protocol
Water
Blocking Agent:
Herring Sperm DNA(Source: Promega)100pg/ml
Acetylated BSA(Source: Sigma-Aldrich)0.1mg/ml
Wash Procedure:
Step 1(Source: Affymetrix)10 cycles of 2 mixes/cycle with Non-Stringent buffer
Step 2(Source: Affymetrix)4 cycles of 15 mixes/cycle with Stringent buffer
Step 3(Source: Affymetrix)Stain the probe array for 10 minutes in Streptavaidin Phycoerythrin (SAPE) solution at 25 C
Step 4(Source: Affymetrix)10 cycles of 4 mixes/cycle with Non-Stringent buffer
Step 5(Source: Affymetrix)Stain the probe array for 10 minutes in antibody solution
Step 6(Source: Affymetrix)Stain the probe array for 10 minutes in SAPE solution at 25 C
Step 7(Source: Affymetrix)15 cycles of 4mixes/cycle with Non-Stringent buffer at 30 C
Step 8(Source: Affymetrix)Hold at 25 C
Quantity Used:
Amount15 microgram Fragmented cRNA
Time: 16 hours
Concentration: 50 pg/ml
Volume: 200 microlitres
Temperature: 45 C
Other Information:
Spike(Source: Affymetrix)Control Oligo B2 to 50pM for landing lights
Spike(Source: Affymetrix)20X Eukaryotic Hybridisation Controls (bioB (1.5pM, bioC 5pM, bioD 25pM, cre 100pM)
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

BioSource 1 Information

BioSource Name: Agusti_5dNAA_CAM1_SRC
Organism: Arabidopsis thaliana
Alias: Columbia
Stock Code:
Growth Conditions:
ProtocolLayed out seeds were kept at 4°C for two days. Then, plants were grown for 3 weeks in short day conditions (8h light, 16h darkness) and then shifted into long day conditions (16h light, 8h darkness) to induce flowering.
Soil ConstituentsManufacturer: Frux. Composition: Standard.
Temperature22 °C average, 22.5 °C day, 21.5 °C night
Humidity61 % average, 63 % day, 59 % night
Medium
Lighting(Source: Cool white fluorescent manufactured by Philips. Intensity: 25µEinsteins. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)6.10
Tissue: Starch sheath + interfascicular fibers
in vivo Treatment: Stems from 15cm plants were harvested. Only plants which first internode was at least 5cm long were selected. Stems were surface sterylised and a 1.5cm sample located 2cm away from the rosette was separated for our experiments. The samples were then incubated with NAA in a MS split-plate. The samples were then rapidly embedded in OCT and frozen until used.
Additional Organism Information:
Sample Description15cm plants with a first internode at least 5cm long.
Other Information:
ecotype_habitat
Timecourse start procedureStart point was set when plant were collected.

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:4.482688
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
Spike_AFFX-r2-P1-cre_3-5-ratio1.162376
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.387367
Spike_AFFX-r2-Bs-dap_5_signal145.402893
NoiseAvg:2.69,Std:0.17,Min:2.5,Max:3.5
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal40.042530
#P7715
Spike_AFFX-r2-Bs-phe_M_signal74.936890
Corner-Avg:16887,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal875.923706
Spike_AFFX-r2-Ec-bioB_3_signal1006.902893
Spike_AFFX-r2-Bs-lys_M_signal13.485255
Spike_AFFX-r2-P1-cre_3_signal34493.660156
Spike_AFFX-r2-Bs-lys_3-5-ratio0.775332
Spike_AFFX-r2-Bs-dap_M_signal247.791809
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio4.363880
Spike_AFFX-r2-Ec-bioB_avg-signal869.530579
Spike_AFFX-r2-Bs-thr_avg-signal123.708191
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal12895.094727
Spike_AFFX-r2-Bs-phe_5_signal63.571342
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal17483.882813
RawQ2.607176
Spike_AFFX-r2-Bs-lys_5_signal80.883881
Signal(A)31.929914
%A62.406837
Signal(All)147.367432
Corner+Avg:128,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal3121.952637
Spike_AFFX-r2-Bs-lys_3_detectionA
Spike_AFFX-r2-Bs-phe_3_signal104.388680
Spike_AFFX-r2-Ec-bioD_avg-signal15189.488281
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionM
%P33.822884
Spike_AFFX-r2-Bs-lys_avg-signal52.360332
Spike_AFFX-r2-P1-cre_avg-signal32084.402344
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionA
#Probe Sets Exceeding Probe Pair Threshold22810
%M3.770276
Spike_AFFX-r2-Bs-thr_3_signal174.740799
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionA
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal80.965637
Spike_AFFX-r2-Bs-dap_3_signal459.471588
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.355855
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal3057.413330
#M860
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal62.711864
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.021109
Spike_AFFX-r2-Bs-thr_M_signal156.341232
Signal(P)364.879242
Spike_AFFX-r2-Bs-phe_3-5-ratio1.642071
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:16732,Count:9
Spike_AFFX-r2-P1-cre_5_signal29675.142578
Spike_AFFX-r2-Bs-phe_M_detectionA
#A14235
Signal(M)106.843513
BackgroundAvg:66.95,Std:0.54,Min:65.7,Max:68.7
Spike_AFFX-r2-Ec-bioC_avg-signal3089.683105
Spike_AFFX-r2-Bs-dap_avg-signal284.222107
Spike_AFFX-r2-Bs-dap_3-5-ratio3.159989
Spike_AFFX-r2-Ec-bioB_5_signal725.765259
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF4.482688
NF1.000000
HZ4
Tau0.015000

Slide: Agusti_5dNAA_CAM2_SLD

Add to Slide Selection

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Summary BioSource 1 Information Extraction / Labelling Protocol for Source 1 Information Slide Information Hybridisation Analysis Information for "Affymetrix MAS 5.0 Scaling Protocol" normalised data.

Summary Information

This slide has had 1 extract(s) hybridised to it (1-colour).

  • Extract 1 ("Agusti_5dNAA_CAM2_SRC") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

The slide used was "Affymetrix ATH1 Arabidopsis Genome Array".

Click on the options above for more information about this slide and its preparation.

Hybridisation Protocol Information

Name of Protocol: Affymetrix Antibody Amplification Protocol
Solution:
BufferEDTA, NaCl, Tween20 according to Affymetrix protocol
Water
Blocking Agent:
Herring Sperm DNA(Source: Promega)100pg/ml
Acetylated BSA(Source: Sigma-Aldrich)0.1mg/ml
Wash Procedure:
Step 1(Source: Affymetrix)10 cycles of 2 mixes/cycle with Non-Stringent buffer
Step 2(Source: Affymetrix)4 cycles of 15 mixes/cycle with Stringent buffer
Step 3(Source: Affymetrix)Stain the probe array for 10 minutes in Streptavaidin Phycoerythrin (SAPE) solution at 25 C
Step 4(Source: Affymetrix)10 cycles of 4 mixes/cycle with Non-Stringent buffer
Step 5(Source: Affymetrix)Stain the probe array for 10 minutes in antibody solution
Step 6(Source: Affymetrix)Stain the probe array for 10 minutes in SAPE solution at 25 C
Step 7(Source: Affymetrix)15 cycles of 4mixes/cycle with Non-Stringent buffer at 30 C
Step 8(Source: Affymetrix)Hold at 25 C
Quantity Used:
Amount15 microgram Fragmented cRNA
Time: 16 hours
Concentration: 50 pg/ml
Volume: 200 microlitres
Temperature: 45 C
Other Information:
Spike(Source: Affymetrix)Control Oligo B2 to 50pM for landing lights
Spike(Source: Affymetrix)20X Eukaryotic Hybridisation Controls (bioB (1.5pM, bioC 5pM, bioD 25pM, cre 100pM)
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

BioSource 1 Information

BioSource Name: Agusti_5dNAA_CAM2_SRC
Organism: Arabidopsis thaliana
Alias: Columbia
Stock Code:
Growth Conditions:
ProtocolLayed out seeds were kept at 4°C for two days. Then, plants were grown for 3 weeks in short day conditions (8h light, 16h darkness) and then shifted into long day conditions (16h light, 8h darkness) to induce flowering.
Soil ConstituentsManufacturer: Frux. Composition: Standard.
Temperature22 °C average, 22.5 °C day, 21.5 °C night
Humidity61 % average, 63 % day, 59 % night
Medium
Lighting(Source: Cool white fluorescent manufactured by Philips. Intensity: 25µEinsteins. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)6.10
Tissue: Starch sheath + interfascicular fibers
in vivo Treatment: Stems from 15cm plants were harvested. Only plants which first internode was at least 5cm long were selected. Stems were surface sterylised and a 1.5cm sample located 2cm away from the rosette was separated for our experiments. The samples were then incubated with NAA in a MS split-plate. The samples were then rapidly embedded in OCT and frozen until used.
Additional Organism Information:
Sample Description15cm plants with a first internode at least 5cm long.
Other Information:
ecotype_habitat
Timecourse start procedureStart point was set when plant were collected.

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:2.928059
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
Spike_AFFX-r2-P1-cre_3-5-ratio1.271451
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.491984
Spike_AFFX-r2-Bs-dap_5_signal93.381912
NoiseAvg:3.21,Std:0.13,Min:2.8,Max:3.8
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal51.591526
#P9201
Spike_AFFX-r2-Bs-phe_M_signal38.341660
Corner-Avg:17643,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal611.747742
Spike_AFFX-r2-Ec-bioB_3_signal675.475830
Spike_AFFX-r2-Bs-lys_M_signal36.590332
Spike_AFFX-r2-P1-cre_3_signal23995.917969
Spike_AFFX-r2-Bs-lys_3-5-ratio1.509559
Spike_AFFX-r2-Bs-dap_M_signal127.187180
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.348873
Spike_AFFX-r2-Ec-bioB_avg-signal579.986755
Spike_AFFX-r2-Bs-thr_avg-signal96.793518
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal8480.541016
Spike_AFFX-r2-Bs-phe_5_signal26.153122
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal12475.253906
RawQ2.983015
Spike_AFFX-r2-Bs-lys_5_signal40.049179
Signal(A)23.327562
%A56.391933
Signal(All)141.038284
Corner+Avg:139,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal2015.400757
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal80.378555
Spike_AFFX-r2-Ec-bioD_avg-signal10477.897461
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionA
%P40.337570
Spike_AFFX-r2-Bs-lys_avg-signal45.698700
Spike_AFFX-r2-P1-cre_avg-signal21434.390625
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionA
#Probe Sets Exceeding Probe Pair Threshold22810
%M3.270495
Spike_AFFX-r2-Bs-thr_3_signal121.181953
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionA
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal48.291111
Spike_AFFX-r2-Bs-dap_3_signal357.904022
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.471045
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal2017.845581
#M746
Spike_AFFX-r2-Bs-lys_5_detectionA
Spike_AFFX-r2-Bs-lys_3_signal60.456585
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.998788
Spike_AFFX-r2-Bs-thr_M_signal117.607071
Signal(P)310.746735
Spike_AFFX-r2-Bs-phe_3-5-ratio3.073383
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:16175,Count:9
Spike_AFFX-r2-P1-cre_5_signal18872.865234
Spike_AFFX-r2-Bs-phe_M_detectionA
#A12863
Signal(M)77.533463
BackgroundAvg:76.10,Std:0.58,Min:74.4,Max:77.7
Spike_AFFX-r2-Ec-bioC_avg-signal2016.623169
Spike_AFFX-r2-Bs-dap_avg-signal192.824356
Spike_AFFX-r2-Bs-dap_3-5-ratio3.832691
Spike_AFFX-r2-Ec-bioB_5_signal452.736542
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF2.928059
NF1.000000
HZ4
Tau0.015000

Slide: Agusti_5dNAA_CAM3_SLD

Add to Slide Selection

Get the data!

Summary BioSource 1 Information Extraction / Labelling Protocol for Source 1 Information Slide Information Hybridisation Analysis Information for "Affymetrix MAS 5.0 Scaling Protocol" normalised data.

Summary Information

This slide has had 1 extract(s) hybridised to it (1-colour).

  • Extract 1 ("Agusti_5dNAA_CAM3_SRC") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

The slide used was "Affymetrix ATH1 Arabidopsis Genome Array".

Click on the options above for more information about this slide and its preparation.

Hybridisation Protocol Information

Name of Protocol: Affymetrix Antibody Amplification Protocol
Solution:
BufferEDTA, NaCl, Tween20 according to Affymetrix protocol
Water
Blocking Agent:
Herring Sperm DNA(Source: Promega)100pg/ml
Acetylated BSA(Source: Sigma-Aldrich)0.1mg/ml
Wash Procedure:
Step 1(Source: Affymetrix)10 cycles of 2 mixes/cycle with Non-Stringent buffer
Step 2(Source: Affymetrix)4 cycles of 15 mixes/cycle with Stringent buffer
Step 3(Source: Affymetrix)Stain the probe array for 10 minutes in Streptavaidin Phycoerythrin (SAPE) solution at 25 C
Step 4(Source: Affymetrix)10 cycles of 4 mixes/cycle with Non-Stringent buffer
Step 5(Source: Affymetrix)Stain the probe array for 10 minutes in antibody solution
Step 6(Source: Affymetrix)Stain the probe array for 10 minutes in SAPE solution at 25 C
Step 7(Source: Affymetrix)15 cycles of 4mixes/cycle with Non-Stringent buffer at 30 C
Step 8(Source: Affymetrix)Hold at 25 C
Quantity Used:
Amount15 microgram Fragmented cRNA
Time: 16 hours
Concentration: 50 pg/ml
Volume: 200 microlitres
Temperature: 45 C
Other Information:
Spike(Source: Affymetrix)Control Oligo B2 to 50pM for landing lights
Spike(Source: Affymetrix)20X Eukaryotic Hybridisation Controls (bioB (1.5pM, bioC 5pM, bioD 25pM, cre 100pM)
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

BioSource 1 Information

BioSource Name: Agusti_5dNAA_CAM3_SRC
Organism: Arabidopsis thaliana
Alias: Columbia
Stock Code:
Growth Conditions:
ProtocolLayed out seeds were kept at 4°C for two days. Then, plants were grown for 3 weeks in short day conditions (8h light, 16h darkness) and then shifted into long day conditions (16h light, 8h darkness) to induce flowering.
Soil ConstituentsManufacturer: Frux. Composition: Standard.
Temperature22 °C average, 22.5 °C day, 21.5 °C night
Humidity61 % average, 63 % day, 59 % night
Medium
Lighting(Source: Cool white fluorescent manufactured by Philips. Intensity: 25µEinsteins. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)6.10
Tissue: Starch sheath + interfascicular fibers
in vivo Treatment: Stems from 15cm plants were harvested. Only plants which first internode was at least 5cm long were selected. Stems were surface sterylised and a 1.5cm sample located 2cm away from the rosette was separated for our experiments. The samples were then incubated with NAA in a MS split-plate. The samples were then rapidly embedded in OCT and frozen until used.
Additional Organism Information:
Sample Description15cm plants with a first internode at least 5cm long.
Other Information:
ecotype_habitat
Timecourse start procedureStart point was set when plant were collected.

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:9.689981
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
Spike_AFFX-r2-P1-cre_3-5-ratio0.973747
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.537858
Spike_AFFX-r2-Bs-dap_5_signal220.739761
NoiseAvg:2.58,Std:0.11,Min:2.3,Max:3.0
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal150.456940
#P3922
Spike_AFFX-r2-Bs-phe_M_signal87.504128
Corner-Avg:18705,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal2485.889648
Spike_AFFX-r2-Ec-bioB_3_signal2679.860352
Spike_AFFX-r2-Bs-lys_M_signal113.064056
Spike_AFFX-r2-P1-cre_3_signal66398.515625
Spike_AFFX-r2-Bs-lys_3-5-ratio15.026884
Spike_AFFX-r2-Bs-dap_M_signal195.787796
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio1.706147
Spike_AFFX-r2-Ec-bioB_avg-signal2302.780762
Spike_AFFX-r2-Bs-thr_avg-signal223.726730
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal32415.490234
Spike_AFFX-r2-Bs-phe_5_signal25.633430
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal44878.562500
RawQ2.700838
Spike_AFFX-r2-Bs-lys_5_signal7.422798
Signal(A)58.356876
%A79.649277
Signal(All)150.123840
Corner+Avg:145,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal6718.312500
Spike_AFFX-r2-Bs-lys_3_detectionA
Spike_AFFX-r2-Bs-phe_3_signal34.925640
Spike_AFFX-r2-Ec-bioD_avg-signal38647.027344
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionA
%P17.194214
Spike_AFFX-r2-Bs-lys_avg-signal77.342796
Spike_AFFX-r2-P1-cre_avg-signal67293.609375
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionA
#Probe Sets Exceeding Probe Pair Threshold22810
%M3.156510
Spike_AFFX-r2-Bs-thr_3_signal256.701599
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionA
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal49.354401
Spike_AFFX-r2-Bs-dap_3_signal666.742798
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.384479
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal6894.111328
#M720
Spike_AFFX-r2-Bs-lys_5_detectionA
Spike_AFFX-r2-Bs-lys_3_signal111.541527
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.974500
Spike_AFFX-r2-Bs-thr_M_signal264.021667
Signal(P)566.647400
Spike_AFFX-r2-Bs-phe_3-5-ratio1.362504
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:18025,Count:9
Spike_AFFX-r2-P1-cre_5_signal68188.695313
Spike_AFFX-r2-Bs-phe_M_detectionA
#A18168
Signal(M)196.813751
BackgroundAvg:65.88,Std:0.62,Min:64.7,Max:67.5
Spike_AFFX-r2-Ec-bioC_avg-signal6806.211914
Spike_AFFX-r2-Bs-dap_avg-signal361.090118
Spike_AFFX-r2-Bs-dap_3-5-ratio3.020493
Spike_AFFX-r2-Ec-bioB_5_signal1742.592407
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF9.689981
NF1.000000
HZ4
Tau0.015000

Slide: Agusti_5dNAA_C1_SLD

Add to Slide Selection

Get the data!

Summary BioSource 1 Information Extraction / Labelling Protocol for Source 1 Information Slide Information Hybridisation Analysis Information for "Affymetrix MAS 5.0 Scaling Protocol" normalised data.

Summary Information

This slide has had 1 extract(s) hybridised to it (1-colour).

  • Extract 1 ("Agusti_5dNAA_C1_SRC") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

The slide used was "Affymetrix ATH1 Arabidopsis Genome Array".

Click on the options above for more information about this slide and its preparation.

Hybridisation Protocol Information

Name of Protocol: Affymetrix Antibody Amplification Protocol
Solution:
BufferEDTA, NaCl, Tween20 according to Affymetrix protocol
Water
Blocking Agent:
Herring Sperm DNA(Source: Promega)100pg/ml
Acetylated BSA(Source: Sigma-Aldrich)0.1mg/ml
Wash Procedure:
Step 1(Source: Affymetrix)10 cycles of 2 mixes/cycle with Non-Stringent buffer
Step 2(Source: Affymetrix)4 cycles of 15 mixes/cycle with Stringent buffer
Step 3(Source: Affymetrix)Stain the probe array for 10 minutes in Streptavaidin Phycoerythrin (SAPE) solution at 25 C
Step 4(Source: Affymetrix)10 cycles of 4 mixes/cycle with Non-Stringent buffer
Step 5(Source: Affymetrix)Stain the probe array for 10 minutes in antibody solution
Step 6(Source: Affymetrix)Stain the probe array for 10 minutes in SAPE solution at 25 C
Step 7(Source: Affymetrix)15 cycles of 4mixes/cycle with Non-Stringent buffer at 30 C
Step 8(Source: Affymetrix)Hold at 25 C
Quantity Used:
Amount15 microgram Fragmented cRNA
Time: 16 hours
Concentration: 50 pg/ml
Volume: 200 microlitres
Temperature: 45 C
Other Information:
Spike(Source: Affymetrix)Control Oligo B2 to 50pM for landing lights
Spike(Source: Affymetrix)20X Eukaryotic Hybridisation Controls (bioB (1.5pM, bioC 5pM, bioD 25pM, cre 100pM)
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

BioSource 1 Information

BioSource Name: Agusti_5dNAA_C1_SRC
Organism: Arabidopsis thaliana
Alias: Columbia
Stock Code:
Growth Conditions:
ProtocolLayed out seeds were kept at 4°C for two days. Then, plants were grown for 3 weeks in short day conditions (8h light, 16h darkness) and then shifted into long day conditions (16h light, 8h darkness) to induce flowering.
Soil ConstituentsManufacturer: Frux. Composition: Standard.
Temperature22 °C average, 22.5 °C day, 21.5 °C night
Humidity61 % average, 63 % day, 59 % night
Medium
Lighting(Source: Cool white fluorescent manufactured by Philips. Intensity: 25µEinsteins. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)6.10
Tissue: Stem except stach sheath layer and vascular bundles.
in vivo Treatment: Stems from 15cm plants were harvested. Only plants which first internode was at least 5cm long were selected. Stems were surface sterylised and a 1.5cm sample located 2cm away from the rosette was separated for our experiments. The samples were then incubated with NAA in a MS split-plate. The samples were then rapidly embedded in OCT and frozen until used.
Additional Organism Information:
Sample Description15cm plants with a first internode at least 5cm long.
Other Information:
ecotype_habitat
Timecourse start procedureStart point was set when plant were collected.

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:6.256403
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
Spike_AFFX-r2-P1-cre_3-5-ratio1.114288
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.725975
Spike_AFFX-r2-Bs-dap_5_signal136.598099
NoiseAvg:3.06,Std:0.09,Min:2.8,Max:3.4
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal68.551155
#P5188
Spike_AFFX-r2-Bs-phe_M_signal66.020660
Corner-Avg:19985,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal1739.595459
Spike_AFFX-r2-Ec-bioB_3_signal1811.610718
Spike_AFFX-r2-Bs-lys_M_signal41.529285
Spike_AFFX-r2-P1-cre_3_signal50511.457031
Spike_AFFX-r2-Bs-lys_3-5-ratio2.857766
Spike_AFFX-r2-Bs-dap_M_signal235.051514
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.049430
Spike_AFFX-r2-Ec-bioB_avg-signal1533.607422
Spike_AFFX-r2-Bs-thr_avg-signal143.394577
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal21455.121094
Spike_AFFX-r2-Bs-phe_5_signal86.365608
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal32483.601563
RawQ2.972815
Spike_AFFX-r2-Bs-lys_5_signal53.284801
Signal(A)47.905895
%A74.011398
Signal(All)148.710022
Corner+Avg:162,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal4705.391602
Spike_AFFX-r2-Bs-lys_3_detectionA
Spike_AFFX-r2-Bs-phe_3_signal99.589844
Spike_AFFX-r2-Ec-bioD_avg-signal26969.361328
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionM
%P22.744410
Spike_AFFX-r2-Bs-lys_avg-signal82.363197
Spike_AFFX-r2-P1-cre_avg-signal47921.078125
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionA
#Probe Sets Exceeding Probe Pair Threshold22810
%M3.244191
Spike_AFFX-r2-Bs-thr_3_signal209.041977
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionM
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal83.992035
Spike_AFFX-r2-Bs-dap_3_signal692.980957
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.514026
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal5010.736328
#M740
Spike_AFFX-r2-Bs-lys_5_detectionA
Spike_AFFX-r2-Bs-lys_3_signal152.275497
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.939062
Spike_AFFX-r2-Bs-thr_M_signal152.590576
Signal(P)475.237335
Spike_AFFX-r2-Bs-phe_3-5-ratio1.153119
Spike_AFFX-r2-Bs-thr_3_detectionM
Central-Avg:18478,Count:9
Spike_AFFX-r2-P1-cre_5_signal45330.699219
Spike_AFFX-r2-Bs-phe_M_detectionA
#A16882
Signal(M)159.185257
BackgroundAvg:99.49,Std:0.56,Min:98.1,Max:101.4
Spike_AFFX-r2-Ec-bioC_avg-signal4858.063965
Spike_AFFX-r2-Bs-dap_avg-signal354.876862
Spike_AFFX-r2-Bs-dap_3-5-ratio5.073138
Spike_AFFX-r2-Ec-bioB_5_signal1049.616089
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF6.256403
NF1.000000
HZ4
Tau0.015000

Slide: Agusti_5dNAA_C2_SLD

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Summary BioSource 1 Information Extraction / Labelling Protocol for Source 1 Information Slide Information Hybridisation Analysis Information for "Affymetrix MAS 5.0 Scaling Protocol" normalised data.

Summary Information

This slide has had 1 extract(s) hybridised to it (1-colour).

  • Extract 1 ("Agusti_5dNAA_C2_SRC") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

The slide used was "Affymetrix ATH1 Arabidopsis Genome Array".

Click on the options above for more information about this slide and its preparation.

Hybridisation Protocol Information

Name of Protocol: Affymetrix Antibody Amplification Protocol
Solution:
BufferEDTA, NaCl, Tween20 according to Affymetrix protocol
Water
Blocking Agent:
Herring Sperm DNA(Source: Promega)100pg/ml
Acetylated BSA(Source: Sigma-Aldrich)0.1mg/ml
Wash Procedure:
Step 1(Source: Affymetrix)10 cycles of 2 mixes/cycle with Non-Stringent buffer
Step 2(Source: Affymetrix)4 cycles of 15 mixes/cycle with Stringent buffer
Step 3(Source: Affymetrix)Stain the probe array for 10 minutes in Streptavaidin Phycoerythrin (SAPE) solution at 25 C
Step 4(Source: Affymetrix)10 cycles of 4 mixes/cycle with Non-Stringent buffer
Step 5(Source: Affymetrix)Stain the probe array for 10 minutes in antibody solution
Step 6(Source: Affymetrix)Stain the probe array for 10 minutes in SAPE solution at 25 C
Step 7(Source: Affymetrix)15 cycles of 4mixes/cycle with Non-Stringent buffer at 30 C
Step 8(Source: Affymetrix)Hold at 25 C
Quantity Used:
Amount15 microgram Fragmented cRNA
Time: 16 hours
Concentration: 50 pg/ml
Volume: 200 microlitres
Temperature: 45 C
Other Information:
Spike(Source: Affymetrix)Control Oligo B2 to 50pM for landing lights
Spike(Source: Affymetrix)20X Eukaryotic Hybridisation Controls (bioB (1.5pM, bioC 5pM, bioD 25pM, cre 100pM)
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

BioSource 1 Information

BioSource Name: Agusti_5dNAA_C2_SRC
Organism: Arabidopsis thaliana
Alias: Columbia
Stock Code:
Growth Conditions:
ProtocolLayed out seeds were kept at 4°C for two days. Then, plants were grown for 3 weeks in short day conditions (8h light, 16h darkness) and then shifted into long day conditions (16h light, 8h darkness) to induce flowering.
Soil ConstituentsManufacturer: Frux. Composition: Standard.
Temperature22 °C average, 22.5 °C day, 21.5 °C night
Humidity61 % average, 63 % day, 59 % night
Medium
Lighting(Source: Cool white fluorescent manufactured by Philips. Intensity: 25µEinsteins. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)6.10
Tissue: Stem except stach sheath layer and vascular bundles.
in vivo Treatment: Stems from 15cm plants were harvested. Only plants which first internode was at least 5cm long were selected. Stems were surface sterylised and a 1.5cm sample located 2cm away from the rosette was separated for our experiments. The samples were then incubated with NAA in a MS split-plate. The samples were then rapidly embedded in OCT and frozen until used.
Additional Organism Information:
Sample Description15cm plants with a first internode at least 5cm long.
Other Information:
ecotype_habitat
Timecourse start procedureStart point was set when plant were collected.

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:5.236627
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
Spike_AFFX-r2-P1-cre_3-5-ratio1.101627
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.544087
Spike_AFFX-r2-Bs-dap_5_signal102.527908
NoiseAvg:2.71,Std:0.07,Min:2.5,Max:3.0
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal106.104767
#P6153
Spike_AFFX-r2-Bs-phe_M_signal34.774204
Corner-Avg:8581,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal1432.638916
Spike_AFFX-r2-Ec-bioB_3_signal1401.517822
Spike_AFFX-r2-Bs-lys_M_signal38.498478
Spike_AFFX-r2-P1-cre_3_signal46366.027344
Spike_AFFX-r2-Bs-lys_3-5-ratio3.752250
Spike_AFFX-r2-Bs-dap_M_signal120.141014
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio1.554157
Spike_AFFX-r2-Ec-bioB_avg-signal1247.274780
Spike_AFFX-r2-Bs-thr_avg-signal155.279465
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal16438.027344
Spike_AFFX-r2-Bs-phe_5_signal74.736923
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal22546.332031
RawQ2.743006
Spike_AFFX-r2-Bs-lys_5_signal17.081903
Signal(A)40.063457
%A69.298553
Signal(All)151.291138
Corner+Avg:90,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal5205.048340
Spike_AFFX-r2-Bs-lys_3_detectionA
Spike_AFFX-r2-Bs-phe_3_signal22.384661
Spike_AFFX-r2-Ec-bioD_avg-signal19492.179688
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionA
%P26.975012
Spike_AFFX-r2-Bs-lys_avg-signal39.891987
Spike_AFFX-r2-P1-cre_avg-signal44227.363281
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionA
#Probe Sets Exceeding Probe Pair Threshold22810
%M3.726436
Spike_AFFX-r2-Bs-thr_3_signal164.903458
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionA
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal43.965260
Spike_AFFX-r2-Bs-dap_3_signal393.986267
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.371596
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal4900.217773
#M850
Spike_AFFX-r2-Bs-lys_5_detectionA
Spike_AFFX-r2-Bs-lys_3_signal64.095573
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.062208
Spike_AFFX-r2-Bs-thr_M_signal194.830154
Signal(P)439.807587
Spike_AFFX-r2-Bs-phe_3-5-ratio0.299513
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:6019,Count:9
Spike_AFFX-r2-P1-cre_5_signal42088.699219
Spike_AFFX-r2-Bs-phe_M_detectionA
#A15807
Signal(M)131.213715
BackgroundAvg:90.86,Std:0.59,Min:89.7,Max:92.3
Spike_AFFX-r2-Ec-bioC_avg-signal5052.632813
Spike_AFFX-r2-Bs-dap_avg-signal205.551712
Spike_AFFX-r2-Bs-dap_3-5-ratio3.842722
Spike_AFFX-r2-Ec-bioB_5_signal907.667542
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF5.236627
NF1.000000
HZ4
Tau0.015000

Slide: Agusti_5dNAA_C3_SLD

Add to Slide Selection

Get the data!

Summary BioSource 1 Information Extraction / Labelling Protocol for Source 1 Information Slide Information Hybridisation Analysis Information for "Affymetrix MAS 5.0 Scaling Protocol" normalised data.

Summary Information

This slide has had 1 extract(s) hybridised to it (1-colour).

  • Extract 1 ("Agusti_5dNAA_C3_SRC") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

The slide used was "Affymetrix ATH1 Arabidopsis Genome Array".

Click on the options above for more information about this slide and its preparation.

Hybridisation Protocol Information

Name of Protocol: Affymetrix Antibody Amplification Protocol
Solution:
BufferEDTA, NaCl, Tween20 according to Affymetrix protocol
Water
Blocking Agent:
Herring Sperm DNA(Source: Promega)100pg/ml
Acetylated BSA(Source: Sigma-Aldrich)0.1mg/ml
Wash Procedure:
Step 1(Source: Affymetrix)10 cycles of 2 mixes/cycle with Non-Stringent buffer
Step 2(Source: Affymetrix)4 cycles of 15 mixes/cycle with Stringent buffer
Step 3(Source: Affymetrix)Stain the probe array for 10 minutes in Streptavaidin Phycoerythrin (SAPE) solution at 25 C
Step 4(Source: Affymetrix)10 cycles of 4 mixes/cycle with Non-Stringent buffer
Step 5(Source: Affymetrix)Stain the probe array for 10 minutes in antibody solution
Step 6(Source: Affymetrix)Stain the probe array for 10 minutes in SAPE solution at 25 C
Step 7(Source: Affymetrix)15 cycles of 4mixes/cycle with Non-Stringent buffer at 30 C
Step 8(Source: Affymetrix)Hold at 25 C
Quantity Used:
Amount15 microgram Fragmented cRNA
Time: 16 hours
Concentration: 50 pg/ml
Volume: 200 microlitres
Temperature: 45 C
Other Information:
Spike(Source: Affymetrix)Control Oligo B2 to 50pM for landing lights
Spike(Source: Affymetrix)20X Eukaryotic Hybridisation Controls (bioB (1.5pM, bioC 5pM, bioD 25pM, cre 100pM)
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

BioSource 1 Information

BioSource Name: Agusti_5dNAA_C3_SRC
Organism: Arabidopsis thaliana
Alias: Columbia
Stock Code:
Growth Conditions:
ProtocolLayed out seeds were kept at 4°C for two days. Then, plants were grown for 3 weeks in short day conditions (8h light, 16h darkness) and then shifted into long day conditions (16h light, 8h darkness) to induce flowering.
Soil ConstituentsManufacturer: Frux. Composition: Standard.
Temperature22 °C average, 22.5 °C day, 21.5 °C night
Humidity61 % average, 63 % day, 59 % night
Medium
Lighting(Source: Cool white fluorescent manufactured by Philips. Intensity: 25µEinsteins. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)6.10
Tissue: Stem except stach sheath layer and vascular bundles.
in vivo Treatment: Stems from 15cm plants were harvested. Only plants which first internode was at least 5cm long were selected. Stems were surface sterylised and a 1.5cm sample located 2cm away from the rosette was separated for our experiments. The samples were then incubated with NAA in a MS split-plate. The samples were then rapidly embedded in OCT and frozen until used.
Additional Organism Information:
Sample Description15cm plants with a first internode at least 5cm long.
Other Information:
ecotype_habitat
Timecourse start procedureStart point was set when plant were collected.

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:6.073006
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
Spike_AFFX-r2-P1-cre_3-5-ratio1.004544
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.578535
Spike_AFFX-r2-Bs-dap_5_signal84.004555
NoiseAvg:2.46,Std:0.10,Min:2.2,Max:2.8
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal70.003708
#P6591
Spike_AFFX-r2-Bs-phe_M_signal63.309341
Corner-Avg:15192,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal1389.108643
Spike_AFFX-r2-Ec-bioB_3_signal1289.084229
Spike_AFFX-r2-Bs-lys_M_signal56.810307
Spike_AFFX-r2-P1-cre_3_signal42033.066406
Spike_AFFX-r2-Bs-lys_3-5-ratio4.302347
Spike_AFFX-r2-Bs-dap_M_signal193.037979
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.286776
Spike_AFFX-r2-Ec-bioB_avg-signal1164.942017
Spike_AFFX-r2-Bs-thr_avg-signal133.653671
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal17809.751953
Spike_AFFX-r2-Bs-phe_5_signal64.125900
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal24264.865234
RawQ2.588179
Spike_AFFX-r2-Bs-lys_5_signal21.789450
Signal(A)36.628391
%A67.553703
Signal(All)149.052078
Corner+Avg:127,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal3622.891846
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal54.477486
Spike_AFFX-r2-Ec-bioD_avg-signal21037.308594
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionM
%P28.895222
Spike_AFFX-r2-Bs-lys_avg-signal57.448505
Spike_AFFX-r2-P1-cre_avg-signal41937.992188
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M3.551074
Spike_AFFX-r2-Bs-thr_3_signal160.082764
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionA
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal60.637573
Spike_AFFX-r2-Bs-dap_3_signal401.016174
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.362448
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal3711.367432
#M810
Spike_AFFX-r2-Bs-lys_5_detectionA
Spike_AFFX-r2-Bs-lys_3_signal93.745773
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.976161
Spike_AFFX-r2-Bs-thr_M_signal170.874496
Signal(P)414.851044
Spike_AFFX-r2-Bs-phe_3-5-ratio0.849540
Spike_AFFX-r2-Bs-thr_3_detectionM
Central-Avg:12792,Count:9
Spike_AFFX-r2-P1-cre_5_signal41842.917969
Spike_AFFX-r2-Bs-phe_M_detectionA
#A15409
Signal(M)124.923103
BackgroundAvg:84.06,Std:1.93,Min:81.0,Max:89.8
Spike_AFFX-r2-Ec-bioC_avg-signal3667.129639
Spike_AFFX-r2-Bs-dap_avg-signal226.019577
Spike_AFFX-r2-Bs-dap_3-5-ratio4.773743
Spike_AFFX-r2-Ec-bioB_5_signal816.633179
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF6.073006
NF1.000000
HZ4
Tau0.015000

Slide: Agusti_5dMS_SS1_SLD

Add to Slide Selection

Get the data!

Summary BioSource 1 Information Extraction / Labelling Protocol for Source 1 Information Slide Information Hybridisation Analysis Information for "Affymetrix MAS 5.0 Scaling Protocol" normalised data.

Summary Information

This slide has had 1 extract(s) hybridised to it (1-colour).

  • Extract 1 ("Agusti_5dMS_SS1_SRC") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

The slide used was "Affymetrix ATH1 Arabidopsis Genome Array".

Click on the options above for more information about this slide and its preparation.

Hybridisation Protocol Information

Name of Protocol: Affymetrix Antibody Amplification Protocol
Solution:
BufferEDTA, NaCl, Tween20 according to Affymetrix protocol
Water
Blocking Agent:
Herring Sperm DNA(Source: Promega)100pg/ml
Acetylated BSA(Source: Sigma-Aldrich)0.1mg/ml
Wash Procedure:
Step 1(Source: Affymetrix)10 cycles of 2 mixes/cycle with Non-Stringent buffer
Step 2(Source: Affymetrix)4 cycles of 15 mixes/cycle with Stringent buffer
Step 3(Source: Affymetrix)Stain the probe array for 10 minutes in Streptavaidin Phycoerythrin (SAPE) solution at 25 C
Step 4(Source: Affymetrix)10 cycles of 4 mixes/cycle with Non-Stringent buffer
Step 5(Source: Affymetrix)Stain the probe array for 10 minutes in antibody solution
Step 6(Source: Affymetrix)Stain the probe array for 10 minutes in SAPE solution at 25 C
Step 7(Source: Affymetrix)15 cycles of 4mixes/cycle with Non-Stringent buffer at 30 C
Step 8(Source: Affymetrix)Hold at 25 C
Quantity Used:
Amount15 microgram Fragmented cRNA
Time: 16 hours
Concentration: 50 pg/ml
Volume: 200 microlitres
Temperature: 45 C
Other Information:
Spike(Source: Affymetrix)Control Oligo B2 to 50pM for landing lights
Spike(Source: Affymetrix)20X Eukaryotic Hybridisation Controls (bioB (1.5pM, bioC 5pM, bioD 25pM, cre 100pM)
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

BioSource 1 Information

BioSource Name: Agusti_5dMS_SS1_SRC
Organism: Arabidopsis thaliana
Alias: Columbia
Stock Code:
Growth Conditions:
ProtocolLayed out seeds were kept at 4°C for two days. Then, plants were grown for 3 weeks in short day conditions (8h light, 16h darkness) and then shifted into long day conditions (16h light, 8h darkness) to induce flowering.
Soil ConstituentsManufacturer: Frux. Composition: Standard.
Temperature22 °C average, 22.5 °C day, 21.5 °C night
Humidity61 % average, 63 % day, 59 % night
Medium
Lighting(Source: Cool white fluorescent manufactured by Philips. Intensity: 25µEinsteins. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)6.10
Tissue: Starch sheath + interfascicular fibers
in vivo Treatment: Stems from 15cm plants were harvested. Only plants which first internode was at least 5cm long were selected. Stems were surface sterylised and a 1.5cm sample located 2cm away from the rosette was separated for our experiments. The samples were then incubated in a MS split-plate. The samples were then rapidly embedded in OCT and frozen until used.
Additional Organism Information:
Sample Description15cm plants with a first internode at least 5cm long.
Other Information:
ecotype_habitat
Timecourse start procedureStart point was set when plant were collected.

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:6.769299
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
Spike_AFFX-r2-P1-cre_3-5-ratio1.058744
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.335800
Spike_AFFX-r2-Bs-dap_5_signal133.684601
NoiseAvg:2.41,Std:0.11,Min:2.2,Max:2.7
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal65.222092
#P5665
Spike_AFFX-r2-Bs-phe_M_signal30.041632
Corner-Avg:7565,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal1244.949585
Spike_AFFX-r2-Ec-bioB_3_signal1252.129150
Spike_AFFX-r2-Bs-lys_M_signal36.411297
Spike_AFFX-r2-P1-cre_3_signal42717.386719
Spike_AFFX-r2-Bs-lys_3-5-ratio0.094993
Spike_AFFX-r2-Bs-dap_M_signal78.807953
Spike_AFFX-r2-Bs-thr_M_detectionA
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.895397
Spike_AFFX-r2-Ec-bioB_avg-signal1144.813843
Spike_AFFX-r2-Bs-thr_avg-signal140.952225
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal11861.675781
Spike_AFFX-r2-Bs-phe_5_signal28.517963
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal19917.679688
RawQ2.410195
Spike_AFFX-r2-Bs-lys_5_signal24.800411
Signal(A)43.495480
%A72.021042
Signal(All)148.478271
Corner+Avg:90,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal5296.584473
Spike_AFFX-r2-Bs-lys_3_detectionA
Spike_AFFX-r2-Bs-phe_3_signal36.051971
Spike_AFFX-r2-Ec-bioD_avg-signal15889.677734
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionA
%P24.835598
Spike_AFFX-r2-Bs-lys_avg-signal21.189194
Spike_AFFX-r2-P1-cre_avg-signal41532.312500
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionA
#Probe Sets Exceeding Probe Pair Threshold22810
%M3.143358
Spike_AFFX-r2-Bs-thr_3_signal188.843826
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionA
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal31.537191
Spike_AFFX-r2-Bs-dap_3_signal315.473022
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.679162
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal4567.715332
#M717
Spike_AFFX-r2-Bs-lys_5_detectionA
Spike_AFFX-r2-Bs-lys_3_signal2.355874
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.159570
Spike_AFFX-r2-Bs-thr_M_signal168.790756
Signal(P)453.895233
Spike_AFFX-r2-Bs-phe_3-5-ratio1.264185
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:5687,Count:9
Spike_AFFX-r2-P1-cre_5_signal40347.234375
Spike_AFFX-r2-Bs-phe_M_detectionA
#A16428
Signal(M)140.765762
BackgroundAvg:80.89,Std:1.59,Min:78.0,Max:86.2
Spike_AFFX-r2-Ec-bioC_avg-signal4932.149902
Spike_AFFX-r2-Bs-dap_avg-signal175.988525
Spike_AFFX-r2-Bs-dap_3-5-ratio2.359831
Spike_AFFX-r2-Ec-bioB_5_signal937.362671
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF6.769299
NF1.000000
HZ4
Tau0.015000

Slide: Agusti_5dMS_SS2_SLD

Add to Slide Selection

Get the data!

Summary BioSource 1 Information Extraction / Labelling Protocol for Source 1 Information Slide Information Hybridisation Analysis Information for "Affymetrix MAS 5.0 Scaling Protocol" normalised data.

Summary Information

This slide has had 1 extract(s) hybridised to it (1-colour).

  • Extract 1 ("Agusti_5dMS_SS2_SRC") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

The slide used was "Affymetrix ATH1 Arabidopsis Genome Array".

Click on the options above for more information about this slide and its preparation.

Hybridisation Protocol Information

Name of Protocol: Affymetrix Antibody Amplification Protocol
Solution:
BufferEDTA, NaCl, Tween20 according to Affymetrix protocol
Water
Blocking Agent:
Herring Sperm DNA(Source: Promega)100pg/ml
Acetylated BSA(Source: Sigma-Aldrich)0.1mg/ml
Wash Procedure:
Step 1(Source: Affymetrix)10 cycles of 2 mixes/cycle with Non-Stringent buffer
Step 2(Source: Affymetrix)4 cycles of 15 mixes/cycle with Stringent buffer
Step 3(Source: Affymetrix)Stain the probe array for 10 minutes in Streptavaidin Phycoerythrin (SAPE) solution at 25 C
Step 4(Source: Affymetrix)10 cycles of 4 mixes/cycle with Non-Stringent buffer
Step 5(Source: Affymetrix)Stain the probe array for 10 minutes in antibody solution
Step 6(Source: Affymetrix)Stain the probe array for 10 minutes in SAPE solution at 25 C
Step 7(Source: Affymetrix)15 cycles of 4mixes/cycle with Non-Stringent buffer at 30 C
Step 8(Source: Affymetrix)Hold at 25 C
Quantity Used:
Amount15 microgram Fragmented cRNA
Time: 16 hours
Concentration: 50 pg/ml
Volume: 200 microlitres
Temperature: 45 C
Other Information:
Spike(Source: Affymetrix)Control Oligo B2 to 50pM for landing lights
Spike(Source: Affymetrix)20X Eukaryotic Hybridisation Controls (bioB (1.5pM, bioC 5pM, bioD 25pM, cre 100pM)
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

BioSource 1 Information

BioSource Name: Agusti_5dMS_SS2_SRC
Organism: Arabidopsis thaliana
Alias: Columbia
Stock Code:
Growth Conditions:
ProtocolLayed out seeds were kept at 4°C for two days. Then, plants were grown for 3 weeks in short day conditions (8h light, 16h darkness) and then shifted into long day conditions (16h light, 8h darkness) to induce flowering.
Soil ConstituentsManufacturer: Frux. Composition: Standard.
Temperature22 °C average, 22.5 °C day, 21.5 °C night
Humidity61 % average, 63 % day, 59 % night
Medium
Lighting(Source: Cool white fluorescent manufactured by Philips. Intensity: 25µEinsteins. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)6.10
Tissue: Starch sheath + interfascicular fibers
in vivo Treatment: Stems from 15cm plants were harvested. Only plants which first internode was at least 5cm long were selected. Stems were surface sterylised and a 1.5cm sample located 2cm away from the rosette was separated for our experiments. The samples were then incubated in a MS split-plate. The samples were then rapidly embedded in OCT and frozen until used.
Additional Organism Information:
Sample Description15cm plants with a first internode at least 5cm long.
Other Information:
ecotype_habitat
Timecourse start procedureStart point was set when plant were collected.

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:3.535791
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
Spike_AFFX-r2-P1-cre_3-5-ratio1.183288
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.529828
Spike_AFFX-r2-Bs-dap_5_signal126.560387
NoiseAvg:3.05,Std:0.08,Min:2.8,Max:3.3
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal47.893581
#P7778
Spike_AFFX-r2-Bs-phe_M_signal45.823601
Corner-Avg:18495,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal1080.739868
Spike_AFFX-r2-Ec-bioB_3_signal1041.013550
Spike_AFFX-r2-Bs-lys_M_signal18.724417
Spike_AFFX-r2-P1-cre_3_signal31872.736328
Spike_AFFX-r2-Bs-lys_3-5-ratio14.981184
Spike_AFFX-r2-Bs-dap_M_signal229.525208
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.523994
Spike_AFFX-r2-Ec-bioB_avg-signal934.076965
Spike_AFFX-r2-Bs-thr_avg-signal126.714714
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal11428.681641
Spike_AFFX-r2-Bs-phe_5_signal46.675007
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal17602.138672
RawQ2.977182
Spike_AFFX-r2-Bs-lys_5_signal3.466381
Signal(A)26.573282
%A62.757561
Signal(All)152.640121
Corner+Avg:155,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal2893.524902
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal89.726128
Spike_AFFX-r2-Ec-bioD_avg-signal14515.410156
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionA
%P34.099079
Spike_AFFX-r2-Bs-lys_avg-signal24.707100
Spike_AFFX-r2-P1-cre_avg-signal29404.242188
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionA
#Probe Sets Exceeding Probe Pair Threshold22810
%M3.143358
Spike_AFFX-r2-Bs-thr_3_signal168.776703
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal60.741577
Spike_AFFX-r2-Bs-dap_3_signal457.515686
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.540172
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal2682.772705
#M717
Spike_AFFX-r2-Bs-lys_5_detectionA
Spike_AFFX-r2-Bs-lys_3_signal51.930496
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.078558
Spike_AFFX-r2-Bs-thr_M_signal163.473862
Signal(P)390.168365
Spike_AFFX-r2-Bs-phe_3-5-ratio1.922359
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:16221,Count:9
Spike_AFFX-r2-P1-cre_5_signal26935.748047
Spike_AFFX-r2-Bs-phe_M_detectionA
#A14315
Signal(M)92.880363
BackgroundAvg:100.16,Std:0.87,Min:98.6,Max:102.6
Spike_AFFX-r2-Ec-bioC_avg-signal2788.148926
Spike_AFFX-r2-Bs-dap_avg-signal271.200409
Spike_AFFX-r2-Bs-dap_3-5-ratio3.614999
Spike_AFFX-r2-Ec-bioB_5_signal680.477539
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF3.535791
NF1.000000
HZ4
Tau0.015000

Slide: Agusti_5dMS_SS3_SLD

Add to Slide Selection

Get the data!

Summary BioSource 1 Information Extraction / Labelling Protocol for Source 1 Information Slide Information Hybridisation Analysis Information for "Affymetrix MAS 5.0 Scaling Protocol" normalised data.

Summary Information

This slide has had 1 extract(s) hybridised to it (1-colour).

  • Extract 1 ("Agusti_5dMS_SS3_SRC") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

The slide used was "Affymetrix ATH1 Arabidopsis Genome Array".

Click on the options above for more information about this slide and its preparation.

Hybridisation Protocol Information

Name of Protocol: Affymetrix Antibody Amplification Protocol
Solution:
BufferEDTA, NaCl, Tween20 according to Affymetrix protocol
Water
Blocking Agent:
Herring Sperm DNA(Source: Promega)100pg/ml
Acetylated BSA(Source: Sigma-Aldrich)0.1mg/ml
Wash Procedure:
Step 1(Source: Affymetrix)10 cycles of 2 mixes/cycle with Non-Stringent buffer
Step 2(Source: Affymetrix)4 cycles of 15 mixes/cycle with Stringent buffer
Step 3(Source: Affymetrix)Stain the probe array for 10 minutes in Streptavaidin Phycoerythrin (SAPE) solution at 25 C
Step 4(Source: Affymetrix)10 cycles of 4 mixes/cycle with Non-Stringent buffer
Step 5(Source: Affymetrix)Stain the probe array for 10 minutes in antibody solution
Step 6(Source: Affymetrix)Stain the probe array for 10 minutes in SAPE solution at 25 C
Step 7(Source: Affymetrix)15 cycles of 4mixes/cycle with Non-Stringent buffer at 30 C
Step 8(Source: Affymetrix)Hold at 25 C
Quantity Used:
Amount15 microgram Fragmented cRNA
Time: 16 hours
Concentration: 50 pg/ml
Volume: 200 microlitres
Temperature: 45 C
Other Information:
Spike(Source: Affymetrix)Control Oligo B2 to 50pM for landing lights
Spike(Source: Affymetrix)20X Eukaryotic Hybridisation Controls (bioB (1.5pM, bioC 5pM, bioD 25pM, cre 100pM)
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

BioSource 1 Information

BioSource Name: Agusti_5dMS_SS3_SRC
Organism: Arabidopsis thaliana
Alias: Columbia
Stock Code:
Growth Conditions:
ProtocolLayed out seeds were kept at 4°C for two days. Then, plants were grown for 3 weeks in short day conditions (8h light, 16h darkness) and then shifted into long day conditions (16h light, 8h darkness) to induce flowering.
Soil ConstituentsManufacturer: Frux. Composition: Standard.
Temperature22 °C average, 22.5 °C day, 21.5 °C night
Humidity61 % average, 63 % day, 59 % night
Medium
Lighting(Source: Cool white fluorescent manufactured by Philips. Intensity: 25µEinsteins. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)6.10
Tissue: Starch sheath + interfascicular fibers
in vivo Treatment: Stems from 15cm plants were harvested. Only plants which first internode was at least 5cm long were selected. Stems were surface sterylised and a 1.5cm sample located 2cm away from the rosette was separated for our experiments. The samples were then incubated in a MS split-plate. The samples were then rapidly embedded in OCT and frozen until used.
Additional Organism Information:
Sample Description15cm plants with a first internode at least 5cm long.
Other Information:
ecotype_habitat
Timecourse start procedureStart point was set when plant were collected.

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:7.957303
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
Spike_AFFX-r2-P1-cre_3-5-ratio1.032574
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.320080
Spike_AFFX-r2-Bs-dap_5_signal200.231140
NoiseAvg:2.43,Std:0.13,Min:2.2,Max:2.9
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal91.609688
#P4937
Spike_AFFX-r2-Bs-phe_M_signal62.752945
Corner-Avg:8466,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal1800.905151
Spike_AFFX-r2-Ec-bioB_3_signal1671.314453
Spike_AFFX-r2-Bs-lys_M_signal71.911438
Spike_AFFX-r2-P1-cre_3_signal53941.570313
Spike_AFFX-r2-Bs-lys_3-5-ratio6.755831
Spike_AFFX-r2-Bs-dap_M_signal146.648727
Spike_AFFX-r2-Bs-thr_M_detectionA
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio1.874714
Spike_AFFX-r2-Ec-bioB_avg-signal1579.430176
Spike_AFFX-r2-Bs-thr_avg-signal170.195313
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal17450.986328
Spike_AFFX-r2-Bs-phe_5_signal76.447174
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal25629.060547
RawQ2.427016
Spike_AFFX-r2-Bs-lys_5_signal7.675356
Signal(A)49.993652
%A75.032883
Signal(All)147.869843
Corner+Avg:98,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal7556.989258
Spike_AFFX-r2-Bs-lys_3_detectionA
Spike_AFFX-r2-Bs-phe_3_signal94.729347
Spike_AFFX-r2-Ec-bioD_avg-signal21540.023438
Spike_AFFX-r2-Bs-dap_5_detectionA
Spike_AFFX-r2-Bs-phe_5_detectionP
%P21.644016
Spike_AFFX-r2-Bs-lys_avg-signal43.813400
Spike_AFFX-r2-P1-cre_avg-signal53090.734375
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionA
#Probe Sets Exceeding Probe Pair Threshold22810
%M3.323104
Spike_AFFX-r2-Bs-thr_3_signal171.741974
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionA
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal77.976494
Spike_AFFX-r2-Bs-dap_3_signal372.876312
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.468631
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal6577.468262
#M758
Spike_AFFX-r2-Bs-lys_5_detectionA
Spike_AFFX-r2-Bs-lys_3_signal51.853409
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.148921
Spike_AFFX-r2-Bs-thr_M_signal247.234299
Signal(P)485.268433
Spike_AFFX-r2-Bs-phe_3-5-ratio1.239148
Spike_AFFX-r2-Bs-thr_3_detectionA
Central-Avg:5889,Count:9
Spike_AFFX-r2-P1-cre_5_signal52239.894531
Spike_AFFX-r2-Bs-phe_M_detectionA
#A17115
Signal(M)160.289337
BackgroundAvg:82.02,Std:0.72,Min:80.8,Max:85.0
Spike_AFFX-r2-Ec-bioC_avg-signal7067.228516
Spike_AFFX-r2-Bs-dap_avg-signal239.918716
Spike_AFFX-r2-Bs-dap_3-5-ratio1.862229
Spike_AFFX-r2-Ec-bioB_5_signal1266.070801
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF7.957303
NF1.000000
HZ4
Tau0.015000


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