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Experiment: Role of FVE in plant development

Experiment Description

NASCArrays Experiment Reference Number: NASCARRAYS-632

15-d-old seedlings grown in vitro on horizontal plates containing 1/2 MS, 0,5% sucrose, 0,4% phytoagar under LD (16h light / 8h dark) conditions were collected for analysis. Samples include Col-0 wt control, fve, and mutants of potential FVE-interactors. Three biological replicates are included for each genotype.RNA was prepared using the Qiagen Plant RNEasy kit with additional on-column DNaseI treatment.

About the Experimenter

Name: Gergely Molnar
Head of Lab Name: Rishikesh Bhalerao
Lab:
Address:Department of Forest Genetics and Plant Physiology, Faculty of Forest Sciences , Swedish University of Agricultural Sciences (SLU)
Skogsmarksgrind, Umea, Vasterbottens line,
Postcode: 901 83
Country: SWEDEN
 

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: gene_knock_out
Number of Slides:12
 
Experimental Parameters:
parameter gene_knock_out
Quality Control Measures Taken:
References:
 
Other Information:

Slides in this Experiment

Hybridisation Set: Molnar: Role of FVE in plant development

Slide: Molnar_632-1_WT-Control_Rep1_ATH1

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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 ("Molnar_632-1_WT-Control_Rep1_ATH1") 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: Molnar_632-1_WT-Control_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Age: 15 days
Growth Conditions:
Stratification72h 4 centigrades
Sterilisation5 min in 70% ethanol / 0,1% Tween-20. Rinsed 1x with 95% ethanol, then dried.
ProtocolSurface sterilized and dried seeds were sown on plates containing 1/2xMS (Sigma), supplemented with 0,5% sucrose and 0,4% Phytoagar (Duchefa). The plates were cold-treated at 4C for 3 days and then transferred to the growth room. Plants were grown under LD (16L/8D) conditions for 15 days, then collected, snap-freezed in liquid nitrogen and RNA was purified.
Substrate Sterilising Procedureautoclaving
Plant Spacingseeds sown on grid, approx. 10mm apart from each other
Temperature21 °C average, 22 °C day, 18 °C night
Humidity60 % average, 60 % day, 60 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent. Intensity: 150µEinsteins. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.05
Tissue: whole plant
Additional Organism Information:
Sample DescriptionCol-0, descendant of N1092, wild type control
Other Information:

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:0.563782
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-ratio1.287939
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.697311
Spike_AFFX-r2-Bs-dap_5_signal31.741058
NoiseAvg:3.00,Std:0.08,Min:2.8,Max:3.3
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionA
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal6.006699
#P14965
Spike_AFFX-r2-Bs-phe_M_signal40.705654
Corner-Avg:8881,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal16.375717
Spike_AFFX-r2-Ec-bioB_3_signal18.046364
Spike_AFFX-r2-Bs-lys_M_signal20.681204
Spike_AFFX-r2-P1-cre_3_signal4943.390137
Spike_AFFX-r2-Bs-lys_3-5-ratio2.164695
Spike_AFFX-r2-Bs-dap_M_signal181.173508
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio17.644106
Spike_AFFX-r2-Ec-bioB_avg-signal20.100676
Spike_AFFX-r2-Bs-thr_avg-signal52.993118
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1014.661560
Spike_AFFX-r2-Bs-phe_5_signal21.372749
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1402.637817
RawQ2.580745
Spike_AFFX-r2-Bs-lys_5_signal28.455383
Signal(A)5.577156
%A32.538361
Signal(All)141.996460
Corner+Avg:157,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal324.234680
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal63.656460
Spike_AFFX-r2-Ec-bioD_avg-signal1208.649658
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P65.607193
Spike_AFFX-r2-Bs-lys_avg-signal36.911266
Spike_AFFX-r2-P1-cre_avg-signal4390.803223
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.854450
Spike_AFFX-r2-Bs-thr_3_signal105.982834
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-signal41.911621
Spike_AFFX-r2-Bs-dap_3_signal383.941681
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.382370
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal307.118439
#M423
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal61.597210
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.055732
Spike_AFFX-r2-Bs-thr_M_signal46.989819
Signal(P)213.091537
Spike_AFFX-r2-Bs-phe_3-5-ratio2.978394
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:7005,Count:9
Spike_AFFX-r2-P1-cre_5_signal3838.216309
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7422
Signal(M)20.404152
BackgroundAvg:57.43,Std:0.59,Min:55.7,Max:58.9
Spike_AFFX-r2-Ec-bioC_avg-signal315.676575
Spike_AFFX-r2-Bs-dap_avg-signal198.952072
Spike_AFFX-r2-Bs-dap_3-5-ratio12.096058
Spike_AFFX-r2-Ec-bioB_5_signal25.879946
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.563782
NF1.000000
HZ4
Tau0.015000

Slide: Molnar_632-2_WT-Control_Rep2_ATH1

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 ("Molnar_632-2_WT-Control_Rep2_ATH1") 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: Molnar_632-2_WT-Control_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Age: 15 days
Growth Conditions:
Stratification72h 4 centigrades
Sterilisation5 min in 70% ethanol / 0,1% Tween-20. Rinsed 1x with 95% ethanol, then dried.
ProtocolSurface sterilized and dried seeds were sown on plates containing 1/2xMS (Sigma), supplemented with 0,5% sucrose and 0,4% Phytoagar (Duchefa). The plates were cold-treated at 4C for 3 days and then transferred to the growth room. Plants were grown under LD (16L/8D) conditions for 15 days, then collected, snap-freezed in liquid nitrogen and RNA was purified.
Substrate Sterilising Procedureautoclaving
Plant Spacingseeds sown on grid, approx. 10mm apart from each other
Temperature21 °C average, 22 °C day, 18 °C night
Humidity60 % average, 60 % day, 60 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent. Intensity: 150µEinsteins. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.05
Tissue: whole plant
Additional Organism Information:
Sample DescriptionCol-0, descendant of N1092, wild type control, rep.2
Other Information:

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:0.652148
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-ratio0.918752
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.691414
Spike_AFFX-r2-Bs-dap_5_signal26.252535
NoiseAvg:2.90,Std:0.12,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_signal3.931906
#P15016
Spike_AFFX-r2-Bs-phe_M_signal24.839046
Corner-Avg:8470,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal17.292980
Spike_AFFX-r2-Ec-bioB_3_signal12.953732
Spike_AFFX-r2-Bs-lys_M_signal13.363486
Spike_AFFX-r2-P1-cre_3_signal3829.727051
Spike_AFFX-r2-Bs-lys_3-5-ratio3.153842
Spike_AFFX-r2-Bs-dap_M_signal116.517670
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio19.325787
Spike_AFFX-r2-Ec-bioB_avg-signal16.327284
Spike_AFFX-r2-Bs-thr_avg-signal37.480282
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1015.998169
Spike_AFFX-r2-Bs-phe_5_signal18.594133
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1628.164185
RawQ2.572049
Spike_AFFX-r2-Bs-lys_5_signal11.509895
Signal(A)5.391250
%A32.244629
Signal(All)141.933090
Corner+Avg:147,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal264.742645
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal35.510750
Spike_AFFX-r2-Ec-bioD_avg-signal1322.081177
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P65.830772
Spike_AFFX-r2-Bs-lys_avg-signal20.391256
Spike_AFFX-r2-P1-cre_avg-signal3999.065186
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.924595
Spike_AFFX-r2-Bs-thr_3_signal75.987183
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-signal26.314644
Spike_AFFX-r2-Bs-dap_3_signal265.785980
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.602527
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal250.591156
#M439
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal36.300388
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.056472
Spike_AFFX-r2-Bs-thr_M_signal32.521755
Signal(P)212.417282
Spike_AFFX-r2-Bs-phe_3-5-ratio1.909782
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:7102,Count:9
Spike_AFFX-r2-P1-cre_5_signal4168.403320
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7355
Signal(M)18.640369
BackgroundAvg:59.98,Std:1.20,Min:56.9,Max:63.0
Spike_AFFX-r2-Ec-bioC_avg-signal257.666901
Spike_AFFX-r2-Bs-dap_avg-signal136.185394
Spike_AFFX-r2-Bs-dap_3-5-ratio10.124203
Spike_AFFX-r2-Ec-bioB_5_signal18.735138
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.652148
NF1.000000
HZ4
Tau0.015000

Slide: Molnar_632-3_WT-Control_Rep3_ATH1

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 ("Molnar_632-3_WT-Control_Rep3_ATH1") 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: Molnar_632-3_WT-Control_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Age: 15 days
Growth Conditions:
Stratification72h 4 centigrades
Sterilisation5 min in 70% ethanol / 0,1% Tween-20. Rinsed 1x with 95% ethanol, then dried.
ProtocolSurface sterilized and dried seeds were sown on plates containing 1/2xMS (Sigma), supplemented with 0,5% sucrose and 0,4% Phytoagar (Duchefa). The plates were cold-treated at 4C for 3 days and then transferred to the growth room. Plants were grown under LD (16L/8D) conditions for 15 days, then collected, snap-freezed in liquid nitrogen and RNA was purified.
Substrate Sterilising Procedureautoclaving
Plant Spacingseeds sown on grid, approx. 10mm apart from each other
Temperature21 °C average, 22 °C day, 18 °C night
Humidity60 % average, 60 % day, 60 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent. Intensity: 150µEinsteins. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.05
Tissue: whole plant
Additional Organism Information:
Sample DescriptionCol-0, descendant of N1092, wild type control, rep.3
Other Information:

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:0.539844
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-ratio1.242155
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.922198
Spike_AFFX-r2-Bs-dap_5_signal36.937954
NoiseAvg:2.92,Std:0.09,Min:2.7,Max:3.2
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal9.303449
#P15513
Spike_AFFX-r2-Bs-phe_M_signal37.285042
Corner-Avg:8255,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal12.260988
Spike_AFFX-r2-Ec-bioB_3_signal13.098137
Spike_AFFX-r2-Bs-lys_M_signal25.616079
Spike_AFFX-r2-P1-cre_3_signal4429.021484
Spike_AFFX-r2-Bs-lys_3-5-ratio2.030510
Spike_AFFX-r2-Bs-dap_M_signal230.022614
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio10.246186
Spike_AFFX-r2-Ec-bioB_avg-signal13.187430
Spike_AFFX-r2-Bs-thr_avg-signal50.302921
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal874.375549
Spike_AFFX-r2-Bs-phe_5_signal33.158722
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1226.820190
RawQ2.465255
Spike_AFFX-r2-Bs-lys_5_signal19.980387
Signal(A)4.530966
%A30.249891
Signal(All)139.108002
Corner+Avg:142,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal289.804718
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal61.177944
Spike_AFFX-r2-Ec-bioD_avg-signal1050.597900
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P68.009644
Spike_AFFX-r2-Bs-lys_avg-signal28.722277
Spike_AFFX-r2-P1-cre_avg-signal3997.308105
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.740465
Spike_AFFX-r2-Bs-thr_3_signal95.324867
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-signal43.873901
Spike_AFFX-r2-Bs-dap_3_signal460.517120
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.403082
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal265.729065
#M397
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal40.570370
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.090602
Spike_AFFX-r2-Bs-thr_M_signal46.280441
Signal(P)202.117355
Spike_AFFX-r2-Bs-phe_3-5-ratio1.845003
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:6281,Count:9
Spike_AFFX-r2-P1-cre_5_signal3565.594971
Spike_AFFX-r2-Bs-phe_M_detectionP
#A6900
Signal(M)15.978292
BackgroundAvg:59.91,Std:0.82,Min:58.1,Max:62.2
Spike_AFFX-r2-Ec-bioC_avg-signal277.766907
Spike_AFFX-r2-Bs-dap_avg-signal242.492554
Spike_AFFX-r2-Bs-dap_3-5-ratio12.467316
Spike_AFFX-r2-Ec-bioB_5_signal14.203165
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.539844
NF1.000000
HZ4
Tau0.015000

Slide: Molnar_632-4_N810420+N873162_Rep1_ATH1

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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 ("Molnar_632-4_N810420+N873162_Rep1_ATH1") 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: Molnar_632-4_N810420+N873162_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: pum5-1 pum6-1
Stock Code:
Genetic Background: Col-0
Age: 15 days
Growth Conditions:
Stratification72h 4 centigrades
Sterilisation5 min in 70% ethanol / 0,1% Tween-20. Rinsed 1x with 95% ethanol, then dried.
ProtocolSurface sterilized and dried seeds were sown on plates containing 1/2xMS (Sigma), supplemented with 0,5% sucrose and 0,4% Phytoagar (Duchefa). The plates were cold-treated at 4C for 3 days and then transferred to the growth room. Plants were grown under LD (16L/8D) conditions for 15 days, then collected, snap-freezed in liquid nitrogen and RNA was purified.
Substrate Sterilising Procedureautoclaving
Plant Spacingseeds sown on grid, approx. 10mm apart from each other
Temperature21 °C average, 22 °C day, 18 °C night
Humidity60 % average, 60 % day, 60 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent. Intensity: 150µEinsteins. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.05
Genetic Variation: T-DNA knock out mutation in At3g20250,At4g25880
Tissue: whole plant
Additional Organism Information:
Sample Descriptionpum5-1 pum6-1 double homozygous mutants from a cross of N810420 and N873162, rep.1
Other Information:

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:0.670469
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-ratio1.392238
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.879572
Spike_AFFX-r2-Bs-dap_5_signal25.783710
NoiseAvg:3.13,Std:0.12,Min:2.8,Max:3.5
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionM
Spike_AFFX-r2-Ec-bioB_3_detectionA
Spike_AFFX-r2-Bs-thr_5_signal12.255322
#P14717
Spike_AFFX-r2-Bs-phe_M_signal27.658913
Corner-Avg:6801,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal13.812568
Spike_AFFX-r2-Ec-bioB_3_signal12.072195
Spike_AFFX-r2-Bs-lys_M_signal16.862173
Spike_AFFX-r2-P1-cre_3_signal4106.786621
Spike_AFFX-r2-Bs-lys_3-5-ratio1.748259
Spike_AFFX-r2-Bs-dap_M_signal151.910782
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio4.868013
Spike_AFFX-r2-Ec-bioB_avg-signal13.203280
Spike_AFFX-r2-Bs-thr_avg-signal35.845039
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal894.620789
Spike_AFFX-r2-Bs-phe_5_signal23.478628
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1198.947754
RawQ2.751279
Spike_AFFX-r2-Bs-lys_5_signal15.730796
Signal(A)5.986397
%A33.410786
Signal(All)142.515121
Corner+Avg:120,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal255.053696
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal43.847889
Spike_AFFX-r2-Ec-bioD_avg-signal1046.784302
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P64.519951
Spike_AFFX-r2-Bs-lys_avg-signal20.031492
Spike_AFFX-r2-P1-cre_avg-signal3528.280273
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionA
#Probe Sets Exceeding Probe Pair Threshold22810
%M2.069268
Spike_AFFX-r2-Bs-thr_3_signal59.659065
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-signal31.661812
Spike_AFFX-r2-Bs-dap_3_signal221.381180
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.340174
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal235.400818
#M472
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal27.501503
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.083487
Spike_AFFX-r2-Bs-thr_M_signal35.620728
Signal(P)217.141708
Spike_AFFX-r2-Bs-phe_3-5-ratio1.867566
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:5630,Count:9
Spike_AFFX-r2-P1-cre_5_signal2949.774170
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7621
Signal(M)20.070066
BackgroundAvg:64.60,Std:1.07,Min:61.7,Max:66.5
Spike_AFFX-r2-Ec-bioC_avg-signal245.227264
Spike_AFFX-r2-Bs-dap_avg-signal133.025223
Spike_AFFX-r2-Bs-dap_3-5-ratio8.586087
Spike_AFFX-r2-Ec-bioB_5_signal13.725078
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.670469
NF1.000000
HZ4
Tau0.015000

Slide: Molnar_632-5_N810420+N873162_Rep2_ATH1

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 ("Molnar_632-5_N810420+N873162_Rep2_ATH1") 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: Molnar_632-5_N810420+N873162_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: pum5-1 pum6-1
Stock Code:
Genetic Background: Col-0
Age: 15 days
Growth Conditions:
Stratification72h 4 centigrades
Sterilisation5 min in 70% ethanol / 0,1% Tween-20. Rinsed 1x with 95% ethanol, then dried.
ProtocolSurface sterilized and dried seeds were sown on plates containing 1/2xMS (Sigma), supplemented with 0,5% sucrose and 0,4% Phytoagar (Duchefa). The plates were cold-treated at 4C for 3 days and then transferred to the growth room. Plants were grown under LD (16L/8D) conditions for 15 days, then collected, snap-freezed in liquid nitrogen and RNA was purified.
Substrate Sterilising Procedureautoclaving
Plant Spacingseeds sown on grid, approx. 10mm apart from each other
Temperature21 °C average, 22 °C day, 18 °C night
Humidity60 % average, 60 % day, 60 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent. Intensity: 150µEinsteins. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.05
Genetic Variation: T-DNA knock out mutation in At3g20250,At4g25880
Tissue: whole plant
Additional Organism Information:
Sample Descriptionpum5-1 pum6-1 double homozygous mutants from a cross of N810420 and N873162, rep.2
Other Information:

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:0.440709
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-ratio1.294515
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.675648
Spike_AFFX-r2-Bs-dap_5_signal56.713306
NoiseAvg:3.24,Std:0.06,Min:3.1,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_signal17.694935
#P15539
Spike_AFFX-r2-Bs-phe_M_signal56.482391
Corner-Avg:9334,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal9.768338
Spike_AFFX-r2-Ec-bioB_3_signal13.570424
Spike_AFFX-r2-Bs-lys_M_signal18.687305
Spike_AFFX-r2-P1-cre_3_signal4095.125488
Spike_AFFX-r2-Bs-lys_3-5-ratio2.307506
Spike_AFFX-r2-Bs-dap_M_signal269.391174
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio8.883587
Spike_AFFX-r2-Ec-bioB_avg-signal14.474602
Spike_AFFX-r2-Bs-thr_avg-signal79.749443
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal973.791626
Spike_AFFX-r2-Bs-phe_5_signal37.383148
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1303.487305
RawQ2.667940
Spike_AFFX-r2-Bs-lys_5_signal30.354303
Signal(A)4.246768
%A30.201666
Signal(All)137.227234
Corner+Avg:185,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal275.278229
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal63.387642
Spike_AFFX-r2-Ec-bioD_avg-signal1138.639404
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P68.123627
Spike_AFFX-r2-Bs-lys_avg-signal39.694775
Spike_AFFX-r2-P1-cre_avg-signal3629.284668
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.674704
Spike_AFFX-r2-Bs-thr_3_signal157.194489
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-signal52.417725
Spike_AFFX-r2-Bs-dap_3_signal498.466370
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.338569
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal282.919739
#M382
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal70.042725
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.972991
Spike_AFFX-r2-Bs-thr_M_signal64.358917
Signal(P)199.193680
Spike_AFFX-r2-Bs-phe_3-5-ratio1.695621
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:7941,Count:9
Spike_AFFX-r2-P1-cre_5_signal3163.443848
Spike_AFFX-r2-Bs-phe_M_detectionP
#A6889
Signal(M)14.729625
BackgroundAvg:64.59,Std:0.45,Min:63.5,Max:65.8
Spike_AFFX-r2-Ec-bioC_avg-signal279.098999
Spike_AFFX-r2-Bs-dap_avg-signal274.856964
Spike_AFFX-r2-Bs-dap_3-5-ratio8.789231
Spike_AFFX-r2-Ec-bioB_5_signal20.085045
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.440709
NF1.000000
HZ4
Tau0.015000

Slide: Molnar_632-6_N810420+N873162_Rep3_ATH1

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 ("Molnar_632-6_N810420+N873162_Rep3_ATH1") 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: Molnar_632-6_N810420+N873162_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: pum5-1 pum6-1
Stock Code:
Genetic Background: Col-0
Age: 15 days
Growth Conditions:
Stratification72h 4 centigrades
Sterilisation5 min in 70% ethanol / 0,1% Tween-20. Rinsed 1x with 95% ethanol, then dried.
ProtocolSurface sterilized and dried seeds were sown on plates containing 1/2xMS (Sigma), supplemented with 0,5% sucrose and 0,4% Phytoagar (Duchefa). The plates were cold-treated at 4C for 3 days and then transferred to the growth room. Plants were grown under LD (16L/8D) conditions for 15 days, then collected, snap-freezed in liquid nitrogen and RNA was purified.
Substrate Sterilising Procedureautoclaving
Plant Spacingseeds sown on grid, approx. 10mm apart from each other
Temperature21 °C average, 22 °C day, 18 °C night
Humidity60 % average, 60 % day, 60 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent. Intensity: 150µEinsteins. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.05
Genetic Variation: T-DNA knock out mutation in At3g20250,At4g25880
Tissue: whole plant
Additional Organism Information:
Sample Descriptionpum5-1 pum6-1 double homozygous mutants from a cross of N810420 and N873162, rep.3
Other Information:

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:0.38272
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-ratio1.207950
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.833934
Spike_AFFX-r2-Bs-dap_5_signal25.001673
NoiseAvg:3.63,Std:0.14,Min:3.2,Max:4.0
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal7.705838
#P15704
Spike_AFFX-r2-Bs-phe_M_signal25.067686
Corner-Avg:9266,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal11.492609
Spike_AFFX-r2-Ec-bioB_3_signal11.465008
Spike_AFFX-r2-Bs-lys_M_signal14.344589
Spike_AFFX-r2-P1-cre_3_signal3289.875732
Spike_AFFX-r2-Bs-lys_3-5-ratio3.301634
Spike_AFFX-r2-Bs-dap_M_signal147.261414
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio8.464712
Spike_AFFX-r2-Ec-bioB_avg-signal12.235240
Spike_AFFX-r2-Bs-thr_avg-signal34.370304
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal806.953613
Spike_AFFX-r2-Bs-phe_5_signal13.436090
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1082.771729
RawQ2.931799
Spike_AFFX-r2-Bs-lys_5_signal14.522787
Signal(A)4.190932
%A29.526524
Signal(All)135.555756
Corner+Avg:164,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal239.790146
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal31.931208
Spike_AFFX-r2-Ec-bioD_avg-signal944.862671
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P68.847000
Spike_AFFX-r2-Bs-lys_avg-signal25.605436
Spike_AFFX-r2-P1-cre_avg-signal3006.698242
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.626480
Spike_AFFX-r2-Bs-thr_3_signal65.227699
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-signal23.478327
Spike_AFFX-r2-Bs-dap_3_signal244.157883
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.341802
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal224.706131
#M371
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal47.948933
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.067128
Spike_AFFX-r2-Bs-thr_M_signal30.177380
Signal(P)194.756668
Spike_AFFX-r2-Bs-phe_3-5-ratio2.376525
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:7281,Count:9
Spike_AFFX-r2-P1-cre_5_signal2723.520752
Spike_AFFX-r2-Bs-phe_M_detectionP
#A6735
Signal(M)14.399456
BackgroundAvg:70.69,Std:0.79,Min:68.1,Max:72.5
Spike_AFFX-r2-Ec-bioC_avg-signal232.248138
Spike_AFFX-r2-Bs-dap_avg-signal138.806992
Spike_AFFX-r2-Bs-dap_3-5-ratio9.765662
Spike_AFFX-r2-Ec-bioB_5_signal13.748103
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.382720
NF1.000000
HZ4
Tau0.015000

Slide: Molnar_632-7_Mutant-N802366_Rep1_ATH1

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 ("Molnar_632-7_Mutant-N802366_Rep1_ATH1") 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: Molnar_632-7_Mutant-N802366_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Age: 15 days
Growth Conditions:
Stratification72h 4 centigrades
Sterilisation5 min in 70% ethanol / 0,1% Tween-20. Rinsed 1x with 95% ethanol, then dried.
ProtocolSurface sterilized and dried seeds were sown on plates containing 1/2xMS (Sigma), supplemented with 0,5% sucrose and 0,4% Phytoagar (Duchefa). The plates were cold-treated at 4C for 3 days and then transferred to the growth room. Plants were grown under LD (16L/8D) conditions for 15 days, then collected, snap-freezed in liquid nitrogen and RNA was purified.
Substrate Sterilising Procedureautoclaving
Plant Spacingseeds sown on grid, approx. 10mm apart from each other
Temperature21 °C average, 22 °C day, 18 °C night
Humidity60 % average, 60 % day, 60 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent. Intensity: 150µEinsteins. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.05
Tissue: whole plant
Additional Organism Information:
Sample DescriptionCol-0, descendant of N1092, wild type control
Other Information:

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:0.391569
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-ratio1.213824
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.176880
Spike_AFFX-r2-Bs-dap_5_signal48.513680
NoiseAvg:3.53,Std:0.13,Min:3.1,Max:3.9
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal13.189553
#P15442
Spike_AFFX-r2-Bs-phe_M_signal47.159241
Corner-Avg:10135,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal12.342230
Spike_AFFX-r2-Ec-bioB_3_signal15.201720
Spike_AFFX-r2-Bs-lys_M_signal20.792173
Spike_AFFX-r2-P1-cre_3_signal3910.445557
Spike_AFFX-r2-Bs-lys_3-5-ratio1.916918
Spike_AFFX-r2-Bs-dap_M_signal231.301910
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio12.092361
Spike_AFFX-r2-Ec-bioB_avg-signal13.486972
Spike_AFFX-r2-Bs-thr_avg-signal74.961983
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal924.517944
Spike_AFFX-r2-Bs-phe_5_signal29.845936
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1303.355713
RawQ2.756077
Spike_AFFX-r2-Bs-lys_5_signal27.819031
Signal(A)4.501553
%A30.420868
Signal(All)137.805496
Corner+Avg:180,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal242.422745
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal88.519707
Spike_AFFX-r2-Ec-bioD_avg-signal1113.936768
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P67.698380
Spike_AFFX-r2-Bs-lys_avg-signal33.979336
Spike_AFFX-r2-P1-cre_avg-signal3566.019043
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.880754
Spike_AFFX-r2-Bs-thr_3_signal159.492844
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-signal55.174961
Spike_AFFX-r2-Bs-dap_3_signal495.408875
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.409768
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal254.711441
#M429
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal53.326805
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.951754
Spike_AFFX-r2-Bs-thr_M_signal52.203548
Signal(P)201.093109
Spike_AFFX-r2-Bs-phe_3-5-ratio2.965888
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:8488,Count:9
Spike_AFFX-r2-P1-cre_5_signal3221.592285
Spike_AFFX-r2-Bs-phe_M_detectionP
#A6939
Signal(M)15.914368
BackgroundAvg:67.68,Std:0.75,Min:65.8,Max:69.0
Spike_AFFX-r2-Ec-bioC_avg-signal248.567093
Spike_AFFX-r2-Bs-dap_avg-signal258.408173
Spike_AFFX-r2-Bs-dap_3-5-ratio10.211736
Spike_AFFX-r2-Ec-bioB_5_signal12.916966
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.391569
NF1.000000
HZ4
Tau0.015000

Slide: Molnar_632-8_Mutant-N802366_Rep2_ATH1

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 ("Molnar_632-8_Mutant-N802366_Rep2_ATH1") 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: Molnar_632-8_Mutant-N802366_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: SAIL_50_D10
Stock Code: N802366
Age: 15 days
Growth Conditions:
Stratification72h 4 centigrades
Sterilisation5 min in 70% ethanol / 0,1% Tween-20. Rinsed 1x with 95% ethanol, then dried.
ProtocolSurface sterilized and dried seeds were sown on plates containing 1/2xMS (Sigma), supplemented with 0,5% sucrose and 0,4% Phytoagar (Duchefa). The plates were cold-treated at 4C for 3 days and then transferred to the growth room. Plants were grown under LD (16L/8D) conditions for 15 days, then collected, snap-freezed in liquid nitrogen and RNA was purified.
Substrate Sterilising Procedureautoclaving
Plant Spacingseeds sown on grid, approx. 10mm apart from each other
Temperature21 °C average, 22 °C day, 18 °C night
Humidity60 % average, 60 % day, 60 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent. Intensity: 150µEinsteins. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.05
Tissue: whole plant
Additional Organism Information:
Sample DescriptionHomozygous mutants from N802366, rep.2
Other Information:

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:0.566812
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-ratio1.189041
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.183609
Spike_AFFX-r2-Bs-dap_5_signal30.313589
NoiseAvg:3.29,Std:0.11,Min:2.9,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_signal12.993040
#P15047
Spike_AFFX-r2-Bs-phe_M_signal31.160204
Corner-Avg:11801,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal12.615305
Spike_AFFX-r2-Ec-bioB_3_signal15.928399
Spike_AFFX-r2-Bs-lys_M_signal16.292288
Spike_AFFX-r2-P1-cre_3_signal3986.567383
Spike_AFFX-r2-Bs-lys_3-5-ratio2.004337
Spike_AFFX-r2-Bs-dap_M_signal175.119934
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio7.523038
Spike_AFFX-r2-Ec-bioB_avg-signal14.000397
Spike_AFFX-r2-Bs-thr_avg-signal49.336533
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal825.709717
Spike_AFFX-r2-Bs-phe_5_signal20.596210
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1245.030884
RawQ2.769246
Spike_AFFX-r2-Bs-lys_5_signal19.024126
Signal(A)5.694327
%A32.152565
Signal(All)139.442612
Corner+Avg:227,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal209.539764
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal50.230900
Spike_AFFX-r2-Ec-bioD_avg-signal1035.370361
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P65.966682
Spike_AFFX-r2-Bs-lys_avg-signal24.482391
Spike_AFFX-r2-P1-cre_avg-signal3669.662598
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.880754
Spike_AFFX-r2-Bs-thr_3_signal97.747139
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-signal33.995773
Spike_AFFX-r2-Bs-dap_3_signal339.740997
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.507831
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal245.533493
#M429
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal38.130764
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.853406
Spike_AFFX-r2-Bs-thr_M_signal37.269413
Signal(P)208.045563
Spike_AFFX-r2-Bs-phe_3-5-ratio2.438842
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:10920,Count:9
Spike_AFFX-r2-P1-cre_5_signal3352.757813
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7334
Signal(M)19.725653
BackgroundAvg:66.63,Std:0.38,Min:65.8,Max:68.0
Spike_AFFX-r2-Ec-bioC_avg-signal227.536621
Spike_AFFX-r2-Bs-dap_avg-signal181.724854
Spike_AFFX-r2-Bs-dap_3-5-ratio11.207548
Spike_AFFX-r2-Ec-bioB_5_signal13.457484
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.566812
NF1.000000
HZ4
Tau0.015000

Slide: Molnar_632-9_Mutant-N802366_Rep3_ATH1

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 ("Molnar_632-9_Mutant-N802366_Rep3_ATH1") 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: Molnar_632-9_Mutant-N802366_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: SAIL_50_D10
Stock Code: N802366
Age: 15 days
Growth Conditions:
Stratification72h 4 centigrades
Sterilisation5 min in 70% ethanol / 0,1% Tween-20. Rinsed 1x with 95% ethanol, then dried.
ProtocolSurface sterilized and dried seeds were sown on plates containing 1/2xMS (Sigma), supplemented with 0,5% sucrose and 0,4% Phytoagar (Duchefa). The plates were cold-treated at 4C for 3 days and then transferred to the growth room. Plants were grown under LD (16L/8D) conditions for 15 days, then collected, snap-freezed in liquid nitrogen and RNA was purified.
Substrate Sterilising Procedureautoclaving
Plant Spacingseeds sown on grid, approx. 10mm apart from each other
Temperature21 °C average, 22 °C day, 18 °C night
Humidity60 % average, 60 % day, 60 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent. Intensity: 150µEinsteins. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.05
Tissue: whole plant
Additional Organism Information:
Sample DescriptionHomozygous mutants from N802366, rep.3
Other Information:

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:0.622267
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-ratio1.196080
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.993265
Spike_AFFX-r2-Bs-dap_5_signal43.113033
NoiseAvg:2.66,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_signal8.261659
#P15216
Spike_AFFX-r2-Bs-phe_M_signal36.055649
Corner-Avg:7706,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal14.901784
Spike_AFFX-r2-Ec-bioB_3_signal14.160543
Spike_AFFX-r2-Bs-lys_M_signal17.421328
Spike_AFFX-r2-P1-cre_3_signal4903.918457
Spike_AFFX-r2-Bs-lys_3-5-ratio2.077840
Spike_AFFX-r2-Bs-dap_M_signal198.340759
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio18.885571
Spike_AFFX-r2-Ec-bioB_avg-signal14.439630
Spike_AFFX-r2-Bs-thr_avg-signal68.698364
Spike_AFFX-r2-Bs-thr_5_detectionM
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1101.857422
Spike_AFFX-r2-Bs-phe_5_signal28.267109
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1450.911743
RawQ2.339675
Spike_AFFX-r2-Bs-lys_5_signal23.166594
Signal(A)4.991186
%A31.464270
Signal(All)139.970139
Corner+Avg:139,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal271.200317
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal63.090942
Spike_AFFX-r2-Ec-bioD_avg-signal1276.384521
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P66.707588
Spike_AFFX-r2-Bs-lys_avg-signal29.574797
Spike_AFFX-r2-P1-cre_avg-signal4501.955078
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.828146
Spike_AFFX-r2-Bs-thr_3_signal156.026138
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-signal42.471233
Spike_AFFX-r2-Bs-dap_3_signal412.817413
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.316787
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal276.918915
#M417
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal48.136467
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.979349
Spike_AFFX-r2-Bs-thr_M_signal41.807289
Signal(P)206.995468
Spike_AFFX-r2-Bs-phe_3-5-ratio2.231956
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:5617,Count:9
Spike_AFFX-r2-P1-cre_5_signal4099.991211
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7177
Signal(M)17.396175
BackgroundAvg:55.51,Std:0.42,Min:54.4,Max:56.9
Spike_AFFX-r2-Ec-bioC_avg-signal274.059631
Spike_AFFX-r2-Bs-dap_avg-signal218.090408
Spike_AFFX-r2-Bs-dap_3-5-ratio9.575234
Spike_AFFX-r2-Ec-bioB_5_signal14.256562
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.622267
NF1.000000
HZ4
Tau0.015000

Slide: Molnar_632-10_Mutant-N513789_Rep1_ATH1

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 ("Molnar_632-10_Mutant-N513789_Rep1_ATH1") 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: Molnar_632-10_Mutant-N513789_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: SALK_013789 (H) (R)
Stock Code: N513789
Genetic Background: Col-0 (Columbia, N60000)
Age: 15 days
Growth Conditions:
Stratification72h 4 centigrades
Sterilisation5 min in 70% ethanol / 0,1% Tween-20. Rinsed 1x with 95% ethanol, then dried.
ProtocolSurface sterilized and dried seeds were sown on plates containing 1/2xMS (Sigma), supplemented with 0,5% sucrose and 0,4% Phytoagar (Duchefa). The plates were cold-treated at 4C for 3 days and then transferred to the growth room. Plants were grown under LD (16L/8D) conditions for 15 days, then collected, snap-freezed in liquid nitrogen and RNA was purified.
Substrate Sterilising Procedureautoclaving
Plant Spacingseeds sown on grid, approx. 10mm apart from each other
Temperature21 °C average, 22 °C day, 18 °C night
Humidity60 % average, 60 % day, 60 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent. Intensity: 150µEinsteins. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.05
Genetic Variation: T-DNA Insertion
Tissue: whole plant
Additional Organism Information:
Sample DescriptionHomozygous mutants from N513789, rep.1
Other Information:

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:0.445072
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-ratio1.261027
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.334803
Spike_AFFX-r2-Bs-dap_5_signal36.348877
NoiseAvg:3.11,Std:0.09,Min:2.9,Max:3.4
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionM
Spike_AFFX-r2-Bs-thr_5_signal7.892601
#P15639
Spike_AFFX-r2-Bs-phe_M_signal32.860500
Corner-Avg:7940,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal9.780848
Spike_AFFX-r2-Ec-bioB_3_signal15.800751
Spike_AFFX-r2-Bs-lys_M_signal16.199823
Spike_AFFX-r2-P1-cre_3_signal3965.235352
Spike_AFFX-r2-Bs-lys_3-5-ratio2.040393
Spike_AFFX-r2-Bs-dap_M_signal192.361221
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio13.907507
Spike_AFFX-r2-Ec-bioB_avg-signal12.473038
Spike_AFFX-r2-Bs-thr_avg-signal53.946396
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal897.848083
Spike_AFFX-r2-Bs-phe_5_signal24.005869
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1057.755981
RawQ2.593666
Spike_AFFX-r2-Bs-lys_5_signal22.487705
Signal(A)4.052345
%A29.614204
Signal(All)138.468063
Corner+Avg:143,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal226.731583
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal64.020439
Spike_AFFX-r2-Ec-bioD_avg-signal977.802002
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P68.562035
Spike_AFFX-r2-Bs-lys_avg-signal28.190430
Spike_AFFX-r2-P1-cre_avg-signal3554.841797
Spike_AFFX-r2-Ec-bioB_M_detectionM
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.823761
Spike_AFFX-r2-Bs-thr_3_signal109.766396
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-signal40.295601
Spike_AFFX-r2-Bs-dap_3_signal389.296844
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.178101
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal199.600723
#M416
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal45.883762
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.135926
Spike_AFFX-r2-Bs-thr_M_signal44.180191
Signal(P)199.809967
Spike_AFFX-r2-Bs-phe_3-5-ratio2.666866
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:5839,Count:9
Spike_AFFX-r2-P1-cre_5_signal3144.448486
Spike_AFFX-r2-Bs-phe_M_detectionP
#A6755
Signal(M)15.035809
BackgroundAvg:62.21,Std:0.72,Min:60.0,Max:63.9
Spike_AFFX-r2-Ec-bioC_avg-signal213.166153
Spike_AFFX-r2-Bs-dap_avg-signal206.002319
Spike_AFFX-r2-Bs-dap_3-5-ratio10.710011
Spike_AFFX-r2-Ec-bioB_5_signal11.837514
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.445072
NF1.000000
HZ4
Tau0.015000

Slide: Molnar_632-11_Mutant-N513789_Rep2_ATH1

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 ("Molnar_632-11_Mutant-N513789_Rep2_ATH1") 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: Molnar_632-11_Mutant-N513789_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: SALK_013789 (H) (R)
Stock Code: N513789
Genetic Background: Col-0 (Columbia, N60000)
Age: 15 days
Growth Conditions:
Stratification72h 4 centigrades
Sterilisation5 min in 70% ethanol / 0,1% Tween-20. Rinsed 1x with 95% ethanol, then dried.
ProtocolSurface sterilized and dried seeds were sown on plates containing 1/2xMS (Sigma), supplemented with 0,5% sucrose and 0,4% Phytoagar (Duchefa). The plates were cold-treated at 4C for 3 days and then transferred to the growth room. Plants were grown under LD (16L/8D) conditions for 15 days, then collected, snap-freezed in liquid nitrogen and RNA was purified.
Substrate Sterilising Procedureautoclaving
Plant Spacingseeds sown on grid, approx. 10mm apart from each other
Temperature21 °C average, 22 °C day, 18 °C night
Humidity60 % average, 60 % day, 60 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent. Intensity: 150µEinsteins. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.05
Genetic Variation: T-DNA Insertion
Tissue: whole plant
Additional Organism Information:
Sample DescriptionHomozygous mutants from N513789, rep.2
Other Information:

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:0.566464
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-ratio1.207360
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.667179
Spike_AFFX-r2-Bs-dap_5_signal22.832806
NoiseAvg:3.17,Std:0.11,Min:2.9,Max:3.5
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionA
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal5.896899
#P15211
Spike_AFFX-r2-Bs-phe_M_signal18.535261
Corner-Avg:7948,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal9.053784
Spike_AFFX-r2-Ec-bioB_3_signal9.096534
Spike_AFFX-r2-Bs-lys_M_signal11.100636
Spike_AFFX-r2-P1-cre_3_signal3672.141113
Spike_AFFX-r2-Bs-lys_3-5-ratio2.388729
Spike_AFFX-r2-Bs-dap_M_signal87.268791
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio7.400189
Spike_AFFX-r2-Ec-bioB_avg-signal10.594882
Spike_AFFX-r2-Bs-thr_avg-signal25.038872
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal732.568298
Spike_AFFX-r2-Bs-phe_5_signal15.386299
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1149.515015
RawQ2.662975
Spike_AFFX-r2-Bs-lys_5_signal12.559340
Signal(A)5.470252
%A31.407278
Signal(All)139.377151
Corner+Avg:149,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal243.701248
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal30.427900
Spike_AFFX-r2-Ec-bioD_avg-signal941.041626
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P66.685661
Spike_AFFX-r2-Bs-lys_avg-signal17.886946
Spike_AFFX-r2-P1-cre_avg-signal3356.801758
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.907058
Spike_AFFX-r2-Bs-thr_3_signal43.638172
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-signal21.449820
Spike_AFFX-r2-Bs-dap_3_signal189.796707
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.569157
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal221.997665
#M435
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal30.000858
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.097765
Spike_AFFX-r2-Bs-thr_M_signal25.581545
Signal(P)205.904022
Spike_AFFX-r2-Bs-phe_3-5-ratio1.977597
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:6707,Count:9
Spike_AFFX-r2-P1-cre_5_signal3041.462402
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7164
Signal(M)18.386372
BackgroundAvg:65.71,Std:0.69,Min:63.4,Max:67.2
Spike_AFFX-r2-Ec-bioC_avg-signal232.849457
Spike_AFFX-r2-Bs-dap_avg-signal99.966095
Spike_AFFX-r2-Bs-dap_3-5-ratio8.312457
Spike_AFFX-r2-Ec-bioB_5_signal13.634328
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.566464
NF1.000000
HZ4
Tau0.015000

Slide: Molnar_632-12_Mutant-N513789_Rep3_ATH1

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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 ("Molnar_632-12_Mutant-N513789_Rep3_ATH1") 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: Molnar_632-12_Mutant-N513789_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: SALK_013789 (H) (R)
Stock Code: N513789
Genetic Background: Col-0 (Columbia, N60000)
Age: 15 days
Growth Conditions:
Stratification72h 4 centigrades
Sterilisation5 min in 70% ethanol / 0,1% Tween-20. Rinsed 1x with 95% ethanol, then dried.
ProtocolSurface sterilized and dried seeds were sown on plates containing 1/2xMS (Sigma), supplemented with 0,5% sucrose and 0,4% Phytoagar (Duchefa). The plates were cold-treated at 4C for 3 days and then transferred to the growth room. Plants were grown under LD (16L/8D) conditions for 15 days, then collected, snap-freezed in liquid nitrogen and RNA was purified.
Substrate Sterilising Procedureautoclaving
Plant Spacingseeds sown on grid, approx. 10mm apart from each other
Temperature21 °C average, 22 °C day, 18 °C night
Humidity60 % average, 60 % day, 60 % night
MediumMurashige & Skoog basal salt mixture
Lighting(Source: Cool white fluorescent. Intensity: 150µEinsteins. Wavelength: White)
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.05
Genetic Variation: T-DNA Insertion
Tissue: whole plant
Additional Organism Information:
Sample DescriptionHomozygous mutants from N513789, rep.3
Other Information:

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:0.43288
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-ratio1.188708
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.968330
Spike_AFFX-r2-Bs-dap_5_signal19.071674
NoiseAvg:3.23,Std:0.16,Min:2.9,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_signal13.221969
#P15665
Spike_AFFX-r2-Bs-phe_M_signal33.169979
Corner-Avg:8677,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal10.742435
Spike_AFFX-r2-Ec-bioB_3_signal15.734770
Spike_AFFX-r2-Bs-lys_M_signal18.160635
Spike_AFFX-r2-P1-cre_3_signal3678.786377
Spike_AFFX-r2-Bs-lys_3-5-ratio2.068529
Spike_AFFX-r2-Bs-dap_M_signal173.790527
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio9.618357
Spike_AFFX-r2-Ec-bioB_avg-signal14.242195
Spike_AFFX-r2-Bs-thr_avg-signal60.311172
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal887.349426
Spike_AFFX-r2-Bs-phe_5_signal24.574453
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1132.355957
RawQ2.724272
Spike_AFFX-r2-Bs-lys_5_signal23.790661
Signal(A)4.087929
%A29.587900
Signal(All)136.235413
Corner+Avg:148,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal237.658890
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal57.901585
Spike_AFFX-r2-Ec-bioD_avg-signal1009.852661
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P68.676018
Spike_AFFX-r2-Bs-lys_avg-signal30.387659
Spike_AFFX-r2-P1-cre_avg-signal3386.781738
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.736081
Spike_AFFX-r2-Bs-thr_3_signal127.173615
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-signal38.548672
Spike_AFFX-r2-Bs-dap_3_signal375.719269
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.276111
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal221.049957
#M396
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal49.211681
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.075137
Spike_AFFX-r2-Bs-thr_M_signal40.537930
Signal(P)196.243973
Spike_AFFX-r2-Bs-phe_3-5-ratio2.356170
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:6494,Count:9
Spike_AFFX-r2-P1-cre_5_signal3094.777100
Spike_AFFX-r2-Bs-phe_M_detectionP
#A6749
Signal(M)14.592553
BackgroundAvg:66.50,Std:0.72,Min:63.5,Max:68.3
Spike_AFFX-r2-Ec-bioC_avg-signal229.354431
Spike_AFFX-r2-Bs-dap_avg-signal189.527145
Spike_AFFX-r2-Bs-dap_3-5-ratio19.700382
Spike_AFFX-r2-Ec-bioB_5_signal16.249380
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.432880
NF1.000000
HZ4
Tau0.015000


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