NASC's International Affymetrix Service

AI logo

NASCArrays

home, selection, spot history, gene swinger, two gene scatterplot, digital northern, bulk gene download, tutorial, help, Affymetrix site, NASC

Experiment: Comparison of wt and biotin-deficient mutant

Experiment Description

NASCArrays Experiment Reference Number: NASCARRAYS-549

In this experiment we have compared gene expression in wild-type Arabidopsis COL-ecotype and a T-DNA insertion mutant bio4-1 that has an altered biotin synthesis. The bio4-1 plants were either grown normally or watered with 200 µM biotin solution.

About the Experimenter

Name: Elina Helenius
Head of Lab Name: T. Palva
Lab:
Institute: Adaptive Responses in Plants Group, Genetics, Department of Biological and Environmental Sciences, Faculty of Biosciences, University of Helsinki
Address:
P.O. Box 56 (Viikinkaari 5D), Helsinki, Helsingfors
Postcode: 00014
Country: FINLAND
 
Telephone Number: +3589191959085
Fax Number: +3589191959079

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: genetic_modification_design
Number of Slides:6
 
Experimental Parameters:
parametergene_knock_out
Quality Control Measures Taken:
References:
 
Other Information:

Slides in this Experiment

Hybridisation Set: Helenius: Comparison of wt and biotin-deficient mutant

Slide: Helenius_549-1_Col-0_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 ("Helenius_549-1_Col-0_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: Helenius_549-1_Col-0_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Age: 35 days
Growth Conditions:
StratificationThe seeds were kept in the dark at +4ºC for 3 days before move to growth room.
SterilisationThe seeds were stored at +4ºC.
ProtocolThe seeds were germinated on pots containing a mixture of peat and vermiculite (1:1). After 7 days the seedlings were transferred to individual pots containing a mixture of peat and vermiculite (1:1). The plants were grown in a growth room with a temperature of 23ºC (day)/19 ºC (night) and a relative humidity of 50-60%. The photoperiod was 12 h of light and 12 h of dark. The light intensity was 220-280 µmol s-2 m-2 .
Soil ConstituentsKekkilä Natural peat B2 mixed 1:1 with vermiculite.
Plant Spacingone/pot
waterwatered with tap water twice a week
Temperature22 °C average, 23 °C day, 19 °C night
Humidity55 % average, 50 % day, 60 % night
Medium
Lighting(Source: Unknown manufactured by Osram L36W/865. Intensity: 220-280µEinsteins. Wavelength: White)12 hour days, 12 hour nights
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)
Tissue: rosette leaves
Additional Organism Information:
Sample DescriptionSamples were collected from 35 day-old plants. Rosette leaves from five plants were pooled for one sample.
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:0.486841
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-ratio1.319803
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.129942
Spike_AFFX-r2-Bs-dap_5_signal58.242451
NoiseAvg:2.50,Std:0.06,Min:2.3,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_signal32.753773
#P14522
Spike_AFFX-r2-Bs-phe_M_signal46.772423
Corner-Avg:12409,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal66.633698
Spike_AFFX-r2-Ec-bioB_3_signal56.535839
Spike_AFFX-r2-Bs-lys_M_signal17.085653
Spike_AFFX-r2-P1-cre_3_signal3571.312744
Spike_AFFX-r2-Bs-lys_3-5-ratio1.403021
Spike_AFFX-r2-Bs-dap_M_signal165.512405
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.965343
Spike_AFFX-r2-Ec-bioB_avg-signal57.734604
Spike_AFFX-r2-Bs-thr_avg-signal69.289825
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal579.298035
Spike_AFFX-r2-Bs-phe_5_signal59.558453
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1057.646362
RawQ2.174968
Spike_AFFX-r2-Bs-lys_5_signal29.008751
Signal(A)3.103356
%A34.875053
Signal(All)143.605667
Corner+Avg:126,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal207.397812
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal102.296341
Spike_AFFX-r2-Ec-bioD_avg-signal818.472168
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P63.665058
Spike_AFFX-r2-Bs-lys_avg-signal28.931429
Spike_AFFX-r2-P1-cre_avg-signal3138.627930
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.459886
Spike_AFFX-r2-Bs-thr_3_signal97.126183
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-signal69.542404
Spike_AFFX-r2-Bs-dap_3_signal255.285233
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.825738
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal194.382156
#M333
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal40.699883
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.066959
Spike_AFFX-r2-Bs-thr_M_signal77.989525
Signal(P)223.579468
Spike_AFFX-r2-Bs-phe_3-5-ratio1.717579
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:11946,Count:9
Spike_AFFX-r2-P1-cre_5_signal2705.943115
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7955
Signal(M)12.423601
BackgroundAvg:78.89,Std:0.45,Min:78.0,Max:79.9
Spike_AFFX-r2-Ec-bioC_avg-signal200.889984
Spike_AFFX-r2-Bs-dap_avg-signal159.680038
Spike_AFFX-r2-Bs-dap_3-5-ratio4.383147
Spike_AFFX-r2-Ec-bioB_5_signal50.034275
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.486841
NF1.000000
HZ4
Tau0.015000

Slide: Helenius_549-2_Col-0_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 ("Helenius_549-2_Col-0_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: Helenius_549-2_Col-0_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Age: 35 days
Growth Conditions:
StratificationThe seeds were kept in the dark at +4ºC for 3 days before move to growth room.
SterilisationThe seeds were stored at +4ºC.
ProtocolThe seeds were germinated on pots containing a mixture of peat and vermiculite (1:1). After 7 days the seedlings were transferred to individual pots containing a mixture of peat and vermiculite (1:1). The plants were grown in a growth room with a temperature of 23ºC (day)/19 ºC (night) and a relative humidity of 50-60%. The photoperiod was 12 h of light and 12 h of dark. The light intensity was 220-280 µmol s-2 m-2 .
Soil ConstituentsKekkilä Natural peat B2 mixed 1:1 with vermiculite.
Plant Spacingone/pot
waterwatered with tap water twice a week
Temperature22 °C average, 23 °C day, 19 °C night
Humidity55 % average, 50 % day, 60 % night
Medium
Lighting(Source: Unknown manufactured by Osram L36W/865. Intensity: 220-280µEinsteins. Wavelength: White)12 hour days, 12 hour nights
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)
Tissue: rosette leaves
Additional Organism Information:
Sample DescriptionSamples were collected from 35 day-old plants. Rosette leaves from five plants were pooled for one sample.
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:0.55509
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-ratio1.198770
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.153264
Spike_AFFX-r2-Bs-dap_5_signal51.762787
NoiseAvg:2.56,Std:0.08,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_signal32.165760
#P14090
Spike_AFFX-r2-Bs-phe_M_signal26.681551
Corner-Avg:7871,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal66.287651
Spike_AFFX-r2-Ec-bioB_3_signal50.803162
Spike_AFFX-r2-Bs-lys_M_signal12.528531
Spike_AFFX-r2-P1-cre_3_signal3516.859131
Spike_AFFX-r2-Bs-lys_3-5-ratio1.361045
Spike_AFFX-r2-Bs-dap_M_signal146.710419
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.087359
Spike_AFFX-r2-Ec-bioB_avg-signal53.714146
Spike_AFFX-r2-Bs-thr_avg-signal54.965176
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal502.816742
Spike_AFFX-r2-Bs-phe_5_signal37.969311
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal913.277222
RawQ2.340508
Spike_AFFX-r2-Bs-lys_5_signal18.326212
Signal(A)3.441317
%A36.690048
Signal(All)145.911179
Corner+Avg:90,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal197.355957
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal47.623253
Spike_AFFX-r2-Ec-bioD_avg-signal708.046997
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P61.771152
Spike_AFFX-r2-Bs-lys_avg-signal18.599182
Spike_AFFX-r2-P1-cre_avg-signal3225.291260
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.538799
Spike_AFFX-r2-Bs-thr_3_signal67.141479
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-signal37.424702
Spike_AFFX-r2-Bs-dap_3_signal139.826630
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.816322
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal208.918198
#M351
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal24.942802
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.944657
Spike_AFFX-r2-Bs-thr_M_signal65.588280
Signal(P)233.820084
Spike_AFFX-r2-Bs-phe_3-5-ratio1.254256
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:6965,Count:9
Spike_AFFX-r2-P1-cre_5_signal2933.723389
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8369
Signal(M)13.984880
BackgroundAvg:82.16,Std:0.81,Min:80.2,Max:84.2
Spike_AFFX-r2-Ec-bioC_avg-signal203.137085
Spike_AFFX-r2-Bs-dap_avg-signal112.766609
Spike_AFFX-r2-Bs-dap_3-5-ratio2.701296
Spike_AFFX-r2-Ec-bioB_5_signal44.051632
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.555090
NF1.000000
HZ4
Tau0.015000

Slide: Helenius_549-3_Bio4-1_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 ("Helenius_549-3_Bio4-1_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: Helenius_549-3_Bio4-1_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: bio4-1
Stock Code:
Genetic Background: Col-0
Age: 35 days
Growth Conditions:
StratificationThe seeds were kept in the dark at +4ºC for 3 days before move to growth room.
SterilisationThe seeds were stored at +4ºC.
ProtocolThe seeds were germinated on pots containing a mixture of peat and vermiculite (1:1). After 7 days the seedlings were transferred to individual pots containing a mixture of peat and vermiculite (1:1). The plants were grown in a growth room with a temperature of 23ºC (day)/19 ºC (night) and a relative humidity of 50-60%. The photoperiod was 12 h of light and 12 h of dark. The light intensity was 220-280 µmol s-2 m-2 .
Soil ConstituentsKekkilä Natural peat B2 mixed 1:1 with vermiculite.
Plant Spacingone/pot
waterwatered with tap water twice a week
Temperature22 °C average, 23 °C day, 19 °C night
Humidity55 % average, 50 % day, 60 % night
Medium
Lighting(Source: Unknown manufactured by Osram L36W/865. Intensity: 220-280µEinsteins. Wavelength: White)12 hour days, 12 hour nights
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)
Genetic Variation: T-DNA knock out mutation in At5g04620
Tissue: rosette leaves
Additional Organism Information:
Sample DescriptionSamples were collected from 35 day-old plants. Rosette leaves from five plants were pooled for one sample.
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:0.688789
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-ratio1.216521
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.022838
Spike_AFFX-r2-Bs-dap_5_signal33.957161
NoiseAvg:2.00,Std:0.08,Min:1.8,Max:2.3
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal24.632710
#P14368
Spike_AFFX-r2-Bs-phe_M_signal23.857042
Corner-Avg:7705,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal60.130981
Spike_AFFX-r2-Ec-bioB_3_signal49.487400
Spike_AFFX-r2-Bs-lys_M_signal7.919672
Spike_AFFX-r2-P1-cre_3_signal3120.453857
Spike_AFFX-r2-Bs-lys_3-5-ratio2.158312
Spike_AFFX-r2-Bs-dap_M_signal92.725464
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.872282
Spike_AFFX-r2-Ec-bioB_avg-signal52.666935
Spike_AFFX-r2-Bs-thr_avg-signal54.549129
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal497.297058
Spike_AFFX-r2-Bs-phe_5_signal34.067814
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal757.492859
RawQ2.089181
Spike_AFFX-r2-Bs-lys_5_signal12.922639
Signal(A)3.294071
%A35.537045
Signal(All)142.458450
Corner+Avg:84,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal246.596725
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal47.117527
Spike_AFFX-r2-Ec-bioD_avg-signal627.394958
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P62.989918
Spike_AFFX-r2-Bs-lys_avg-signal16.244465
Spike_AFFX-r2-P1-cre_avg-signal2842.758545
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionA
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.473038
Spike_AFFX-r2-Bs-thr_3_signal70.752075
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-signal35.014130
Spike_AFFX-r2-Bs-dap_3_signal131.351669
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.523220
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal184.693573
#M336
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal27.891085
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.335167
Spike_AFFX-r2-Bs-thr_M_signal68.262596
Signal(P)224.001007
Spike_AFFX-r2-Bs-phe_3-5-ratio1.383051
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:5149,Count:9
Spike_AFFX-r2-P1-cre_5_signal2565.063232
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8106
Signal(M)12.883817
BackgroundAvg:73.45,Std:0.57,Min:71.6,Max:75.1
Spike_AFFX-r2-Ec-bioC_avg-signal215.645142
Spike_AFFX-r2-Bs-dap_avg-signal86.011436
Spike_AFFX-r2-Bs-dap_3-5-ratio3.868158
Spike_AFFX-r2-Ec-bioB_5_signal48.382431
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.688789
NF1.000000
HZ4
Tau0.015000

Slide: Helenius_549-4_Bio4-1_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 ("Helenius_549-4_Bio4-1_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: Helenius_549-4_Bio4-1_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: bio4-1
Stock Code:
Genetic Background: Col-0
Age: 35 days
Growth Conditions:
StratificationThe seeds were kept in the dark at +4ºC for 3 days before move to growth room.
SterilisationThe seeds were stored at +4ºC.
ProtocolThe seeds were germinated on pots containing a mixture of peat and vermiculite (1:1). After 7 days the seedlings were transferred to individual pots containing a mixture of peat and vermiculite (1:1). The plants were grown in a growth room with a temperature of 23ºC (day)/19 ºC (night) and a relative humidity of 50-60%. The photoperiod was 12 h of light and 12 h of dark. The light intensity was 220-280 µmol s-2 m-2 .
Soil ConstituentsKekkilä Natural peat B2 mixed 1:1 with vermiculite.
Plant Spacingone/pot
waterwatered with tap water twice a week
Temperature22 °C average, 23 °C day, 19 °C night
Humidity55 % average, 50 % day, 60 % night
Medium
Lighting(Source: Unknown manufactured by Osram L36W/865. Intensity: 220-280µEinsteins. Wavelength: White)12 hour days, 12 hour nights
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)
Genetic Variation: T-DNA knock out mutation in At5g04620
Tissue: rosette leaves
Additional Organism Information:
Sample DescriptionSamples were collected from 35 day-old plants. Rosette leaves from five plants were pooled for one sample.
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:0.415714
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-ratio1.289903
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.810709
Spike_AFFX-r2-Bs-dap_5_signal48.384026
NoiseAvg:2.44,Std:0.05,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_signal28.847122
#P14819
Spike_AFFX-r2-Bs-phe_M_signal29.098551
Corner-Avg:7847,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal53.672714
Spike_AFFX-r2-Ec-bioB_3_signal37.330704
Spike_AFFX-r2-Bs-lys_M_signal9.536436
Spike_AFFX-r2-P1-cre_3_signal2916.143799
Spike_AFFX-r2-Bs-lys_3-5-ratio1.994728
Spike_AFFX-r2-Bs-dap_M_signal119.152626
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.480787
Spike_AFFX-r2-Ec-bioB_avg-signal45.683472
Spike_AFFX-r2-Bs-thr_avg-signal56.009853
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal413.703064
Spike_AFFX-r2-Bs-phe_5_signal35.569031
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal767.148499
RawQ2.313929
Spike_AFFX-r2-Bs-lys_5_signal17.420549
Signal(A)2.465194
%A33.735203
Signal(All)139.169113
Corner+Avg:92,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal181.833710
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal46.056938
Spike_AFFX-r2-Ec-bioD_avg-signal590.425781
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P64.967117
Spike_AFFX-r2-Bs-lys_avg-signal20.568747
Spike_AFFX-r2-P1-cre_avg-signal2588.444824
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.297676
Spike_AFFX-r2-Bs-thr_3_signal71.563560
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-signal36.908173
Spike_AFFX-r2-Bs-dap_3_signal161.403107
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.854346
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal173.274643
#M296
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal34.749256
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.049396
Spike_AFFX-r2-Bs-thr_M_signal67.618881
Signal(P)212.719681
Spike_AFFX-r2-Bs-phe_3-5-ratio1.294861
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:5641,Count:9
Spike_AFFX-r2-P1-cre_5_signal2260.746094
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7695
Signal(M)10.759397
BackgroundAvg:80.30,Std:0.57,Min:78.7,Max:81.8
Spike_AFFX-r2-Ec-bioC_avg-signal177.554169
Spike_AFFX-r2-Bs-dap_avg-signal109.646584
Spike_AFFX-r2-Bs-dap_3-5-ratio3.335876
Spike_AFFX-r2-Ec-bioB_5_signal46.047001
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.415714
NF1.000000
HZ4
Tau0.015000

Slide: Helenius_549-5_Bio4-1+Biotin__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 ("Helenius_549-5_Bio4-1+Biotin__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: Helenius_549-5_Bio4-1+Biotin__Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: bio4-1
Stock Code:
Genetic Background: Col-0
Age: 35 days
Growth Conditions:
StratificationThe seeds were kept in the dark at +4ºC for 3 days before move to growth room.
SterilisationThe seeds were stored at +4ºC.
ProtocolThe seeds were germinated on pots containing a mixture of peat and vermiculite (1:1). After 7 days the seedlings were transferred to individual pots containing a mixture of peat and vermiculite (1:1). The plants were grown in a growth room with a temperature of 23ºC (day)/19 ºC (night) and a relative humidity of 50-60%. The photoperiod was 12 h of light and 12 h of dark. The light intensity was 220-280 µmol s-2 m-2 .
Soil ConstituentsKekkilä Natural peat B2 mixed 1:1 with vermiculite.
Plant Spacingone/pot
waterwatered with tap water twice a week
Temperature22 °C average, 23 °C day, 19 °C night
Humidity55 % average, 50 % day, 60 % night
Medium
Lighting(Source: Unknown manufactured by Osram L36W/865. Intensity: 220-280µEinsteins. Wavelength: White)12 hour days, 12 hour nights
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)
Genetic Variation: T-DNA knock out mutation in At5g04620
Tissue: rosette leaves
in vivo Treatment: The biotin treatment was done by watering the plants with 200µM biotin (in tap water) twice a week.
Additional Organism Information:
Sample DescriptionSamples were collected from 35 day-old plants. Rosette leaves from five plants were pooled for one sample.
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:0.543844
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-ratio1.247815
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.788948
Spike_AFFX-r2-Bs-dap_5_signal54.547951
NoiseAvg:2.42,Std:0.05,Min:2.2,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_signal35.691872
#P14368
Spike_AFFX-r2-Bs-phe_M_signal37.173637
Corner-Avg:8099,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal64.488953
Spike_AFFX-r2-Ec-bioB_3_signal38.162029
Spike_AFFX-r2-Bs-lys_M_signal11.195799
Spike_AFFX-r2-P1-cre_3_signal3303.959961
Spike_AFFX-r2-Bs-lys_3-5-ratio1.209328
Spike_AFFX-r2-Bs-dap_M_signal155.217438
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.417276
Spike_AFFX-r2-Ec-bioB_avg-signal50.340595
Spike_AFFX-r2-Bs-thr_avg-signal65.661469
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal520.103027
Spike_AFFX-r2-Bs-phe_5_signal35.770523
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1062.689209
RawQ2.202105
Spike_AFFX-r2-Bs-lys_5_signal18.133530
Signal(A)3.417308
%A35.401138
Signal(All)143.708115
Corner+Avg:97,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal215.770386
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal35.263489
Spike_AFFX-r2-Ec-bioD_avg-signal791.396118
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P62.989918
Spike_AFFX-r2-Bs-lys_avg-signal17.086237
Spike_AFFX-r2-P1-cre_avg-signal2975.877686
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.608943
Spike_AFFX-r2-Bs-thr_3_signal86.277122
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-signal36.069218
Spike_AFFX-r2-Bs-dap_3_signal149.634964
Spike_AFFX-r2-Ec-bioD_3-5-ratio2.043228
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal204.377243
#M367
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal21.929384
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.055746
Spike_AFFX-r2-Bs-thr_M_signal75.015427
Signal(P)225.872757
Spike_AFFX-r2-Bs-phe_3-5-ratio0.985825
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:4826,Count:9
Spike_AFFX-r2-P1-cre_5_signal2647.795410
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8075
Signal(M)13.753395
BackgroundAvg:76.70,Std:0.59,Min:74.9,Max:78.4
Spike_AFFX-r2-Ec-bioC_avg-signal210.073822
Spike_AFFX-r2-Bs-dap_avg-signal119.800117
Spike_AFFX-r2-Bs-dap_3-5-ratio2.743182
Spike_AFFX-r2-Ec-bioB_5_signal48.370800
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.543844
NF1.000000
HZ4
Tau0.015000

Slide: Helenius_549-6_Bio4-1+Biotin_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 ("Helenius_549-6_Bio4-1+Biotin_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: Helenius_549-6_Bio4-1+Biotin_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: bio4-1
Stock Code:
Genetic Background: Col-0
Age: 35 days
Growth Conditions:
StratificationThe seeds were kept in the dark at +4ºC for 3 days before move to growth room.
SterilisationThe seeds were stored at +4ºC.
ProtocolThe seeds were germinated on pots containing a mixture of peat and vermiculite (1:1). After 7 days the seedlings were transferred to individual pots containing a mixture of peat and vermiculite (1:1). The plants were grown in a growth room with a temperature of 23ºC (day)/19 ºC (night) and a relative humidity of 50-60%. The photoperiod was 12 h of light and 12 h of dark. The light intensity was 220-280 µmol s-2 m-2 .
Soil ConstituentsKekkilä Natural peat B2 mixed 1:1 with vermiculite.
Plant Spacingone/pot
waterwatered with tap water twice a week
Temperature22 °C average, 23 °C day, 19 °C night
Humidity55 % average, 50 % day, 60 % night
Medium
Lighting(Source: Unknown manufactured by Osram L36W/865. Intensity: 220-280µEinsteins. Wavelength: White)12 hour days, 12 hour nights
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)
Genetic Variation: T-DNA knock out mutation in At5g04620
Tissue: rosette leaves
in vivo Treatment: The biotin treatment was done by watering the plants with 200µM biotin (in tap water) twice a week.
Additional Organism Information:
Sample DescriptionSamples were collected from 35 day-old plants. Rosette leaves from five plants were pooled for one sample.
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:0.540049
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-ratio1.248138
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.927361
Spike_AFFX-r2-Bs-dap_5_signal62.376583
NoiseAvg:2.33,Std:0.08,Min:2.2,Max:2.5
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal42.699574
#P14071
Spike_AFFX-r2-Bs-phe_M_signal42.086754
Corner-Avg:7620,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal57.754181
Spike_AFFX-r2-Ec-bioB_3_signal45.702366
Spike_AFFX-r2-Bs-lys_M_signal11.870383
Spike_AFFX-r2-P1-cre_3_signal3470.507813
Spike_AFFX-r2-Bs-lys_3-5-ratio2.311829
Spike_AFFX-r2-Bs-dap_M_signal198.081924
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.864640
Spike_AFFX-r2-Ec-bioB_avg-signal50.912914
Spike_AFFX-r2-Bs-thr_avg-signal91.237183
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal537.388794
Spike_AFFX-r2-Bs-phe_5_signal49.465649
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal925.137695
RawQ2.120242
Spike_AFFX-r2-Bs-lys_5_signal26.371588
Signal(A)3.446028
%A36.690048
Signal(All)147.434799
Corner+Avg:90,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal262.041656
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal53.649773
Spike_AFFX-r2-Ec-bioD_avg-signal731.263245
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P61.687855
Spike_AFFX-r2-Bs-lys_avg-signal33.069527
Spike_AFFX-r2-P1-cre_avg-signal3125.527832
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.622096
Spike_AFFX-r2-Bs-thr_3_signal122.318909
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-signal48.400726
Spike_AFFX-r2-Bs-dap_3_signal240.311691
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.721543
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal220.741913
#M370
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal60.966610
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.187095
Spike_AFFX-r2-Bs-thr_M_signal108.693054
Signal(P)236.562881
Spike_AFFX-r2-Bs-phe_3-5-ratio1.084587
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:5496,Count:9
Spike_AFFX-r2-P1-cre_5_signal2780.548096
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8369
Signal(M)14.788154
BackgroundAvg:79.45,Std:0.38,Min:78.3,Max:80.4
Spike_AFFX-r2-Ec-bioC_avg-signal241.391785
Spike_AFFX-r2-Bs-dap_avg-signal166.923401
Spike_AFFX-r2-Bs-dap_3-5-ratio3.852595
Spike_AFFX-r2-Ec-bioB_5_signal49.282192
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.540049
NF1.000000
HZ4
Tau0.015000


Problems? Comments? Suggestions? Contact the Affymetrix Team