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Experiment: Exogenous glucose treatment for Arabidopsis thaliana seedlings (Col-0)

Experiment Description

NASCArrays Experiment Reference Number: NASCARRAYS-580

Glucose regulation of auxin (IAA) synthesis has recently been suggested in Maize (LeClere et al. 2010). The experiment in hand involves long glucose treatment of wild-type Arabidopsis thaliana seedlings. The purpose of the gene chip analysis is to pinpoint carbohydrate-regulated genes which are involved in IAA homeostasis and to monitor the metabolic status of the seedlings during the incubation with/without glucose.Wild type Arabidopsis thaliana (Col-0) seedlings were grown on 1% agarose plates (pH 5.7) under long day light period for 10 days. On day 10, one hour after the onset of light, the seedlings were transferred into liquid MS (1x, pH 5.7). After four hours of incubation in the dark, a treatment meant to drain the soluable carbohydrate pools of the plants, the material was transferred into liquid media (1xMS, ph 5.7) with varying amounts of glucose (0%, 1%, 5%). Pooled samples of approximately 30-50 whole seedlings were harvested at the point of glucose application (t0) and after 15 hours of incubation (t15) with/without exogenous glucose.LeClere et al. Plant Physiology (2010) 153, 306-318.

About the Experimenter

Name:Dr Karin Ljung
Head of Lab Name:Dr Karin Ljung
Lab:
Address:Department of Forest Genetics and Plant Physiology, Faculty of Forest Sciences , Swedish University of Agricultural Sciences (SLU)
Skogsmarksgrand, Umea, Vasterbottens lan, 901 83, SWEDEN
Postcode:
Country:
 
Telephone Number: +46-90-7868355

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

About this Experiment

Experiment Type: compound_based_treatment
Number of Slides:16
 
Experimental Parameters:
parametercompound_based_treatment
parameterincubate
parameterstarvation
parametertimepoint
parameternutrients
Quality Control Measures Taken:
References: LeClere et al. Plant Physiology (2010) 153, 306-318.
 
Other Information:

Slides in this Experiment

Hybridisation Set: Ljung: Exogenous glucose treatment for Arabidopsis thaliana seedlings (Col-0)

Slide: Ljung_580-1_3_0h_sugar__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 ("Ljung_580-1_3_0h_sugar__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: Ljung_580-1_3_0h_sugar__Rep1_ATH1
Organism: Arabidopsis thaliana
Stock Code:
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:0.31711
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-ratio1.266039
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.837555
Spike_AFFX-r2-Bs-dap_5_signal41.591816
NoiseAvg:3.32,Std:0.14,Min:3.0,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_signal21.072351
#P14871
Spike_AFFX-r2-Bs-phe_M_signal21.525206
Corner-Avg:10113,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal65.012192
Spike_AFFX-r2-Ec-bioB_3_signal44.769302
Spike_AFFX-r2-Bs-lys_M_signal12.616367
Spike_AFFX-r2-P1-cre_3_signal3339.709229
Spike_AFFX-r2-Bs-lys_3-5-ratio2.071313
Spike_AFFX-r2-Bs-dap_M_signal141.773239
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.537757
Spike_AFFX-r2-Ec-bioB_avg-signal54.411285
Spike_AFFX-r2-Bs-thr_avg-signal47.670628
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal526.039307
Spike_AFFX-r2-Bs-phe_5_signal27.337078
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal771.587402
RawQ2.943868
Spike_AFFX-r2-Bs-lys_5_signal13.209278
Signal(A)2.609877
%A33.235424
Signal(All)142.452332
Corner+Avg:158,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal183.704437
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal30.193075
Spike_AFFX-r2-Ec-bioD_avg-signal648.813354
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P65.195091
Spike_AFFX-r2-Bs-lys_avg-signal17.728731
Spike_AFFX-r2-P1-cre_avg-signal2988.814941
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.569487
Spike_AFFX-r2-Bs-thr_3_signal74.548851
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-signal26.351786
Spike_AFFX-r2-Bs-dap_3_signal167.371597
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.466787
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal186.231476
#M358
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal27.360544
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.986431
Spike_AFFX-r2-Bs-thr_M_signal47.390686
Signal(P)216.920761
Spike_AFFX-r2-Bs-phe_3-5-ratio1.104473
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:7894,Count:9
Spike_AFFX-r2-P1-cre_5_signal2637.920410
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7581
Signal(M)10.400781
BackgroundAvg:75.07,Std:0.97,Min:72.0,Max:78.1
Spike_AFFX-r2-Ec-bioC_avg-signal184.967957
Spike_AFFX-r2-Bs-dap_avg-signal116.912224
Spike_AFFX-r2-Bs-dap_3-5-ratio4.024148
Spike_AFFX-r2-Ec-bioB_5_signal53.452366
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.317110
NF1.000000
HZ4
Tau0.015000

Slide: Ljung_580-2_1_0h_sugar_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 ("Ljung_580-2_1_0h_sugar_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: Ljung_580-2_1_0h_sugar_Rep2_ATH1
Organism: Arabidopsis thaliana
Stock Code:
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:0.393524
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-ratio1.268196
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.771232
Spike_AFFX-r2-Bs-dap_5_signal29.461475
NoiseAvg:3.47,Std:0.11,Min:3.2,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_signal12.450269
#P14544
Spike_AFFX-r2-Bs-phe_M_signal18.670847
Corner-Avg:10855,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal84.339729
Spike_AFFX-r2-Ec-bioB_3_signal49.554668
Spike_AFFX-r2-Bs-lys_M_signal10.854249
Spike_AFFX-r2-P1-cre_3_signal3105.289551
Spike_AFFX-r2-Bs-lys_3-5-ratio1.706383
Spike_AFFX-r2-Bs-dap_M_signal90.736107
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio5.102389
Spike_AFFX-r2-Ec-bioB_avg-signal66.049423
Spike_AFFX-r2-Bs-thr_avg-signal40.520596
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal571.001648
Spike_AFFX-r2-Bs-phe_5_signal15.675443
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal975.672791
RawQ3.108185
Spike_AFFX-r2-Bs-lys_5_signal11.455667
Signal(A)3.116277
%A34.664619
Signal(All)142.837128
Corner+Avg:179,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal205.469147
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal23.694405
Spike_AFFX-r2-Ec-bioD_avg-signal773.337219
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P63.761509
Spike_AFFX-r2-Bs-lys_avg-signal13.952558
Spike_AFFX-r2-P1-cre_avg-signal2776.938477
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.573871
Spike_AFFX-r2-Bs-thr_3_signal63.526115
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-signal19.346897
Spike_AFFX-r2-Bs-dap_3_signal106.183784
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.708704
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal228.165100
#M359
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal19.547760
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.900528
Spike_AFFX-r2-Bs-thr_M_signal45.585400
Signal(P)222.033737
Spike_AFFX-r2-Bs-phe_3-5-ratio1.511562
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:8029,Count:9
Spike_AFFX-r2-P1-cre_5_signal2448.587402
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7907
Signal(M)11.742842
BackgroundAvg:79.07,Std:0.97,Min:77.3,Max:81.5
Spike_AFFX-r2-Ec-bioC_avg-signal216.817123
Spike_AFFX-r2-Bs-dap_avg-signal75.460457
Spike_AFFX-r2-Bs-dap_3-5-ratio3.604157
Spike_AFFX-r2-Ec-bioB_5_signal64.253876
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.393524
NF1.000000
HZ4
Tau0.015000

Slide: Ljung_580-3_24_0h_sugar_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 ("Ljung_580-3_24_0h_sugar_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: Ljung_580-3_24_0h_sugar_Rep3_ATH1
Organism: Arabidopsis thaliana
Stock Code:
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:0.377953
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-ratio1.078405
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.977728
Spike_AFFX-r2-Bs-dap_5_signal47.196781
NoiseAvg:3.09,Std:0.08,Min:2.8,Max:3.3
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal15.474485
#P14854
Spike_AFFX-r2-Bs-phe_M_signal19.395967
Corner-Avg:9619,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal83.146172
Spike_AFFX-r2-Ec-bioB_3_signal60.271862
Spike_AFFX-r2-Bs-lys_M_signal14.251311
Spike_AFFX-r2-P1-cre_3_signal3349.815918
Spike_AFFX-r2-Bs-lys_3-5-ratio3.281566
Spike_AFFX-r2-Bs-dap_M_signal109.232117
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio5.108493
Spike_AFFX-r2-Ec-bioB_avg-signal68.354286
Spike_AFFX-r2-Bs-thr_avg-signal49.331364
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal586.503479
Spike_AFFX-r2-Bs-phe_5_signal22.668447
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal919.359924
RawQ2.910115
Spike_AFFX-r2-Bs-lys_5_signal11.525789
Signal(A)2.679438
%A33.415169
Signal(All)142.625656
Corner+Avg:155,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal255.265884
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal22.450130
Spike_AFFX-r2-Ec-bioD_avg-signal752.931702
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P65.120560
Spike_AFFX-r2-Bs-lys_avg-signal21.199913
Spike_AFFX-r2-P1-cre_avg-signal3228.042480
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.464270
Spike_AFFX-r2-Bs-thr_3_signal79.051300
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-signal21.504850
Spike_AFFX-r2-Bs-dap_3_signal153.897690
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.567527
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal239.595779
#M334
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal37.822639
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.065402
Spike_AFFX-r2-Bs-thr_M_signal53.468307
Signal(P)217.415726
Spike_AFFX-r2-Bs-phe_3-5-ratio0.990369
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:7781,Count:9
Spike_AFFX-r2-P1-cre_5_signal3106.269287
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7622
Signal(M)10.106187
BackgroundAvg:69.82,Std:0.60,Min:68.3,Max:71.4
Spike_AFFX-r2-Ec-bioC_avg-signal247.430832
Spike_AFFX-r2-Bs-dap_avg-signal103.442200
Spike_AFFX-r2-Bs-dap_3-5-ratio3.260767
Spike_AFFX-r2-Ec-bioB_5_signal61.644817
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.377953
NF1.000000
HZ4
Tau0.015000

Slide: Ljung_580-4_12_0h_sugar_Rep4_ATH1

Add to Slide Selection

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

Summary Information

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

  • Extract 1 ("Ljung_580-4_12_0h_sugar_Rep4_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: Ljung_580-4_12_0h_sugar_Rep4_ATH1
Organism: Arabidopsis thaliana
Stock Code:
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:0.240569
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-ratio1.235476
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.896645
Spike_AFFX-r2-Bs-dap_5_signal57.145180
NoiseAvg:3.79,Std:0.11,Min:3.4,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_signal19.605206
#P15358
Spike_AFFX-r2-Bs-phe_M_signal20.856995
Corner-Avg:11691,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal63.986595
Spike_AFFX-r2-Ec-bioB_3_signal47.657532
Spike_AFFX-r2-Bs-lys_M_signal8.361727
Spike_AFFX-r2-P1-cre_3_signal2884.749512
Spike_AFFX-r2-Bs-lys_3-5-ratio1.911557
Spike_AFFX-r2-Bs-dap_M_signal144.358063
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio4.042281
Spike_AFFX-r2-Ec-bioB_avg-signal54.931690
Spike_AFFX-r2-Bs-thr_avg-signal47.520092
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal538.610779
Spike_AFFX-r2-Bs-phe_5_signal28.125200
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal759.112427
RawQ3.198818
Spike_AFFX-r2-Bs-lys_5_signal14.109138
Signal(A)2.189703
%A31.429197
Signal(All)136.998337
Corner+Avg:187,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal192.138718
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal23.492081
Spike_AFFX-r2-Ec-bioD_avg-signal648.861572
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P67.330116
Spike_AFFX-r2-Bs-lys_avg-signal16.480429
Spike_AFFX-r2-P1-cre_avg-signal2609.839600
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.240684
Spike_AFFX-r2-Bs-thr_3_signal79.249756
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-signal24.158091
Spike_AFFX-r2-Bs-dap_3_signal181.342361
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.409390
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal178.650742
#M283
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal26.970419
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.075499
Spike_AFFX-r2-Bs-thr_M_signal43.705311
Signal(P)202.284027
Spike_AFFX-r2-Bs-phe_3-5-ratio0.835268
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:8928,Count:9
Spike_AFFX-r2-P1-cre_5_signal2334.929688
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7169
Signal(M)9.032481
BackgroundAvg:83.54,Std:0.69,Min:81.8,Max:85.4
Spike_AFFX-r2-Ec-bioC_avg-signal185.394730
Spike_AFFX-r2-Bs-dap_avg-signal127.615204
Spike_AFFX-r2-Bs-dap_3-5-ratio3.173362
Spike_AFFX-r2-Ec-bioB_5_signal53.150940
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.240569
NF1.000000
HZ4
Tau0.015000

Slide: Ljung_580-5_10_15h_1per-glucose_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 ("Ljung_580-5_10_15h_1per-glucose_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: Ljung_580-5_10_15h_1per-glucose_Rep1_ATH1
Organism: Arabidopsis thaliana
Stock Code:
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:0.431521
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-ratio1.006031
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.873191
Spike_AFFX-r2-Bs-dap_5_signal5.997025
NoiseAvg:3.03,Std:0.09,Min:2.8,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_signal1.691629
#P15374
Spike_AFFX-r2-Bs-phe_M_signal11.104818
Corner-Avg:9065,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal72.949280
Spike_AFFX-r2-Ec-bioB_3_signal49.217075
Spike_AFFX-r2-Bs-lys_M_signal8.327570
Spike_AFFX-r2-P1-cre_3_signal2531.762451
Spike_AFFX-r2-Bs-lys_3-5-ratio1.924454
Spike_AFFX-r2-Bs-dap_M_signal44.464592
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio25.341022
Spike_AFFX-r2-Ec-bioB_avg-signal59.510319
Spike_AFFX-r2-Bs-thr_avg-signal21.487055
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal441.742432
Spike_AFFX-r2-Bs-phe_5_signal11.629557
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal707.370789
RawQ2.956888
Spike_AFFX-r2-Bs-lys_5_signal8.512722
Signal(A)2.718286
%A31.188076
Signal(All)134.919098
Corner+Avg:145,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal179.734085
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal21.966736
Spike_AFFX-r2-Ec-bioD_avg-signal574.556641
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P67.400261
Spike_AFFX-r2-Bs-lys_avg-signal11.074212
Spike_AFFX-r2-P1-cre_avg-signal2524.173828
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.411662
Spike_AFFX-r2-Bs-thr_3_signal42.867615
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-signal14.900371
Spike_AFFX-r2-Bs-dap_3_signal119.919922
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.601320
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal207.487305
#M322
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal16.382345
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.866241
Spike_AFFX-r2-Bs-thr_M_signal19.901922
Signal(P)198.683578
Spike_AFFX-r2-Bs-phe_3-5-ratio1.888871
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:6836,Count:9
Spike_AFFX-r2-P1-cre_5_signal2516.584961
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7114
Signal(M)11.197304
BackgroundAvg:70.69,Std:0.71,Min:69.0,Max:72.0
Spike_AFFX-r2-Ec-bioC_avg-signal193.610687
Spike_AFFX-r2-Bs-dap_avg-signal56.793850
Spike_AFFX-r2-Bs-dap_3-5-ratio19.996569
Spike_AFFX-r2-Ec-bioB_5_signal56.364605
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.431521
NF1.000000
HZ4
Tau0.015000

Slide: Ljung_580-6_18_15h_1per-glucose_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 ("Ljung_580-6_18_15h_1per-glucose_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: Ljung_580-6_18_15h_1per-glucose_Rep2_ATH1
Organism: Arabidopsis thaliana
Stock Code:
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:0.401788
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-ratio0.960737
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.676210
Spike_AFFX-r2-Bs-dap_5_signal31.996611
NoiseAvg:3.04,Std:0.09,Min:2.8,Max:3.4
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal13.583076
#P15545
Spike_AFFX-r2-Bs-phe_M_signal15.838864
Corner-Avg:8648,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal76.595711
Spike_AFFX-r2-Ec-bioB_3_signal45.200443
Spike_AFFX-r2-Bs-lys_M_signal7.330994
Spike_AFFX-r2-P1-cre_3_signal2513.021484
Spike_AFFX-r2-Bs-lys_3-5-ratio1.666058
Spike_AFFX-r2-Bs-dap_M_signal81.404144
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio5.503864
Spike_AFFX-r2-Ec-bioB_avg-signal62.879986
Spike_AFFX-r2-Bs-thr_avg-signal39.663528
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal497.488098
Spike_AFFX-r2-Bs-phe_5_signal13.198514
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal725.347900
RawQ2.770492
Spike_AFFX-r2-Bs-lys_5_signal11.838221
Signal(A)2.662912
%A30.491013
Signal(All)134.742584
Corner+Avg:140,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal227.164413
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal19.544888
Spike_AFFX-r2-Ec-bioD_avg-signal611.417969
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P68.149933
Spike_AFFX-r2-Bs-lys_avg-signal12.964127
Spike_AFFX-r2-P1-cre_avg-signal2564.371582
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.359053
Spike_AFFX-r2-Bs-thr_3_signal74.759407
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-signal16.194088
Spike_AFFX-r2-Bs-dap_3_signal125.467720
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.458021
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal210.950470
#M310
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal19.723164
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.076861
Spike_AFFX-r2-Bs-thr_M_signal30.648100
Signal(P)196.310989
Spike_AFFX-r2-Bs-phe_3-5-ratio1.480840
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:7014,Count:9
Spike_AFFX-r2-P1-cre_5_signal2615.721436
Spike_AFFX-r2-Bs-phe_M_detectionP
#A6955
Signal(M)10.656963
BackgroundAvg:69.01,Std:0.60,Min:67.4,Max:70.8
Spike_AFFX-r2-Ec-bioC_avg-signal219.057434
Spike_AFFX-r2-Bs-dap_avg-signal79.622826
Spike_AFFX-r2-Bs-dap_3-5-ratio3.921282
Spike_AFFX-r2-Ec-bioB_5_signal66.843803
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.401788
NF1.000000
HZ4
Tau0.015000

Slide: Ljung_580-7_8_15h_1per-glucose_Rep3_ATH1

Add to Slide Selection

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

Summary Information

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

  • Extract 1 ("Ljung_580-7_8_15h_1per-glucose_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: Ljung_580-7_8_15h_1per-glucose_Rep3_ATH1
Organism: Arabidopsis thaliana
Stock Code:
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:0.275019
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-ratio1.172820
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.891469
Spike_AFFX-r2-Bs-dap_5_signal33.049141
NoiseAvg:3.87,Std:0.14,Min:3.6,Max:4.2
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal13.339003
#P15608
Spike_AFFX-r2-Bs-phe_M_signal11.107848
Corner-Avg:10004,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal60.783012
Spike_AFFX-r2-Ec-bioB_3_signal40.385323
Spike_AFFX-r2-Bs-lys_M_signal9.610118
Spike_AFFX-r2-P1-cre_3_signal2198.184814
Spike_AFFX-r2-Bs-lys_3-5-ratio1.991564
Spike_AFFX-r2-Bs-dap_M_signal79.785240
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio4.530491
Spike_AFFX-r2-Ec-bioB_avg-signal48.823444
Spike_AFFX-r2-Bs-thr_avg-signal35.283154
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal398.881592
Spike_AFFX-r2-Bs-phe_5_signal20.002253
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal653.214600
RawQ3.353632
Spike_AFFX-r2-Bs-lys_5_signal12.864060
Signal(A)2.426375
%A30.320036
Signal(All)131.168350
Corner+Avg:163,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal171.713669
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal20.360958
Spike_AFFX-r2-Ec-bioD_avg-signal526.048096
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P68.426132
Spike_AFFX-r2-Bs-lys_avg-signal16.031260
Spike_AFFX-r2-P1-cre_avg-signal2036.229004
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.253836
Spike_AFFX-r2-Bs-thr_3_signal60.432236
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-signal17.157021
Spike_AFFX-r2-Bs-dap_3_signal137.483948
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.637615
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal145.589935
#M286
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal25.619598
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.179434
Spike_AFFX-r2-Bs-thr_M_signal32.078224
Signal(P)190.448792
Spike_AFFX-r2-Bs-phe_3-5-ratio1.017933
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:7559,Count:9
Spike_AFFX-r2-P1-cre_5_signal1874.273315
Spike_AFFX-r2-Bs-phe_M_detectionP
#A6916
Signal(M)9.246159
BackgroundAvg:86.72,Std:1.04,Min:84.8,Max:89.1
Spike_AFFX-r2-Ec-bioC_avg-signal158.651794
Spike_AFFX-r2-Bs-dap_avg-signal83.439445
Spike_AFFX-r2-Bs-dap_3-5-ratio4.159986
Spike_AFFX-r2-Ec-bioB_5_signal45.302006
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.275019
NF1.000000
HZ4
Tau0.015000

Slide: Ljung_580-8_22_15h_1per-glucose_Rep4_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 ("Ljung_580-8_22_15h_1per-glucose_Rep4_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: Ljung_580-8_22_15h_1per-glucose_Rep4_ATH1
Organism: Arabidopsis thaliana
Stock Code:
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:0.501785
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-ratio1.262757
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.944919
Spike_AFFX-r2-Bs-dap_5_signal35.658649
NoiseAvg:3.11,Std:0.08,Min:2.9,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_signal16.468378
#P15173
Spike_AFFX-r2-Bs-phe_M_signal14.944201
Corner-Avg:10042,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal77.368973
Spike_AFFX-r2-Ec-bioB_3_signal57.199867
Spike_AFFX-r2-Bs-lys_M_signal5.205085
Spike_AFFX-r2-P1-cre_3_signal3478.264160
Spike_AFFX-r2-Bs-lys_3-5-ratio1.359811
Spike_AFFX-r2-Bs-dap_M_signal88.345497
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio4.516281
Spike_AFFX-r2-Ec-bioB_avg-signal65.034325
Spike_AFFX-r2-Bs-thr_avg-signal45.658737
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal633.261658
Spike_AFFX-r2-Bs-phe_5_signal12.150571
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal855.564270
RawQ2.942032
Spike_AFFX-r2-Bs-lys_5_signal13.431915
Signal(A)3.331634
%A31.885138
Signal(All)136.021454
Corner+Avg:163,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal178.053955
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal20.331276
Spike_AFFX-r2-Ec-bioD_avg-signal744.412964
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P66.519073
Spike_AFFX-r2-Bs-lys_avg-signal12.300624
Spike_AFFX-r2-P1-cre_avg-signal3116.381836
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.595791
Spike_AFFX-r2-Bs-thr_3_signal74.375816
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-signal15.808681
Spike_AFFX-r2-Bs-dap_3_signal150.810623
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.351044
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal248.492767
#M364
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal18.264870
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.716536
Spike_AFFX-r2-Bs-thr_M_signal46.132011
Signal(P)202.589188
Spike_AFFX-r2-Bs-phe_3-5-ratio1.673277
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:5888,Count:9
Spike_AFFX-r2-P1-cre_5_signal2754.499268
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7273
Signal(M)12.452192
BackgroundAvg:73.02,Std:0.63,Min:71.2,Max:74.5
Spike_AFFX-r2-Ec-bioC_avg-signal213.273361
Spike_AFFX-r2-Bs-dap_avg-signal91.604927
Spike_AFFX-r2-Bs-dap_3-5-ratio4.229286
Spike_AFFX-r2-Ec-bioB_5_signal60.534134
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.501785
NF1.000000
HZ4
Tau0.015000

Slide: Ljung_580-9_14_15h_5per-glucose_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 ("Ljung_580-9_14_15h_5per-glucose_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: Ljung_580-9_14_15h_5per-glucose_Rep1_ATH1
Organism: Arabidopsis thaliana
Stock Code:
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:0.500019
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-ratio1.214617
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.884150
Spike_AFFX-r2-Bs-dap_5_signal40.628654
NoiseAvg:2.73,Std:0.09,Min:2.5,Max:3.0
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal10.625004
#P15407
Spike_AFFX-r2-Bs-phe_M_signal11.068132
Corner-Avg:9074,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal84.262688
Spike_AFFX-r2-Ec-bioB_3_signal70.224640
Spike_AFFX-r2-Bs-lys_M_signal9.068554
Spike_AFFX-r2-P1-cre_3_signal3406.379883
Spike_AFFX-r2-Bs-lys_3-5-ratio2.189419
Spike_AFFX-r2-Bs-dap_M_signal87.253334
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio4.563911
Spike_AFFX-r2-Ec-bioB_avg-signal77.971184
Spike_AFFX-r2-Bs-thr_avg-signal30.389368
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal575.171021
Spike_AFFX-r2-Bs-phe_5_signal12.831969
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal976.599976
RawQ2.701120
Spike_AFFX-r2-Bs-lys_5_signal6.347078
Signal(A)3.215354
%A30.920649
Signal(All)137.784897
Corner+Avg:143,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal312.149078
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal20.719793
Spike_AFFX-r2-Ec-bioD_avg-signal775.885498
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P67.544937
Spike_AFFX-r2-Bs-lys_avg-signal9.770682
Spike_AFFX-r2-P1-cre_avg-signal3105.434570
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionA
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.534415
Spike_AFFX-r2-Bs-thr_3_signal48.491577
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-signal14.873299
Spike_AFFX-r2-Bs-dap_3_signal125.683578
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.697930
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal258.982330
#M350
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal13.896416
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.205291
Spike_AFFX-r2-Bs-thr_M_signal32.051529
Signal(P)202.237396
Spike_AFFX-r2-Bs-phe_3-5-ratio1.614701
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:6819,Count:9
Spike_AFFX-r2-P1-cre_5_signal2804.489014
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7053
Signal(M)12.354984
BackgroundAvg:64.81,Std:0.53,Min:63.6,Max:66.2
Spike_AFFX-r2-Ec-bioC_avg-signal285.565704
Spike_AFFX-r2-Bs-dap_avg-signal84.521858
Spike_AFFX-r2-Bs-dap_3-5-ratio3.093471
Spike_AFFX-r2-Ec-bioB_5_signal79.426201
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.500019
NF1.000000
HZ4
Tau0.015000

Slide: Ljung_580-10_19_15h_5per-glucose_Rep2_ATH1

Add to Slide Selection

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

Summary Information

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

  • Extract 1 ("Ljung_580-10_19_15h_5per-glucose_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: Ljung_580-10_19_15h_5per-glucose_Rep2_ATH1
Organism: Arabidopsis thaliana
Stock Code:
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:0.230553
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-ratio1.176285
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.803595
Spike_AFFX-r2-Bs-dap_5_signal38.032288
NoiseAvg:3.54,Std:0.16,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_signal12.774014
#P16111
Spike_AFFX-r2-Bs-phe_M_signal9.902409
Corner-Avg:10824,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal71.709045
Spike_AFFX-r2-Ec-bioB_3_signal44.195484
Spike_AFFX-r2-Bs-lys_M_signal7.030358
Spike_AFFX-r2-P1-cre_3_signal2518.062012
Spike_AFFX-r2-Bs-lys_3-5-ratio2.205806
Spike_AFFX-r2-Bs-dap_M_signal91.923164
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio4.757108
Spike_AFFX-r2-Ec-bioB_avg-signal56.967255
Spike_AFFX-r2-Bs-thr_avg-signal33.767406
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal467.989807
Spike_AFFX-r2-Bs-phe_5_signal17.199196
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal743.464417
RawQ2.957391
Spike_AFFX-r2-Bs-lys_5_signal9.509043
Signal(A)1.932595
%A28.114862
Signal(All)131.704376
Corner+Avg:177,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal181.834442
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal15.038058
Spike_AFFX-r2-Ec-bioD_avg-signal605.727112
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P70.631302
Spike_AFFX-r2-Bs-lys_avg-signal12.504834
Spike_AFFX-r2-P1-cre_avg-signal2329.376465
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.253836
Spike_AFFX-r2-Bs-thr_3_signal60.767368
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-signal14.046555
Spike_AFFX-r2-Bs-dap_3_signal135.965668
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.588634
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal178.319733
#M286
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal20.975103
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.019710
Spike_AFFX-r2-Bs-thr_M_signal27.760828
Signal(P)185.552444
Spike_AFFX-r2-Bs-phe_3-5-ratio0.874347
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:8006,Count:9
Spike_AFFX-r2-P1-cre_5_signal2140.690674
Spike_AFFX-r2-Bs-phe_M_detectionP
#A6413
Signal(M)8.208496
BackgroundAvg:74.27,Std:0.91,Min:71.7,Max:76.9
Spike_AFFX-r2-Ec-bioC_avg-signal180.077087
Spike_AFFX-r2-Bs-dap_avg-signal88.640373
Spike_AFFX-r2-Bs-dap_3-5-ratio3.575006
Spike_AFFX-r2-Ec-bioB_5_signal54.997238
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.230553
NF1.000000
HZ4
Tau0.015000

Slide: Ljung_580-11_23_15h_5per-glucose_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 ("Ljung_580-11_23_15h_5per-glucose_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: Ljung_580-11_23_15h_5per-glucose_Rep3_ATH1
Organism: Arabidopsis thaliana
Stock Code:
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:0.390164
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-ratio1.133959
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.012145
Spike_AFFX-r2-Bs-dap_5_signal41.380253
NoiseAvg:3.42,Std:0.11,Min:3.1,Max:3.8
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal13.836610
#P15477
Spike_AFFX-r2-Bs-phe_M_signal13.653521
Corner-Avg:9991,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal80.136711
Spike_AFFX-r2-Ec-bioB_3_signal50.372410
Spike_AFFX-r2-Bs-lys_M_signal8.271471
Spike_AFFX-r2-P1-cre_3_signal2584.910889
Spike_AFFX-r2-Bs-lys_3-5-ratio2.781078
Spike_AFFX-r2-Bs-dap_M_signal86.522057
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio4.922699
Spike_AFFX-r2-Ec-bioB_avg-signal60.092377
Spike_AFFX-r2-Bs-thr_avg-signal39.107372
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal564.134705
Spike_AFFX-r2-Bs-phe_5_signal20.826900
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal792.970276
RawQ3.058141
Spike_AFFX-r2-Bs-lys_5_signal6.084205
Signal(A)2.853531
%A30.710215
Signal(All)134.740784
Corner+Avg:163,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal224.845673
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal14.218464
Spike_AFFX-r2-Ec-bioD_avg-signal678.552490
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P67.851822
Spike_AFFX-r2-Bs-lys_avg-signal10.425441
Spike_AFFX-r2-P1-cre_avg-signal2432.227783
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.437966
Spike_AFFX-r2-Bs-thr_3_signal68.113464
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-signal16.232962
Spike_AFFX-r2-Bs-dap_3_signal126.408463
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.405640
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal221.746262
#M328
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal16.920647
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.013977
Spike_AFFX-r2-Bs-thr_M_signal35.372047
Signal(P)197.042374
Spike_AFFX-r2-Bs-phe_3-5-ratio0.682697
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:7332,Count:9
Spike_AFFX-r2-P1-cre_5_signal2279.544678
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7005
Signal(M)11.657463
BackgroundAvg:79.71,Std:0.74,Min:77.9,Max:82.0
Spike_AFFX-r2-Ec-bioC_avg-signal223.295959
Spike_AFFX-r2-Bs-dap_avg-signal84.770256
Spike_AFFX-r2-Bs-dap_3-5-ratio3.054802
Spike_AFFX-r2-Ec-bioB_5_signal49.767998
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.390164
NF1.000000
HZ4
Tau0.015000

Slide: Ljung_580-12_4_15h_5per-glucose_Rep4_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 ("Ljung_580-12_4_15h_5per-glucose_Rep4_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: Ljung_580-12_4_15h_5per-glucose_Rep4_ATH1
Organism: Arabidopsis thaliana
Stock Code:
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:0.330285
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-ratio1.204559
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.688802
Spike_AFFX-r2-Bs-dap_5_signal31.634979
NoiseAvg:3.55,Std:0.07,Min:3.2,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_signal14.084105
#P15726
Spike_AFFX-r2-Bs-phe_M_signal14.989147
Corner-Avg:9928,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal61.512348
Spike_AFFX-r2-Ec-bioB_3_signal39.324131
Spike_AFFX-r2-Bs-lys_M_signal6.347532
Spike_AFFX-r2-P1-cre_3_signal2431.534424
Spike_AFFX-r2-Bs-lys_3-5-ratio2.978082
Spike_AFFX-r2-Bs-dap_M_signal80.253006
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio5.220572
Spike_AFFX-r2-Ec-bioB_avg-signal52.642365
Spike_AFFX-r2-Bs-thr_avg-signal39.385834
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal437.131165
Spike_AFFX-r2-Bs-phe_5_signal17.836964
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal687.942444
RawQ3.160797
Spike_AFFX-r2-Bs-lys_5_signal8.541389
Signal(A)2.609560
%A29.631741
Signal(All)132.966293
Corner+Avg:161,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal168.453674
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal20.781517
Spike_AFFX-r2-Ec-bioD_avg-signal562.536804
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P68.943443
Spike_AFFX-r2-Bs-lys_avg-signal13.441959
Spike_AFFX-r2-P1-cre_avg-signal2225.072021
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.424814
Spike_AFFX-r2-Bs-thr_3_signal73.527077
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-signal17.869209
Spike_AFFX-r2-Bs-dap_3_signal115.179214
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.573767
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal170.341843
#M325
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal25.436956
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.988915
Spike_AFFX-r2-Bs-thr_M_signal30.546316
Signal(P)191.540497
Spike_AFFX-r2-Bs-phe_3-5-ratio1.165082
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:8809,Count:9
Spike_AFFX-r2-P1-cre_5_signal2018.609741
Spike_AFFX-r2-Bs-phe_M_detectionP
#A6759
Signal(M)9.714954
BackgroundAvg:78.01,Std:0.87,Min:75.7,Max:80.3
Spike_AFFX-r2-Ec-bioC_avg-signal169.397766
Spike_AFFX-r2-Bs-dap_avg-signal75.689064
Spike_AFFX-r2-Bs-dap_3-5-ratio3.640882
Spike_AFFX-r2-Ec-bioB_5_signal57.090607
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.330285
NF1.000000
HZ4
Tau0.015000

Slide: Ljung_580-13_16_15h_0per-glucose_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 ("Ljung_580-13_16_15h_0per-glucose_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: Ljung_580-13_16_15h_0per-glucose_Rep1_ATH1
Organism: Arabidopsis thaliana
Stock Code:
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:0.571289
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-ratio1.420356
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.728180
Spike_AFFX-r2-Bs-dap_5_signal9.737702
NoiseAvg:2.24,Std:0.06,Min:2.1,Max:2.4
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal6.080288
#P14303
Spike_AFFX-r2-Bs-phe_M_signal13.224496
Corner-Avg:8573,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal168.451767
Spike_AFFX-r2-Ec-bioB_3_signal83.921913
Spike_AFFX-r2-Bs-lys_M_signal20.597519
Spike_AFFX-r2-P1-cre_3_signal6238.541016
Spike_AFFX-r2-Bs-lys_3-5-ratio1.917128
Spike_AFFX-r2-Bs-dap_M_signal68.894585
Spike_AFFX-r2-Bs-thr_M_detectionA
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio12.418293
Spike_AFFX-r2-Ec-bioB_avg-signal122.540863
Spike_AFFX-r2-Bs-thr_avg-signal34.980659
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1131.262451
Spike_AFFX-r2-Bs-phe_5_signal6.477066
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1468.197144
RawQ2.396323
Spike_AFFX-r2-Bs-lys_5_signal22.301132
Signal(A)2.938149
%A35.611572
Signal(All)151.323578
Corner+Avg:133,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal409.615234
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal21.307392
Spike_AFFX-r2-Ec-bioD_avg-signal1299.729736
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P62.704952
Spike_AFFX-r2-Bs-lys_avg-signal28.550926
Spike_AFFX-r2-P1-cre_avg-signal5315.389648
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.683472
Spike_AFFX-r2-Bs-thr_3_signal75.506805
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-signal13.669651
Spike_AFFX-r2-Bs-dap_3_signal172.475143
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.297840
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal411.209106
#M384
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal42.754128
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.996124
Spike_AFFX-r2-Bs-thr_M_signal23.354879
Signal(P)239.351013
Spike_AFFX-r2-Bs-phe_3-5-ratio3.289668
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:6308,Count:9
Spike_AFFX-r2-P1-cre_5_signal4392.238281
Spike_AFFX-r2-Bs-phe_M_detectionA
#A8123
Signal(M)11.424222
BackgroundAvg:53.92,Std:0.32,Min:53.1,Max:54.7
Spike_AFFX-r2-Ec-bioC_avg-signal410.412170
Spike_AFFX-r2-Bs-dap_avg-signal83.702477
Spike_AFFX-r2-Bs-dap_3-5-ratio17.712099
Spike_AFFX-r2-Ec-bioB_5_signal115.248901
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.571289
NF1.000000
HZ4
Tau0.015000

Slide: Ljung_580-14_13_15h_0per-glucose_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 ("Ljung_580-14_13_15h_0per-glucose_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: Ljung_580-14_13_15h_0per-glucose_Rep2_ATH1
Organism: Arabidopsis thaliana
Stock Code:
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:0.367322
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-ratio1.217046
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.873869
Spike_AFFX-r2-Bs-dap_5_signal55.166660
NoiseAvg:2.90,Std:0.14,Min:2.6,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_signal16.178759
#P15076
Spike_AFFX-r2-Bs-phe_M_signal19.452908
Corner-Avg:10013,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal97.590538
Spike_AFFX-r2-Ec-bioB_3_signal61.207035
Spike_AFFX-r2-Bs-lys_M_signal9.238373
Spike_AFFX-r2-P1-cre_3_signal3447.610352
Spike_AFFX-r2-Bs-lys_3-5-ratio1.410640
Spike_AFFX-r2-Bs-dap_M_signal137.561737
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio6.341159
Spike_AFFX-r2-Ec-bioB_avg-signal76.279671
Spike_AFFX-r2-Bs-thr_avg-signal60.963169
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal673.272766
Spike_AFFX-r2-Bs-phe_5_signal20.245209
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal921.004333
RawQ2.745798
Spike_AFFX-r2-Bs-lys_5_signal13.923647
Signal(A)2.373639
%A32.437527
Signal(All)139.717621
Corner+Avg:158,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal262.631287
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal26.874495
Spike_AFFX-r2-Ec-bioD_avg-signal797.138550
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P66.093819
Spike_AFFX-r2-Bs-lys_avg-signal14.267756
Spike_AFFX-r2-P1-cre_avg-signal3140.189209
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.468654
Spike_AFFX-r2-Bs-thr_3_signal102.592087
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-signal22.190870
Spike_AFFX-r2-Bs-dap_3_signal192.570007
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.367951
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal259.523132
#M335
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal19.641247
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.011976
Spike_AFFX-r2-Bs-thr_M_signal64.118675
Signal(P)210.022583
Spike_AFFX-r2-Bs-phe_3-5-ratio1.327450
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:7089,Count:9
Spike_AFFX-r2-P1-cre_5_signal2832.768066
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7399
Signal(M)9.241788
BackgroundAvg:65.39,Std:0.57,Min:64.1,Max:66.8
Spike_AFFX-r2-Ec-bioC_avg-signal261.077209
Spike_AFFX-r2-Bs-dap_avg-signal128.432800
Spike_AFFX-r2-Bs-dap_3-5-ratio3.490695
Spike_AFFX-r2-Ec-bioB_5_signal70.041428
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.367322
NF1.000000
HZ4
Tau0.015000

Slide: Ljung_580-15_20_15h_0per-glucose_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 ("Ljung_580-15_20_15h_0per-glucose_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: Ljung_580-15_20_15h_0per-glucose_Rep3_ATH1
Organism: Arabidopsis thaliana
Stock Code:
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:0.539641
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-ratio0.954669
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.790235
Spike_AFFX-r2-Bs-dap_5_signal51.427292
NoiseAvg:2.75,Std:0.11,Min:2.4,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_signal21.225676
#P14488
Spike_AFFX-r2-Bs-phe_M_signal24.126652
Corner-Avg:8773,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal99.985138
Spike_AFFX-r2-Ec-bioB_3_signal64.043327
Spike_AFFX-r2-Bs-lys_M_signal20.632454
Spike_AFFX-r2-P1-cre_3_signal3106.660400
Spike_AFFX-r2-Bs-lys_3-5-ratio1.412789
Spike_AFFX-r2-Bs-dap_M_signal163.932236
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio6.462158
Spike_AFFX-r2-Ec-bioB_avg-signal81.690636
Spike_AFFX-r2-Bs-thr_avg-signal78.544701
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal730.285095
Spike_AFFX-r2-Bs-phe_5_signal27.435064
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1004.266846
RawQ2.694431
Spike_AFFX-r2-Bs-lys_5_signal18.920069
Signal(A)3.025933
%A35.015343
Signal(All)143.096802
Corner+Avg:136,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal256.443451
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal30.328625
Spike_AFFX-r2-Ec-bioD_avg-signal867.276001
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P63.516003
Spike_AFFX-r2-Bs-lys_avg-signal22.094198
Spike_AFFX-r2-P1-cre_avg-signal3180.418457
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.468654
Spike_AFFX-r2-Bs-thr_3_signal137.163666
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-signal27.296782
Spike_AFFX-r2-Bs-dap_3_signal221.400726
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.375171
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal292.161377
#M335
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal26.730068
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.877746
Spike_AFFX-r2-Bs-thr_M_signal77.244751
Signal(P)223.352722
Spike_AFFX-r2-Bs-phe_3-5-ratio1.105469
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:6310,Count:9
Spike_AFFX-r2-P1-cre_5_signal3254.176514
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7987
Signal(M)11.748652
BackgroundAvg:64.30,Std:0.56,Min:63.3,Max:65.8
Spike_AFFX-r2-Ec-bioC_avg-signal274.302429
Spike_AFFX-r2-Bs-dap_avg-signal145.586746
Spike_AFFX-r2-Bs-dap_3-5-ratio4.305121
Spike_AFFX-r2-Ec-bioB_5_signal81.043419
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.539641
NF1.000000
HZ4
Tau0.015000

Slide: Ljung_580-16_9_15h_0per-glucose_Rep4_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 ("Ljung_580-16_9_15h_0per-glucose_Rep4_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: Ljung_580-16_9_15h_0per-glucose_Rep4_ATH1
Organism: Arabidopsis thaliana
Stock Code:
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:0.547678
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-ratio1.266140
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.534026
Spike_AFFX-r2-Bs-dap_5_signal45.921413
NoiseAvg:2.93,Std:0.07,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_signal22.775627
#P14217
Spike_AFFX-r2-Bs-phe_M_signal25.555328
Corner-Avg:8350,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal93.423264
Spike_AFFX-r2-Ec-bioB_3_signal39.708897
Spike_AFFX-r2-Bs-lys_M_signal20.074150
Spike_AFFX-r2-P1-cre_3_signal3598.446289
Spike_AFFX-r2-Bs-lys_3-5-ratio1.402455
Spike_AFFX-r2-Bs-dap_M_signal137.150665
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio6.472648
Spike_AFFX-r2-Ec-bioB_avg-signal69.163231
Spike_AFFX-r2-Bs-thr_avg-signal75.385506
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal630.727539
Spike_AFFX-r2-Bs-phe_5_signal32.501621
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal829.179016
RawQ2.869464
Spike_AFFX-r2-Bs-lys_5_signal15.718969
Signal(A)3.838897
%A35.957912
Signal(All)142.268539
Corner+Avg:135,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal256.260956
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal24.324625
Spike_AFFX-r2-Ec-bioD_avg-signal729.953247
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P62.327927
Spike_AFFX-r2-Bs-lys_avg-signal19.279421
Spike_AFFX-r2-P1-cre_avg-signal3220.253418
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.714160
Spike_AFFX-r2-Bs-thr_3_signal147.418610
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-signal27.460526
Spike_AFFX-r2-Bs-dap_3_signal177.328186
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.314639
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal267.351471
#M391
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal22.045141
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.958517
Spike_AFFX-r2-Bs-thr_M_signal55.962284
Signal(P)225.675201
Spike_AFFX-r2-Bs-phe_3-5-ratio0.748413
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:5539,Count:9
Spike_AFFX-r2-P1-cre_5_signal2842.060303
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8202
Signal(M)13.387849
BackgroundAvg:73.35,Std:0.59,Min:71.9,Max:74.7
Spike_AFFX-r2-Ec-bioC_avg-signal261.806213
Spike_AFFX-r2-Bs-dap_avg-signal120.133423
Spike_AFFX-r2-Bs-dap_3-5-ratio3.861558
Spike_AFFX-r2-Ec-bioB_5_signal74.357544
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.547678
NF1.000000
HZ4
Tau0.015000


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