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Experiment: Expression analysis on low phosphate conditions

Experiment Description

NASCArrays Experiment Reference Number: NASCARRAYS-648

Low phosphate conditions induce massive changes in the root system architecture (RSA). Our aim was to find differences in the expression pattern of Pi starvation related genes under high and low phosphate conditions in the wild type versus starvation hypersensitive and insensitive (double-) mutants pdr2 and lpr1lpr2, respectively. For this, we used RNA from root tissue of 5 days old seedlings which were grown for 4 days on high phosphate medium and subsequently transferred to low phosphate medium for 20h.

About the Experimenter

Name:Mr Jens Mueller
Head of Lab Name:Prof Steffen Abel
Lab:
Address:Department of Molecular Signal Processing, Leibniz Institute of Plant Biochemistry
Weinberg 3 , Halle, Sachsen-Anhalt, 06120, GERMANY
Postcode: 06120
Country: GERMANY
 
Telephone Number: +4934555821240

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: starvation
Number of Slides:18
 
Experimental Parameters:
parameterstarvation
Quality Control Measures Taken:
References:
 
Other Information:

Slides in this Experiment

Hybridisation Set: Mueller: Expression analysis on low phosphate conditions

Slide: Mueller_648-18_lpr1lpr2(-)_Rep3_ATH1

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

Summary Information

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

  • Extract 1 ("Mueller_648-18_lpr1lpr2(-)_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: Mueller_648-18_lpr1lpr2(-)_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: lpr1lpr2
Stock Code:
Genetic Background: Col-0
Growth Conditions:
Stratification3-5 mg of seeds were stratified over night in agar solution (0,1% Agar in sterile dd. water) in an 2ml centrifugation tube at 4°C.
Sterilisation3-5 mg seeds were incubated for 35 min in an exicator containing a mixture of 6 ml HCl (37%) and 10 ml sodium hypochlorite (12%).
ProtocolAfter surface sterilization and stratification Arabidopsis seeds were germinated and grown for 4 days on 1% Phytagar medium (pH 5.6) containing 5 mM KNO3, 2.5 mM KH2PO4, 2 mM MgSO4, 2 mM Ca(NO3)2, 50 µM Fe-EDTA, 70 µM H3BO3, 14 µM MnCl2, 0.5 µM CuSO4, 1 µM ZnSO4, 0.2 µM NaMoO4, 10 µM NaCl, and 0.01 µM CoCl2. In addition, 2.5 mM Mes-KOH (pH 5.6) and 0.5% sucrose were included. This medium is referred to as high or +Pi medium. For low or -Pi medium, KH2PO4 was omitted from the above nutrient solution. To remove remnants of phosphorus from Phytagar we included washing steps using dialysis before preparing the medium. Plants were grown on long day conditions (16h light/ 8h dark) at 20°C in a growth room.
Substrate Sterilising Proceduresterilisation by autoclaving
Plant Spacingca 5 mg seeds in 3 rows on square dishes
Temperature20 °C average, 20 °C day, 20 °C night
Humidity60 % average, 60 % day, 60 % night
MediumOwn medium: 1% Phytagar medium (pH 5.6) containing 5 mM KNO3, 2.5 mM KH2PO4, 2 mM MgSO4, 2 mM Ca(NO3)2, 50 µM Fe-EDTA, 70 µM H3BO3, 14 µM MnCl2, 0.5 µM CuSO4, 1 µM ZnSO4, 0.2 µM NaMoO4, 10 µM NaCl, and 0.01 µM CoCl2. In addition, 2.5 mM Mes-KOH (pH 5.6) and 0.5% sucrose were included
Lighting
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)
Genetic Variation: T-DNA knock out mutation in AT1G23010,AT1G71040
Tissue: whole root
in vivo Treatment: Plants were germinated and grown for 4 days on medium with high phosphate (2,5mM / (+)) and subsequently transferred for 20h to either medium with no phosphate (0mM / (-)) or to medium with high phosphate (control plants).
Additional Organism Information:
Sample DescriptionSamples were derived from roots of 5 days old seedlings.
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:0.190703
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-ratio1.145811
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.623538
Spike_AFFX-r2-Bs-dap_5_signal9.109216
NoiseAvg:7.71,Std:0.18,Min:7.3,Max:8.2
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionA
Spike_AFFX-r2-Ec-bioB_3_detectionA
Spike_AFFX-r2-Bs-thr_5_signal3.353389
#P15378
Spike_AFFX-r2-Bs-phe_M_signal7.068611
Corner-Avg:13835,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal1.123509
Spike_AFFX-r2-Ec-bioB_3_signal2.346767
Spike_AFFX-r2-Bs-lys_M_signal6.962833
Spike_AFFX-r2-P1-cre_3_signal1342.291992
Spike_AFFX-r2-Bs-lys_3-5-ratio2.448543
Spike_AFFX-r2-Bs-dap_M_signal48.119698
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio11.777310
Spike_AFFX-r2-Ec-bioB_avg-signal2.411302
Spike_AFFX-r2-Bs-thr_avg-signal19.383112
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal219.556000
Spike_AFFX-r2-Bs-phe_5_signal5.685984
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal337.430817
RawQ5.308672
Spike_AFFX-r2-Bs-lys_5_signal5.298440
Signal(A)3.419936
%A31.091627
Signal(All)127.036552
Corner+Avg:290,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal62.388699
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal13.100038
Spike_AFFX-r2-Ec-bioD_avg-signal278.493408
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionA
%P67.417801
Spike_AFFX-r2-Bs-lys_avg-signal8.411576
Spike_AFFX-r2-P1-cre_avg-signal1256.884766
Spike_AFFX-r2-Ec-bioB_M_detectionA
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.490574
Spike_AFFX-r2-Bs-thr_3_signal39.493896
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionA
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal8.618211
Spike_AFFX-r2-Bs-dap_3_signal105.866173
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.536878
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal59.207016
#M340
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal12.973457
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.053738
Spike_AFFX-r2-Bs-thr_M_signal15.302046
Signal(P)186.566605
Spike_AFFX-r2-Bs-phe_3-5-ratio2.303918
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:12914,Count:9
Spike_AFFX-r2-P1-cre_5_signal1171.477539
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7092
Signal(M)13.024618
BackgroundAvg:178.11,Std:1.66,Min:173.9,Max:182.7
Spike_AFFX-r2-Ec-bioC_avg-signal60.797859
Spike_AFFX-r2-Bs-dap_avg-signal54.365032
Spike_AFFX-r2-Bs-dap_3-5-ratio11.621876
Spike_AFFX-r2-Ec-bioB_5_signal3.763630
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.190703
NF1.000000
HZ4
Tau0.015000

Slide: Mueller_648-17_pdr2(-)_Rep3_ATH1

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

Summary Information

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

  • Extract 1 ("Mueller_648-17_pdr2(-)_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: Mueller_648-17_pdr2(-)_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: pdr2
Stock Code:
Genetic Background: Col-0
Growth Conditions:
Stratification3-5 mg of seeds were stratified over night in agar solution (0,1% Agar in sterile dd. water) in an 2ml centrifugation tube at 4°C.
Sterilisation3-5 mg seeds were incubated for 35 min in an exicator containing a mixture of 6 ml HCl (37%) and 10 ml sodium hypochlorite (12%).
ProtocolAfter surface sterilization and stratification Arabidopsis seeds were germinated and grown for 4 days on 1% Phytagar medium (pH 5.6) containing 5 mM KNO3, 2.5 mM KH2PO4, 2 mM MgSO4, 2 mM Ca(NO3)2, 50 µM Fe-EDTA, 70 µM H3BO3, 14 µM MnCl2, 0.5 µM CuSO4, 1 µM ZnSO4, 0.2 µM NaMoO4, 10 µM NaCl, and 0.01 µM CoCl2. In addition, 2.5 mM Mes-KOH (pH 5.6) and 0.5% sucrose were included. This medium is referred to as high or +Pi medium. For low or -Pi medium, KH2PO4 was omitted from the above nutrient solution. To remove remnants of phosphorus from Phytagar we included washing steps using dialysis before preparing the medium. Plants were grown on long day conditions (16h light/ 8h dark) at 20°C in a growth room.
Substrate Sterilising Proceduresterilisation by autoclaving
Plant Spacingca 5 mg seeds in 3 rows on square dishes
Temperature20 °C average, 20 °C day, 20 °C night
Humidity60 % average, 60 % day, 60 % night
MediumOwn medium: 1% Phytagar medium (pH 5.6) containing 5 mM KNO3, 2.5 mM KH2PO4, 2 mM MgSO4, 2 mM Ca(NO3)2, 50 µM Fe-EDTA, 70 µM H3BO3, 14 µM MnCl2, 0.5 µM CuSO4, 1 µM ZnSO4, 0.2 µM NaMoO4, 10 µM NaCl, and 0.01 µM CoCl2. In addition, 2.5 mM Mes-KOH (pH 5.6) and 0.5% sucrose were included
Lighting
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)
Genetic Variation: EMS induced mutation mutation in AT5G23630
Tissue: whole root
in vivo Treatment: Plants were germinated and grown for 4 days on medium with high phosphate (2,5mM / (+)) and subsequently transferred for 20h to either medium with no phosphate (0mM / (-)) or to medium with high phosphate (control plants).
Additional Organism Information:
Sample DescriptionSamples were derived from roots of 5 days old seedlings.
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:0.628091
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-ratio1.183735
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.599113
Spike_AFFX-r2-Bs-dap_5_signal61.821697
NoiseAvg:3.28,Std:0.11,Min:3.0,Max:3.5
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal26.614382
#P14929
Spike_AFFX-r2-Bs-phe_M_signal32.326443
Corner-Avg:13511,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal10.523208
Spike_AFFX-r2-Ec-bioB_3_signal8.307972
Spike_AFFX-r2-Bs-lys_M_signal39.071220
Spike_AFFX-r2-P1-cre_3_signal5272.272461
Spike_AFFX-r2-Bs-lys_3-5-ratio1.831762
Spike_AFFX-r2-Bs-dap_M_signal239.561935
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio6.426201
Spike_AFFX-r2-Ec-bioB_avg-signal10.899433
Spike_AFFX-r2-Bs-thr_avg-signal88.690102
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1091.568481
Spike_AFFX-r2-Bs-phe_5_signal35.373837
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1646.013184
RawQ2.924690
Spike_AFFX-r2-Bs-lys_5_signal27.969477
Signal(A)4.494394
%A32.766331
Signal(All)140.457047
Corner+Avg:257,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal316.270599
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal84.646942
Spike_AFFX-r2-Ec-bioD_avg-signal1368.790771
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P65.449364
Spike_AFFX-r2-Bs-lys_avg-signal39.424706
Spike_AFFX-r2-P1-cre_avg-signal4863.101074
Spike_AFFX-r2-Ec-bioB_M_detectionA
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.784305
Spike_AFFX-r2-Bs-thr_3_signal171.029373
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-signal50.782410
Spike_AFFX-r2-Bs-dap_3_signal448.944519
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.507934
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal293.420532
#M407
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal51.233418
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.077875
Spike_AFFX-r2-Bs-thr_M_signal68.426544
Signal(P)211.886307
Spike_AFFX-r2-Bs-phe_3-5-ratio2.392925
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:12776,Count:9
Spike_AFFX-r2-P1-cre_5_signal4453.929688
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7474
Signal(M)17.158915
BackgroundAvg:75.89,Std:0.82,Min:73.4,Max:77.6
Spike_AFFX-r2-Ec-bioC_avg-signal304.845581
Spike_AFFX-r2-Bs-dap_avg-signal250.109390
Spike_AFFX-r2-Bs-dap_3-5-ratio7.261925
Spike_AFFX-r2-Ec-bioB_5_signal13.867120
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.628091
NF1.000000
HZ4
Tau0.015000

Slide: Mueller_648-16_Col (-)_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 ("Mueller_648-16_Col (-)_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: Mueller_648-16_Col (-)_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: Columbia-0
Stock Code:
Growth Conditions:
Stratification3-5 mg of seeds were stratified over night in agar solution (0,1% Agar in sterile dd. water) in an 2ml centrifugation tube at 4°C.
Sterilisation3-5 mg seeds were incubated for 35 min in an exicator containing a mixture of 6 ml HCl (37%) and 10 ml sodium hypochlorite (12%).
ProtocolAfter surface sterilization and stratification Arabidopsis seeds were germinated and grown for 4 days on 1% Phytagar medium (pH 5.6) containing 5 mM KNO3, 2.5 mM KH2PO4, 2 mM MgSO4, 2 mM Ca(NO3)2, 50 µM Fe-EDTA, 70 µM H3BO3, 14 µM MnCl2, 0.5 µM CuSO4, 1 µM ZnSO4, 0.2 µM NaMoO4, 10 µM NaCl, and 0.01 µM CoCl2. In addition, 2.5 mM Mes-KOH (pH 5.6) and 0.5% sucrose were included. This medium is referred to as high or +Pi medium. For low or -Pi medium, KH2PO4 was omitted from the above nutrient solution. To remove remnants of phosphorus from Phytagar we included washing steps using dialysis before preparing the medium. Plants were grown on long day conditions (16h light/ 8h dark) at 20°C in a growth room.
Substrate Sterilising Proceduresterilisation by autoclaving
Plant Spacingca 5 mg seeds in 3 rows on square dishes
Temperature20 °C average, 20 °C day, 20 °C night
Humidity60 % average, 60 % day, 60 % night
MediumOwn medium: 1% Phytagar medium (pH 5.6) containing 5 mM KNO3, 2.5 mM KH2PO4, 2 mM MgSO4, 2 mM Ca(NO3)2, 50 µM Fe-EDTA, 70 µM H3BO3, 14 µM MnCl2, 0.5 µM CuSO4, 1 µM ZnSO4, 0.2 µM NaMoO4, 10 µM NaCl, and 0.01 µM CoCl2. In addition, 2.5 mM Mes-KOH (pH 5.6) and 0.5% sucrose were included
Lighting
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)
Tissue: whole root
in vivo Treatment: Plants were germinated and grown for 4 days on medium with high phosphate (2,5mM / (+)) and subsequently transferred for 20h to either medium with no phosphate (0mM / (-)) or to medium with high phosphate (control plants).
Additional Organism Information:
Sample DescriptionSamples were derived from roots of 5 days old seedlings.
Other Information:
ecotype_habitat

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:0.285737
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-ratio1.264266
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.055392
Spike_AFFX-r2-Bs-dap_5_signal22.750914
NoiseAvg:7.61,Std:0.26,Min:6.9,Max:8.4
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionA
Spike_AFFX-r2-Ec-bioB_3_detectionA
Spike_AFFX-r2-Bs-thr_5_signal5.044284
#P14838
Spike_AFFX-r2-Bs-phe_M_signal4.848184
Corner-Avg:12522,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal3.677606
Spike_AFFX-r2-Ec-bioB_3_signal0.700724
Spike_AFFX-r2-Bs-lys_M_signal4.609657
Spike_AFFX-r2-P1-cre_3_signal1681.728149
Spike_AFFX-r2-Bs-lys_3-5-ratio2.635463
Spike_AFFX-r2-Bs-dap_M_signal42.280674
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio4.284894
Spike_AFFX-r2-Ec-bioB_avg-signal5.676191
Spike_AFFX-r2-Bs-thr_avg-signal14.550251
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal213.084946
Spike_AFFX-r2-Bs-phe_5_signal8.473521
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal377.347168
RawQ5.522881
Spike_AFFX-r2-Bs-lys_5_signal7.484577
Signal(A)4.607358
%A33.340641
Signal(All)131.123810
Corner+Avg:252,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal60.765457
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal20.144646
Spike_AFFX-r2-Ec-bioD_avg-signal295.216064
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionA
%P65.050415
Spike_AFFX-r2-Bs-lys_avg-signal10.606520
Spike_AFFX-r2-P1-cre_avg-signal1505.964844
Spike_AFFX-r2-Ec-bioB_M_detectionA
Spike_AFFX-r2-Bs-lys_M_detectionA
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.608943
Spike_AFFX-r2-Bs-thr_3_signal21.614222
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionA
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal11.155450
Spike_AFFX-r2-Bs-dap_3_signal108.694733
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.770877
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal65.173805
#M367
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal19.725325
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.932360
Spike_AFFX-r2-Bs-thr_M_signal16.992245
Signal(P)198.778839
Spike_AFFX-r2-Bs-phe_3-5-ratio2.377364
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:11396,Count:9
Spike_AFFX-r2-P1-cre_5_signal1330.201538
Spike_AFFX-r2-Bs-phe_M_detectionA
#A7605
Signal(M)17.478899
BackgroundAvg:187.33,Std:3.17,Min:179.0,Max:194.8
Spike_AFFX-r2-Ec-bioC_avg-signal62.969631
Spike_AFFX-r2-Bs-dap_avg-signal57.908772
Spike_AFFX-r2-Bs-dap_3-5-ratio4.777598
Spike_AFFX-r2-Ec-bioB_5_signal12.650244
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.285737
NF1.000000
HZ4
Tau0.015000

Slide: Mueller_648-15_lpr1lpr2(+)_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 ("Mueller_648-15_lpr1lpr2(+)_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: Mueller_648-15_lpr1lpr2(+)_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: lpr1lpr2
Stock Code:
Genetic Background: Col-0
Growth Conditions:
Stratification3-5 mg of seeds were stratified over night in agar solution (0,1% Agar in sterile dd. water) in an 2ml centrifugation tube at 4°C.
Sterilisation3-5 mg seeds were incubated for 35 min in an exicator containing a mixture of 6 ml HCl (37%) and 10 ml sodium hypochlorite (12%).
ProtocolAfter surface sterilization and stratification Arabidopsis seeds were germinated and grown for 4 days on 1% Phytagar medium (pH 5.6) containing 5 mM KNO3, 2.5 mM KH2PO4, 2 mM MgSO4, 2 mM Ca(NO3)2, 50 µM Fe-EDTA, 70 µM H3BO3, 14 µM MnCl2, 0.5 µM CuSO4, 1 µM ZnSO4, 0.2 µM NaMoO4, 10 µM NaCl, and 0.01 µM CoCl2. In addition, 2.5 mM Mes-KOH (pH 5.6) and 0.5% sucrose were included. This medium is referred to as high or +Pi medium. For low or -Pi medium, KH2PO4 was omitted from the above nutrient solution. To remove remnants of phosphorus from Phytagar we included washing steps using dialysis before preparing the medium. Plants were grown on long day conditions (16h light/ 8h dark) at 20°C in a growth room.
Substrate Sterilising Proceduresterilisation by autoclaving
Plant Spacingca 5 mg seeds in 3 rows on square dishes
Temperature20 °C average, 20 °C day, 20 °C night
Humidity60 % average, 60 % day, 60 % night
MediumOwn medium: 1% Phytagar medium (pH 5.6) containing 5 mM KNO3, 2.5 mM KH2PO4, 2 mM MgSO4, 2 mM Ca(NO3)2, 50 µM Fe-EDTA, 70 µM H3BO3, 14 µM MnCl2, 0.5 µM CuSO4, 1 µM ZnSO4, 0.2 µM NaMoO4, 10 µM NaCl, and 0.01 µM CoCl2. In addition, 2.5 mM Mes-KOH (pH 5.6) and 0.5% sucrose were included
Lighting
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)
Genetic Variation: T-DNA knock out mutation in AT1G23010,AT1G71040
Tissue: whole root
in vivo Treatment: Plants were germinated and grown for 4 days on medium with high phosphate (2,5mM / (+)) and subsequently transferred for 20h to either medium with no phosphate (0mM / (-)) or to medium with high phosphate (control plants).
Additional Organism Information:
Sample DescriptionSamples were derived from roots of 5 days old seedlings.
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:0.303266
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-ratio1.126386
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.349569
Spike_AFFX-r2-Bs-dap_5_signal17.370667
NoiseAvg:5.96,Std:0.17,Min:5.5,Max:6.5
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionA
Spike_AFFX-r2-Ec-bioB_3_detectionA
Spike_AFFX-r2-Bs-thr_5_signal1.006186
#P15180
Spike_AFFX-r2-Bs-phe_M_signal9.530097
Corner-Avg:12073,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal0.367032
Spike_AFFX-r2-Ec-bioB_3_signal2.260389
Spike_AFFX-r2-Bs-lys_M_signal7.454523
Spike_AFFX-r2-P1-cre_3_signal1566.677490
Spike_AFFX-r2-Bs-lys_3-5-ratio1.799762
Spike_AFFX-r2-Bs-dap_M_signal65.944046
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio38.033413
Spike_AFFX-r2-Ec-bioB_avg-signal3.031212
Spike_AFFX-r2-Bs-thr_avg-signal20.532990
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal219.278763
Spike_AFFX-r2-Bs-phe_5_signal11.626464
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal377.469543
RawQ4.491953
Spike_AFFX-r2-Bs-lys_5_signal8.752322
Signal(A)3.578753
%A32.034195
Signal(All)131.806183
Corner+Avg:227,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal60.266178
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal24.483639
Spike_AFFX-r2-Ec-bioD_avg-signal298.374146
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P66.549759
Spike_AFFX-r2-Bs-lys_avg-signal10.652982
Spike_AFFX-r2-P1-cre_avg-signal1478.782959
Spike_AFFX-r2-Ec-bioB_M_detectionA
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.416046
Spike_AFFX-r2-Bs-thr_3_signal38.268669
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-signal15.213401
Spike_AFFX-r2-Bs-dap_3_signal122.129639
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.721414
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal61.101501
#M323
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal15.752100
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.986329
Spike_AFFX-r2-Bs-thr_M_signal22.324110
Signal(P)196.023132
Spike_AFFX-r2-Bs-phe_3-5-ratio2.105854
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:10508,Count:9
Spike_AFFX-r2-P1-cre_5_signal1390.888550
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7307
Signal(M)14.606388
BackgroundAvg:142.72,Std:2.75,Min:134.2,Max:150.1
Spike_AFFX-r2-Ec-bioC_avg-signal60.683838
Spike_AFFX-r2-Bs-dap_avg-signal68.481453
Spike_AFFX-r2-Bs-dap_3-5-ratio7.030797
Spike_AFFX-r2-Ec-bioB_5_signal6.466214
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.303266
NF1.000000
HZ4
Tau0.015000

Slide: Mueller_648-14_pdr2(+)_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 ("Mueller_648-14_pdr2(+)_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: Mueller_648-14_pdr2(+)_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: pdr2
Stock Code:
Genetic Background: Col-0
Growth Conditions:
Stratification3-5 mg of seeds were stratified over night in agar solution (0,1% Agar in sterile dd. water) in an 2ml centrifugation tube at 4°C.
Sterilisation3-5 mg seeds were incubated for 35 min in an exicator containing a mixture of 6 ml HCl (37%) and 10 ml sodium hypochlorite (12%).
ProtocolAfter surface sterilization and stratification Arabidopsis seeds were germinated and grown for 4 days on 1% Phytagar medium (pH 5.6) containing 5 mM KNO3, 2.5 mM KH2PO4, 2 mM MgSO4, 2 mM Ca(NO3)2, 50 µM Fe-EDTA, 70 µM H3BO3, 14 µM MnCl2, 0.5 µM CuSO4, 1 µM ZnSO4, 0.2 µM NaMoO4, 10 µM NaCl, and 0.01 µM CoCl2. In addition, 2.5 mM Mes-KOH (pH 5.6) and 0.5% sucrose were included. This medium is referred to as high or +Pi medium. For low or -Pi medium, KH2PO4 was omitted from the above nutrient solution. To remove remnants of phosphorus from Phytagar we included washing steps using dialysis before preparing the medium. Plants were grown on long day conditions (16h light/ 8h dark) at 20°C in a growth room.
Substrate Sterilising Proceduresterilisation by autoclaving
Plant Spacingca 5 mg seeds in 3 rows on square dishes
Temperature20 °C average, 20 °C day, 20 °C night
Humidity60 % average, 60 % day, 60 % night
MediumOwn medium: 1% Phytagar medium (pH 5.6) containing 5 mM KNO3, 2.5 mM KH2PO4, 2 mM MgSO4, 2 mM Ca(NO3)2, 50 µM Fe-EDTA, 70 µM H3BO3, 14 µM MnCl2, 0.5 µM CuSO4, 1 µM ZnSO4, 0.2 µM NaMoO4, 10 µM NaCl, and 0.01 µM CoCl2. In addition, 2.5 mM Mes-KOH (pH 5.6) and 0.5% sucrose were included
Lighting
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)
Genetic Variation: EMS induced mutation mutation in AT5G23630
Tissue: whole root
in vivo Treatment: Plants were germinated and grown for 4 days on medium with high phosphate (2,5mM / (+)) and subsequently transferred for 20h to either medium with no phosphate (0mM / (-)) or to medium with high phosphate (control plants).
Additional Organism Information:
Sample DescriptionSamples were derived from roots of 5 days old seedlings.
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:0.424572
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-ratio1.135356
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.587939
Spike_AFFX-r2-Bs-dap_5_signal15.315353
NoiseAvg:3.81,Std:0.16,Min:3.4,Max:4.1
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionA
Spike_AFFX-r2-Ec-bioB_3_detectionA
Spike_AFFX-r2-Bs-thr_5_signal4.563760
#P15196
Spike_AFFX-r2-Bs-phe_M_signal12.506719
Corner-Avg:12456,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal1.861803
Spike_AFFX-r2-Ec-bioB_3_signal4.179606
Spike_AFFX-r2-Bs-lys_M_signal8.379676
Spike_AFFX-r2-P1-cre_3_signal2916.578613
Spike_AFFX-r2-Bs-lys_3-5-ratio1.913552
Spike_AFFX-r2-Bs-dap_M_signal75.273460
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio10.797654
Spike_AFFX-r2-Ec-bioB_avg-signal4.383439
Spike_AFFX-r2-Bs-thr_avg-signal25.966087
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal498.289154
Spike_AFFX-r2-Bs-phe_5_signal9.895948
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal712.072632
RawQ3.311163
Spike_AFFX-r2-Bs-lys_5_signal14.292480
Signal(A)3.510441
%A31.911442
Signal(All)138.157959
Corner+Avg:223,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal135.529343
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal31.859102
Spike_AFFX-r2-Ec-bioD_avg-signal605.180908
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionM
%P66.619904
Spike_AFFX-r2-Bs-lys_avg-signal16.673853
Spike_AFFX-r2-P1-cre_avg-signal2742.723145
Spike_AFFX-r2-Ec-bioB_M_detectionA
Spike_AFFX-r2-Bs-lys_M_detectionA
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.468654
Spike_AFFX-r2-Bs-thr_3_signal49.277905
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-signal18.087257
Spike_AFFX-r2-Bs-dap_3_signal172.353043
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.429035
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal122.924728
#M335
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal27.349405
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.102539
Spike_AFFX-r2-Bs-thr_M_signal24.056599
Signal(P)205.380005
Spike_AFFX-r2-Bs-phe_3-5-ratio3.219409
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:10610,Count:9
Spike_AFFX-r2-P1-cre_5_signal2568.867432
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7279
Signal(M)14.554419
BackgroundAvg:86.16,Std:1.81,Min:81.1,Max:90.4
Spike_AFFX-r2-Ec-bioC_avg-signal129.227036
Spike_AFFX-r2-Bs-dap_avg-signal87.647278
Spike_AFFX-r2-Bs-dap_3-5-ratio11.253612
Spike_AFFX-r2-Ec-bioB_5_signal7.108908
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.424572
NF1.000000
HZ4
Tau0.015000

Slide: Mueller_648-13_Col(+)_Rep3_ATH1

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

Summary Information

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

  • Extract 1 ("Mueller_648-13_Col(+)_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: Mueller_648-13_Col(+)_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: Columbia-0
Stock Code:
Growth Conditions:
Stratification3-5 mg of seeds were stratified over night in agar solution (0,1% Agar in sterile dd. water) in an 2ml centrifugation tube at 4°C.
Sterilisation3-5 mg seeds were incubated for 35 min in an exicator containing a mixture of 6 ml HCl (37%) and 10 ml sodium hypochlorite (12%).
ProtocolAfter surface sterilization and stratification Arabidopsis seeds were germinated and grown for 4 days on 1% Phytagar medium (pH 5.6) containing 5 mM KNO3, 2.5 mM KH2PO4, 2 mM MgSO4, 2 mM Ca(NO3)2, 50 µM Fe-EDTA, 70 µM H3BO3, 14 µM MnCl2, 0.5 µM CuSO4, 1 µM ZnSO4, 0.2 µM NaMoO4, 10 µM NaCl, and 0.01 µM CoCl2. In addition, 2.5 mM Mes-KOH (pH 5.6) and 0.5% sucrose were included. This medium is referred to as high or +Pi medium. For low or -Pi medium, KH2PO4 was omitted from the above nutrient solution. To remove remnants of phosphorus from Phytagar we included washing steps using dialysis before preparing the medium. Plants were grown on long day conditions (16h light/ 8h dark) at 20°C in a growth room.
Substrate Sterilising Proceduresterilisation by autoclaving
Plant Spacingca 5 mg seeds in 3 rows on square dishes
Temperature20 °C average, 20 °C day, 20 °C night
Humidity60 % average, 60 % day, 60 % night
MediumOwn medium: 1% Phytagar medium (pH 5.6) containing 5 mM KNO3, 2.5 mM KH2PO4, 2 mM MgSO4, 2 mM Ca(NO3)2, 50 µM Fe-EDTA, 70 µM H3BO3, 14 µM MnCl2, 0.5 µM CuSO4, 1 µM ZnSO4, 0.2 µM NaMoO4, 10 µM NaCl, and 0.01 µM CoCl2. In addition, 2.5 mM Mes-KOH (pH 5.6) and 0.5% sucrose were included
Lighting
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)
Tissue: whole root
in vivo Treatment: Plants were germinated and grown for 4 days on medium with high phosphate (2,5mM / (+)) and subsequently transferred for 20h to either medium with no phosphate (0mM / (-)) or to medium with high phosphate (control plants).
Additional Organism Information:
Sample DescriptionSamples were derived from roots of 5 days old seedlings.
Other Information:
ecotype_habitat

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:0.363986
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-ratio1.272430
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.523527
Spike_AFFX-r2-Bs-dap_5_signal15.541977
NoiseAvg:5.95,Std:0.17,Min:5.4,Max:6.4
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionA
Spike_AFFX-r2-Ec-bioB_3_detectionA
Spike_AFFX-r2-Bs-thr_5_signal7.694997
#P14671
Spike_AFFX-r2-Bs-phe_M_signal4.386371
Corner-Avg:11913,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal0.717760
Spike_AFFX-r2-Ec-bioB_3_signal2.116796
Spike_AFFX-r2-Bs-lys_M_signal9.394115
Spike_AFFX-r2-P1-cre_3_signal1812.888428
Spike_AFFX-r2-Bs-lys_3-5-ratio2.185455
Spike_AFFX-r2-Bs-dap_M_signal49.662365
Spike_AFFX-r2-Bs-thr_M_detectionM
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio4.483341
Spike_AFFX-r2-Ec-bioB_avg-signal2.292631
Spike_AFFX-r2-Bs-thr_avg-signal19.708364
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal210.010391
Spike_AFFX-r2-Bs-phe_5_signal6.546183
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal360.239807
RawQ4.709966
Spike_AFFX-r2-Bs-lys_5_signal9.776814
Signal(A)4.948836
%A33.967560
Signal(All)133.906052
Corner+Avg:228,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal70.741982
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal26.036158
Spike_AFFX-r2-Ec-bioD_avg-signal285.125092
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionA
%P64.318283
Spike_AFFX-r2-Bs-lys_avg-signal13.512572
Spike_AFFX-r2-P1-cre_avg-signal1618.816650
Spike_AFFX-r2-Ec-bioB_M_detectionA
Spike_AFFX-r2-Bs-lys_M_detectionA
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.714160
Spike_AFFX-r2-Bs-thr_3_signal34.499294
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionA
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal12.322904
Spike_AFFX-r2-Bs-dap_3_signal114.453285
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.715343
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal70.325691
#M391
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal21.366785
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.005919
Spike_AFFX-r2-Bs-thr_M_signal16.930801
Signal(P)205.080307
Spike_AFFX-r2-Bs-phe_3-5-ratio3.977304
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:10454,Count:9
Spike_AFFX-r2-P1-cre_5_signal1424.744873
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7748
Signal(M)18.721619
BackgroundAvg:147.05,Std:2.32,Min:140.3,Max:152.3
Spike_AFFX-r2-Ec-bioC_avg-signal70.533836
Spike_AFFX-r2-Bs-dap_avg-signal59.885876
Spike_AFFX-r2-Bs-dap_3-5-ratio7.364140
Spike_AFFX-r2-Ec-bioB_5_signal4.043336
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.363986
NF1.000000
HZ4
Tau0.015000

Slide: Mueller_648-12_lpr1lpr2(-)_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 ("Mueller_648-12_lpr1lpr2(-)_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: Mueller_648-12_lpr1lpr2(-)_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: lpr1lpr2
Stock Code:
Genetic Background: Col-0
Growth Conditions:
Stratification3-5 mg of seeds were stratified over night in agar solution (0,1% Agar in sterile dd. water) in an 2ml centrifugation tube at 4°C.
Sterilisation3-5 mg seeds were incubated for 35 min in an exicator containing a mixture of 6 ml HCl (37%) and 10 ml sodium hypochlorite (12%).
ProtocolAfter surface sterilization and stratification Arabidopsis seeds were germinated and grown for 4 days on 1% Phytagar medium (pH 5.6) containing 5 mM KNO3, 2.5 mM KH2PO4, 2 mM MgSO4, 2 mM Ca(NO3)2, 50 µM Fe-EDTA, 70 µM H3BO3, 14 µM MnCl2, 0.5 µM CuSO4, 1 µM ZnSO4, 0.2 µM NaMoO4, 10 µM NaCl, and 0.01 µM CoCl2. In addition, 2.5 mM Mes-KOH (pH 5.6) and 0.5% sucrose were included. This medium is referred to as high or +Pi medium. For low or -Pi medium, KH2PO4 was omitted from the above nutrient solution. To remove remnants of phosphorus from Phytagar we included washing steps using dialysis before preparing the medium. Plants were grown on long day conditions (16h light/ 8h dark) at 20°C in a growth room.
Substrate Sterilising Proceduresterilisation by autoclaving
Plant Spacingca 5 mg seeds in 3 rows on square dishes
Temperature20 °C average, 20 °C day, 20 °C night
Humidity60 % average, 60 % day, 60 % night
MediumOwn medium: 1% Phytagar medium (pH 5.6) containing 5 mM KNO3, 2.5 mM KH2PO4, 2 mM MgSO4, 2 mM Ca(NO3)2, 50 µM Fe-EDTA, 70 µM H3BO3, 14 µM MnCl2, 0.5 µM CuSO4, 1 µM ZnSO4, 0.2 µM NaMoO4, 10 µM NaCl, and 0.01 µM CoCl2. In addition, 2.5 mM Mes-KOH (pH 5.6) and 0.5% sucrose were included
Lighting
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)
Genetic Variation: T-DNA knock out mutation in AT1G23010,AT1G71040
Tissue: whole root
in vivo Treatment: Plants were germinated and grown for 4 days on medium with high phosphate (2,5mM / (+)) and subsequently transferred for 20h to either medium with no phosphate (0mM / (-)) or to medium with high phosphate (control plants).
Additional Organism Information:
Sample DescriptionSamples were derived from roots of 5 days old seedlings.
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:0.405275
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-ratio1.166010
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.622067
Spike_AFFX-r2-Bs-dap_5_signal4.076034
NoiseAvg:3.79,Std:0.06,Min:3.6,Max:4.0
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionA
Spike_AFFX-r2-Ec-bioB_3_detectionA
Spike_AFFX-r2-Bs-thr_5_signal3.742176
#P15103
Spike_AFFX-r2-Bs-phe_M_signal3.937462
Corner-Avg:11021,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal4.617859
Spike_AFFX-r2-Ec-bioB_3_signal6.509258
Spike_AFFX-r2-Bs-lys_M_signal0.865982
Spike_AFFX-r2-P1-cre_3_signal3145.810303
Spike_AFFX-r2-Bs-lys_3-5-ratio3.620639
Spike_AFFX-r2-Bs-dap_M_signal30.235888
Spike_AFFX-r2-Bs-thr_M_detectionA
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio5.386216
Spike_AFFX-r2-Ec-bioB_avg-signal7.197010
Spike_AFFX-r2-Bs-thr_avg-signal11.521386
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal621.157043
Spike_AFFX-r2-Bs-phe_5_signal5.004852
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal797.750305
RawQ3.084631
Spike_AFFX-r2-Bs-lys_5_signal3.472144
Signal(A)4.020029
%A32.301620
Signal(All)136.345764
Corner+Avg:200,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal159.169571
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal2.979156
Spike_AFFX-r2-Ec-bioD_avg-signal709.453674
Spike_AFFX-r2-Bs-dap_5_detectionA
Spike_AFFX-r2-Bs-phe_5_detectionA
%P66.212189
Spike_AFFX-r2-Bs-lys_avg-signal5.636501
Spike_AFFX-r2-P1-cre_avg-signal2921.869385
Spike_AFFX-r2-Ec-bioB_M_detectionA
Spike_AFFX-r2-Bs-lys_M_detectionA
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.486190
Spike_AFFX-r2-Bs-thr_3_signal20.156168
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionA
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal3.973823
Spike_AFFX-r2-Bs-dap_3_signal59.010166
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.284297
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal143.132858
#M339
Spike_AFFX-r2-Bs-lys_5_detectionA
Spike_AFFX-r2-Bs-lys_3_signal12.571379
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.112041
Spike_AFFX-r2-Bs-thr_M_signal10.665814
Signal(P)203.625412
Spike_AFFX-r2-Bs-phe_3-5-ratio0.595253
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:9365,Count:9
Spike_AFFX-r2-P1-cre_5_signal2697.928467
Spike_AFFX-r2-Bs-phe_M_detectionA
#A7368
Signal(M)14.963949
BackgroundAvg:81.13,Std:1.56,Min:77.3,Max:84.8
Spike_AFFX-r2-Ec-bioC_avg-signal151.151215
Spike_AFFX-r2-Bs-dap_avg-signal31.107363
Spike_AFFX-r2-Bs-dap_3-5-ratio14.477350
Spike_AFFX-r2-Ec-bioB_5_signal10.463913
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.405275
NF1.000000
HZ4
Tau0.015000

Slide: Mueller_648-11_pdr2(-) _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 ("Mueller_648-11_pdr2(-) _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: Mueller_648-11_pdr2(-) _Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: pdr2
Stock Code:
Genetic Background: Col-0
Growth Conditions:
Stratification3-5 mg of seeds were stratified over night in agar solution (0,1% Agar in sterile dd. water) in an 2ml centrifugation tube at 4°C.
Sterilisation3-5 mg seeds were incubated for 35 min in an exicator containing a mixture of 6 ml HCl (37%) and 10 ml sodium hypochlorite (12%).
ProtocolAfter surface sterilization and stratification Arabidopsis seeds were germinated and grown for 4 days on 1% Phytagar medium (pH 5.6) containing 5 mM KNO3, 2.5 mM KH2PO4, 2 mM MgSO4, 2 mM Ca(NO3)2, 50 µM Fe-EDTA, 70 µM H3BO3, 14 µM MnCl2, 0.5 µM CuSO4, 1 µM ZnSO4, 0.2 µM NaMoO4, 10 µM NaCl, and 0.01 µM CoCl2. In addition, 2.5 mM Mes-KOH (pH 5.6) and 0.5% sucrose were included. This medium is referred to as high or +Pi medium. For low or -Pi medium, KH2PO4 was omitted from the above nutrient solution. To remove remnants of phosphorus from Phytagar we included washing steps using dialysis before preparing the medium. Plants were grown on long day conditions (16h light/ 8h dark) at 20°C in a growth room.
Substrate Sterilising Proceduresterilisation by autoclaving
Plant Spacingca 5 mg seeds in 3 rows on square dishes
Temperature20 °C average, 20 °C day, 20 °C night
Humidity60 % average, 60 % day, 60 % night
MediumOwn medium: 1% Phytagar medium (pH 5.6) containing 5 mM KNO3, 2.5 mM KH2PO4, 2 mM MgSO4, 2 mM Ca(NO3)2, 50 µM Fe-EDTA, 70 µM H3BO3, 14 µM MnCl2, 0.5 µM CuSO4, 1 µM ZnSO4, 0.2 µM NaMoO4, 10 µM NaCl, and 0.01 µM CoCl2. In addition, 2.5 mM Mes-KOH (pH 5.6) and 0.5% sucrose were included
Lighting
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)
Genetic Variation: EMS induced mutation mutation in AT5G23630
Tissue: whole root
in vivo Treatment: Plants were germinated and grown for 4 days on medium with high phosphate (2,5mM / (+)) and subsequently transferred for 20h to either medium with no phosphate (0mM / (-)) or to medium with high phosphate (control plants).
Additional Organism Information:
Sample DescriptionSamples were derived from roots of 5 days old seedlings.
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:0.528381
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-ratio1.198918
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.307133
Spike_AFFX-r2-Bs-dap_5_signal35.275574
NoiseAvg:3.00,Std:0.09,Min:2.8,Max:3.3
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionA
Spike_AFFX-r2-Bs-thr_5_signal9.037141
#P15215
Spike_AFFX-r2-Bs-phe_M_signal18.501743
Corner-Avg:10945,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal6.356883
Spike_AFFX-r2-Ec-bioB_3_signal3.870265
Spike_AFFX-r2-Bs-lys_M_signal12.814236
Spike_AFFX-r2-P1-cre_3_signal4112.560547
Spike_AFFX-r2-Bs-lys_3-5-ratio1.835749
Spike_AFFX-r2-Bs-dap_M_signal116.554466
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio6.723822
Spike_AFFX-r2-Ec-bioB_avg-signal7.609479
Spike_AFFX-r2-Bs-thr_avg-signal35.295628
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal702.182251
Spike_AFFX-r2-Bs-phe_5_signal14.626748
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1073.695190
RawQ2.739177
Spike_AFFX-r2-Bs-lys_5_signal13.488649
Signal(A)3.799933
%A31.674704
Signal(All)136.358673
Corner+Avg:182,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal213.842392
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal28.108337
Spike_AFFX-r2-Ec-bioD_avg-signal887.938721
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P66.703201
Spike_AFFX-r2-Bs-lys_avg-signal17.021551
Spike_AFFX-r2-P1-cre_avg-signal3771.393555
Spike_AFFX-r2-Ec-bioB_M_detectionA
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.622096
Spike_AFFX-r2-Bs-thr_3_signal60.764126
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-signal20.412275
Spike_AFFX-r2-Bs-dap_3_signal215.522202
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.529083
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal179.380142
#M370
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal24.761768
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.192119
Spike_AFFX-r2-Bs-thr_M_signal36.085621
Signal(P)202.298141
Spike_AFFX-r2-Bs-phe_3-5-ratio1.921708
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:9559,Count:9
Spike_AFFX-r2-P1-cre_5_signal3430.226318
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7225
Signal(M)13.299563
BackgroundAvg:67.30,Std:1.00,Min:64.2,Max:69.3
Spike_AFFX-r2-Ec-bioC_avg-signal196.611267
Spike_AFFX-r2-Bs-dap_avg-signal122.450745
Spike_AFFX-r2-Bs-dap_3-5-ratio6.109673
Spike_AFFX-r2-Ec-bioB_5_signal12.601289
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.528381
NF1.000000
HZ4
Tau0.015000

Slide: Mueller_648-10_Col(-)_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 ("Mueller_648-10_Col(-)_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: Mueller_648-10_Col(-)_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Columbia-0
Stock Code:
Growth Conditions:
Stratification3-5 mg of seeds were stratified over night in agar solution (0,1% Agar in sterile dd. water) in an 2ml centrifugation tube at 4°C.
Sterilisation3-5 mg seeds were incubated for 35 min in an exicator containing a mixture of 6 ml HCl (37%) and 10 ml sodium hypochlorite (12%).
ProtocolAfter surface sterilization and stratification Arabidopsis seeds were germinated and grown for 4 days on 1% Phytagar medium (pH 5.6) containing 5 mM KNO3, 2.5 mM KH2PO4, 2 mM MgSO4, 2 mM Ca(NO3)2, 50 µM Fe-EDTA, 70 µM H3BO3, 14 µM MnCl2, 0.5 µM CuSO4, 1 µM ZnSO4, 0.2 µM NaMoO4, 10 µM NaCl, and 0.01 µM CoCl2. In addition, 2.5 mM Mes-KOH (pH 5.6) and 0.5% sucrose were included. This medium is referred to as high or +Pi medium. For low or -Pi medium, KH2PO4 was omitted from the above nutrient solution. To remove remnants of phosphorus from Phytagar we included washing steps using dialysis before preparing the medium. Plants were grown on long day conditions (16h light/ 8h dark) at 20°C in a growth room.
Substrate Sterilising Proceduresterilisation by autoclaving
Plant Spacingca 5 mg seeds in 3 rows on square dishes
Temperature20 °C average, 20 °C day, 20 °C night
Humidity60 % average, 60 % day, 60 % night
MediumOwn medium: 1% Phytagar medium (pH 5.6) containing 5 mM KNO3, 2.5 mM KH2PO4, 2 mM MgSO4, 2 mM Ca(NO3)2, 50 µM Fe-EDTA, 70 µM H3BO3, 14 µM MnCl2, 0.5 µM CuSO4, 1 µM ZnSO4, 0.2 µM NaMoO4, 10 µM NaCl, and 0.01 µM CoCl2. In addition, 2.5 mM Mes-KOH (pH 5.6) and 0.5% sucrose were included
Lighting
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)
Tissue: whole root
in vivo Treatment: Plants were germinated and grown for 4 days on medium with high phosphate (2,5mM / (+)) and subsequently transferred for 20h to either medium with no phosphate (0mM / (-)) or to medium with high phosphate (control plants).
Additional Organism Information:
Sample DescriptionSamples were derived from roots of 5 days old seedlings.
Other Information:
ecotype_habitat

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:0.638936
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-ratio1.213187
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.668769
Spike_AFFX-r2-Bs-dap_5_signal28.852093
NoiseAvg:3.19,Std:0.10,Min:2.9,Max:3.5
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionA
Spike_AFFX-r2-Bs-thr_5_signal8.183644
#P14756
Spike_AFFX-r2-Bs-phe_M_signal13.475869
Corner-Avg:10337,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal8.906413
Spike_AFFX-r2-Ec-bioB_3_signal9.262323
Spike_AFFX-r2-Bs-lys_M_signal10.458592
Spike_AFFX-r2-P1-cre_3_signal4739.768555
Spike_AFFX-r2-Bs-lys_3-5-ratio3.518060
Spike_AFFX-r2-Bs-dap_M_signal80.302345
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio5.606206
Spike_AFFX-r2-Ec-bioB_avg-signal10.672849
Spike_AFFX-r2-Bs-thr_avg-signal28.628729
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal789.722046
Spike_AFFX-r2-Bs-phe_5_signal14.278589
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1248.688354
RawQ2.843388
Spike_AFFX-r2-Bs-lys_5_signal7.048168
Signal(A)4.801945
%A33.643139
Signal(All)140.363281
Corner+Avg:171,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal182.727737
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal22.633934
Spike_AFFX-r2-Ec-bioD_avg-signal1019.205200
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionA
%P64.690926
Spike_AFFX-r2-Bs-lys_avg-signal14.100880
Spike_AFFX-r2-P1-cre_avg-signal4323.321289
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionM
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.665936
Spike_AFFX-r2-Bs-thr_3_signal45.879196
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-signal16.796129
Spike_AFFX-r2-Bs-dap_3_signal161.693329
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.581174
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal253.499634
#M380
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal24.795879
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.720821
Spike_AFFX-r2-Bs-thr_M_signal31.823341
Signal(P)214.018402
Spike_AFFX-r2-Bs-phe_3-5-ratio1.585166
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:9091,Count:9
Spike_AFFX-r2-P1-cre_5_signal3906.873779
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7674
Signal(M)17.843533
BackgroundAvg:70.80,Std:0.50,Min:69.1,Max:72.3
Spike_AFFX-r2-Ec-bioC_avg-signal218.113678
Spike_AFFX-r2-Bs-dap_avg-signal90.282585
Spike_AFFX-r2-Bs-dap_3-5-ratio5.604215
Spike_AFFX-r2-Ec-bioB_5_signal13.849811
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.638936
NF1.000000
HZ4
Tau0.015000

Slide: Mueller_648-9_lpr1lpr2(+)_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 ("Mueller_648-9_lpr1lpr2(+)_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: Mueller_648-9_lpr1lpr2(+)_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: lpr1lpr2
Stock Code:
Genetic Background: Col-0
Growth Conditions:
Stratification3-5 mg of seeds were stratified over night in agar solution (0,1% Agar in sterile dd. water) in an 2ml centrifugation tube at 4°C.
Sterilisation3-5 mg seeds were incubated for 35 min in an exicator containing a mixture of 6 ml HCl (37%) and 10 ml sodium hypochlorite (12%).
ProtocolAfter surface sterilization and stratification Arabidopsis seeds were germinated and grown for 4 days on 1% Phytagar medium (pH 5.6) containing 5 mM KNO3, 2.5 mM KH2PO4, 2 mM MgSO4, 2 mM Ca(NO3)2, 50 µM Fe-EDTA, 70 µM H3BO3, 14 µM MnCl2, 0.5 µM CuSO4, 1 µM ZnSO4, 0.2 µM NaMoO4, 10 µM NaCl, and 0.01 µM CoCl2. In addition, 2.5 mM Mes-KOH (pH 5.6) and 0.5% sucrose were included. This medium is referred to as high or +Pi medium. For low or -Pi medium, KH2PO4 was omitted from the above nutrient solution. To remove remnants of phosphorus from Phytagar we included washing steps using dialysis before preparing the medium. Plants were grown on long day conditions (16h light/ 8h dark) at 20°C in a growth room.
Substrate Sterilising Proceduresterilisation by autoclaving
Plant Spacingca 5 mg seeds in 3 rows on square dishes
Temperature20 °C average, 20 °C day, 20 °C night
Humidity60 % average, 60 % day, 60 % night
MediumOwn medium: 1% Phytagar medium (pH 5.6) containing 5 mM KNO3, 2.5 mM KH2PO4, 2 mM MgSO4, 2 mM Ca(NO3)2, 50 µM Fe-EDTA, 70 µM H3BO3, 14 µM MnCl2, 0.5 µM CuSO4, 1 µM ZnSO4, 0.2 µM NaMoO4, 10 µM NaCl, and 0.01 µM CoCl2. In addition, 2.5 mM Mes-KOH (pH 5.6) and 0.5% sucrose were included
Lighting
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)
Genetic Variation: T-DNA knock out mutation in AT1G23010,AT1G71040
Tissue: whole root
in vivo Treatment: Plants were germinated and grown for 4 days on medium with high phosphate (2,5mM / (+)) and subsequently transferred for 20h to either medium with no phosphate (0mM / (-)) or to medium with high phosphate (control plants).
Additional Organism Information:
Sample DescriptionSamples were derived from roots of 5 days old seedlings.
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:0.405666
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-ratio1.179156
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.923983
Spike_AFFX-r2-Bs-dap_5_signal18.535480
NoiseAvg:3.48,Std:0.09,Min:3.3,Max:3.7
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionA
Spike_AFFX-r2-Ec-bioB_3_detectionA
Spike_AFFX-r2-Bs-thr_5_signal6.928370
#P15342
Spike_AFFX-r2-Bs-phe_M_signal5.954241
Corner-Avg:10777,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal6.812735
Spike_AFFX-r2-Ec-bioB_3_signal7.655565
Spike_AFFX-r2-Bs-lys_M_signal7.728758
Spike_AFFX-r2-P1-cre_3_signal3278.376953
Spike_AFFX-r2-Bs-lys_3-5-ratio2.454470
Spike_AFFX-r2-Bs-dap_M_signal51.165604
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio7.010266
Spike_AFFX-r2-Ec-bioB_avg-signal7.584567
Spike_AFFX-r2-Bs-thr_avg-signal23.219322
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal607.391357
Spike_AFFX-r2-Bs-phe_5_signal7.358577
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal832.520142
RawQ2.918770
Spike_AFFX-r2-Bs-lys_5_signal6.741166
Signal(A)3.684708
%A31.196844
Signal(All)135.376663
Corner+Avg:223,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal169.778687
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal18.569002
Spike_AFFX-r2-Ec-bioD_avg-signal719.955750
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionA
%P67.259972
Spike_AFFX-r2-Bs-lys_avg-signal10.338638
Spike_AFFX-r2-P1-cre_avg-signal3029.325439
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.543183
Spike_AFFX-r2-Bs-thr_3_signal48.569721
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-signal10.627274
Spike_AFFX-r2-Bs-dap_3_signal110.315575
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.370649
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal163.428192
#M352
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal16.545990
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.038858
Spike_AFFX-r2-Bs-thr_M_signal14.159874
Signal(P)199.242477
Spike_AFFX-r2-Bs-phe_3-5-ratio2.523450
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:9458,Count:9
Spike_AFFX-r2-P1-cre_5_signal2780.273926
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7116
Signal(M)14.043120
BackgroundAvg:72.46,Std:0.81,Min:70.3,Max:75.0
Spike_AFFX-r2-Ec-bioC_avg-signal166.603439
Spike_AFFX-r2-Bs-dap_avg-signal60.005550
Spike_AFFX-r2-Bs-dap_3-5-ratio5.951590
Spike_AFFX-r2-Ec-bioB_5_signal8.285399
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.405666
NF1.000000
HZ4
Tau0.015000

Slide: Mueller_648-8_pdr2(+)_Rep2_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 ("Mueller_648-8_pdr2(+)_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: Mueller_648-8_pdr2(+)_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: pdr2
Stock Code:
Genetic Background: Col-0
Growth Conditions:
Stratification3-5 mg of seeds were stratified over night in agar solution (0,1% Agar in sterile dd. water) in an 2ml centrifugation tube at 4°C.
Sterilisation3-5 mg seeds were incubated for 35 min in an exicator containing a mixture of 6 ml HCl (37%) and 10 ml sodium hypochlorite (12%).
ProtocolAfter surface sterilization and stratification Arabidopsis seeds were germinated and grown for 4 days on 1% Phytagar medium (pH 5.6) containing 5 mM KNO3, 2.5 mM KH2PO4, 2 mM MgSO4, 2 mM Ca(NO3)2, 50 µM Fe-EDTA, 70 µM H3BO3, 14 µM MnCl2, 0.5 µM CuSO4, 1 µM ZnSO4, 0.2 µM NaMoO4, 10 µM NaCl, and 0.01 µM CoCl2. In addition, 2.5 mM Mes-KOH (pH 5.6) and 0.5% sucrose were included. This medium is referred to as high or +Pi medium. For low or -Pi medium, KH2PO4 was omitted from the above nutrient solution. To remove remnants of phosphorus from Phytagar we included washing steps using dialysis before preparing the medium. Plants were grown on long day conditions (16h light/ 8h dark) at 20°C in a growth room.
Substrate Sterilising Proceduresterilisation by autoclaving
Plant Spacingca 5 mg seeds in 3 rows on square dishes
Temperature20 °C average, 20 °C day, 20 °C night
Humidity60 % average, 60 % day, 60 % night
MediumOwn medium: 1% Phytagar medium (pH 5.6) containing 5 mM KNO3, 2.5 mM KH2PO4, 2 mM MgSO4, 2 mM Ca(NO3)2, 50 µM Fe-EDTA, 70 µM H3BO3, 14 µM MnCl2, 0.5 µM CuSO4, 1 µM ZnSO4, 0.2 µM NaMoO4, 10 µM NaCl, and 0.01 µM CoCl2. In addition, 2.5 mM Mes-KOH (pH 5.6) and 0.5% sucrose were included
Lighting
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)
Genetic Variation: EMS induced mutation mutation in AT5G23630
Tissue: whole root
in vivo Treatment: Plants were germinated and grown for 4 days on medium with high phosphate (2,5mM / (+)) and subsequently transferred for 20h to either medium with no phosphate (0mM / (-)) or to medium with high phosphate (control plants).
Additional Organism Information:
Sample DescriptionSamples were derived from roots of 5 days old seedlings.
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:0.730205
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-ratio1.140556
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.026792
Spike_AFFX-r2-Bs-dap_5_signal16.650112
NoiseAvg:2.94,Std:0.09,Min:2.6,Max:3.2
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionA
Spike_AFFX-r2-Bs-thr_5_signal0.852277
#P14452
Spike_AFFX-r2-Bs-phe_M_signal4.076862
Corner-Avg:10399,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal7.812204
Spike_AFFX-r2-Ec-bioB_3_signal10.767218
Spike_AFFX-r2-Bs-lys_M_signal5.722354
Spike_AFFX-r2-P1-cre_3_signal4639.426270
Spike_AFFX-r2-Bs-lys_3-5-ratio4.376216
Spike_AFFX-r2-Bs-dap_M_signal48.020885
Spike_AFFX-r2-Bs-thr_M_detectionA
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio31.508808
Spike_AFFX-r2-Ec-bioB_avg-signal9.688563
Spike_AFFX-r2-Bs-thr_avg-signal17.868952
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal806.329651
Spike_AFFX-r2-Bs-phe_5_signal11.491816
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1258.185425
RawQ2.570529
Spike_AFFX-r2-Bs-lys_5_signal6.186909
Signal(A)5.625416
%A34.690926
Signal(All)146.320450
Corner+Avg:183,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal190.065353
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal16.317446
Spike_AFFX-r2-Ec-bioD_avg-signal1032.257568
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionA
%P63.358177
Spike_AFFX-r2-Bs-lys_avg-signal12.994838
Spike_AFFX-r2-P1-cre_avg-signal4353.557129
Spike_AFFX-r2-Ec-bioB_M_detectionA
Spike_AFFX-r2-Bs-lys_M_detectionM
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.950899
Spike_AFFX-r2-Bs-thr_3_signal31.508808
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionA
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal10.628708
Spike_AFFX-r2-Bs-dap_3_signal96.515404
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.560386
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal185.436218
#M445
Spike_AFFX-r2-Bs-lys_5_detectionA
Spike_AFFX-r2-Bs-lys_3_signal27.075249
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.024963
Spike_AFFX-r2-Bs-thr_M_signal21.245768
Signal(P)227.274628
Spike_AFFX-r2-Bs-phe_3-5-ratio1.419919
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:8660,Count:9
Spike_AFFX-r2-P1-cre_5_signal4067.687988
Spike_AFFX-r2-Bs-phe_M_detectionA
#A7913
Signal(M)19.062290
BackgroundAvg:65.21,Std:0.77,Min:63.4,Max:66.6
Spike_AFFX-r2-Ec-bioC_avg-signal187.750793
Spike_AFFX-r2-Bs-dap_avg-signal53.728802
Spike_AFFX-r2-Bs-dap_3-5-ratio5.796682
Spike_AFFX-r2-Ec-bioB_5_signal10.486268
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.730205
NF1.000000
HZ4
Tau0.015000

Slide: Mueller_648-7_Col(+)_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 ("Mueller_648-7_Col(+)_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: Mueller_648-7_Col(+)_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Columbia-0
Stock Code:
Growth Conditions:
Stratification3-5 mg of seeds were stratified over night in agar solution (0,1% Agar in sterile dd. water) in an 2ml centrifugation tube at 4°C.
Sterilisation3-5 mg seeds were incubated for 35 min in an exicator containing a mixture of 6 ml HCl (37%) and 10 ml sodium hypochlorite (12%).
ProtocolAfter surface sterilization and stratification Arabidopsis seeds were germinated and grown for 4 days on 1% Phytagar medium (pH 5.6) containing 5 mM KNO3, 2.5 mM KH2PO4, 2 mM MgSO4, 2 mM Ca(NO3)2, 50 µM Fe-EDTA, 70 µM H3BO3, 14 µM MnCl2, 0.5 µM CuSO4, 1 µM ZnSO4, 0.2 µM NaMoO4, 10 µM NaCl, and 0.01 µM CoCl2. In addition, 2.5 mM Mes-KOH (pH 5.6) and 0.5% sucrose were included. This medium is referred to as high or +Pi medium. For low or -Pi medium, KH2PO4 was omitted from the above nutrient solution. To remove remnants of phosphorus from Phytagar we included washing steps using dialysis before preparing the medium. Plants were grown on long day conditions (16h light/ 8h dark) at 20°C in a growth room.
Substrate Sterilising Proceduresterilisation by autoclaving
Plant Spacingca 5 mg seeds in 3 rows on square dishes
Temperature20 °C average, 20 °C day, 20 °C night
Humidity60 % average, 60 % day, 60 % night
MediumOwn medium: 1% Phytagar medium (pH 5.6) containing 5 mM KNO3, 2.5 mM KH2PO4, 2 mM MgSO4, 2 mM Ca(NO3)2, 50 µM Fe-EDTA, 70 µM H3BO3, 14 µM MnCl2, 0.5 µM CuSO4, 1 µM ZnSO4, 0.2 µM NaMoO4, 10 µM NaCl, and 0.01 µM CoCl2. In addition, 2.5 mM Mes-KOH (pH 5.6) and 0.5% sucrose were included
Lighting
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)
Tissue: whole root
in vivo Treatment: Plants were germinated and grown for 4 days on medium with high phosphate (2,5mM / (+)) and subsequently transferred for 20h to either medium with no phosphate (0mM / (-)) or to medium with high phosphate (control plants).
Additional Organism Information:
Sample DescriptionSamples were derived from roots of 5 days old seedlings.
Other Information:
ecotype_habitat

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:0.726358
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-ratio1.235349
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.266282
Spike_AFFX-r2-Bs-dap_5_signal11.125635
NoiseAvg:3.45,Std:0.12,Min:3.2,Max:3.9
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionA
Spike_AFFX-r2-Bs-thr_5_signal0.769573
#P14020
Spike_AFFX-r2-Bs-phe_M_signal8.597127
Corner-Avg:10342,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal3.657691
Spike_AFFX-r2-Ec-bioB_3_signal4.003624
Spike_AFFX-r2-Bs-lys_M_signal7.324451
Spike_AFFX-r2-P1-cre_3_signal4713.658203
Spike_AFFX-r2-Bs-lys_3-5-ratio4.412141
Spike_AFFX-r2-Bs-dap_M_signal28.381708
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio22.720186
Spike_AFFX-r2-Ec-bioB_avg-signal7.565535
Spike_AFFX-r2-Bs-thr_avg-signal16.141699
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal647.873657
Spike_AFFX-r2-Bs-phe_5_signal9.181923
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1026.926636
RawQ2.968837
Spike_AFFX-r2-Bs-lys_5_signal1.878127
Signal(A)7.085706
%A36.523453
Signal(All)144.727463
Corner+Avg:179,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal193.499786
Spike_AFFX-r2-Bs-lys_3_detectionA
Spike_AFFX-r2-Bs-phe_3_signal8.052212
Spike_AFFX-r2-Ec-bioD_avg-signal837.400146
Spike_AFFX-r2-Bs-dap_5_detectionM
Spike_AFFX-r2-Bs-phe_5_detectionA
%P61.464272
Spike_AFFX-r2-Bs-lys_avg-signal5.829714
Spike_AFFX-r2-P1-cre_avg-signal4264.654297
Spike_AFFX-r2-Ec-bioB_M_detectionA
Spike_AFFX-r2-Bs-lys_M_detectionA
#Probe Sets Exceeding Probe Pair Threshold22810
%M2.012275
Spike_AFFX-r2-Bs-thr_3_signal22.720186
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionA
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal8.610420
Spike_AFFX-r2-Bs-dap_3_signal70.148872
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.585072
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal181.234619
#M459
Spike_AFFX-r2-Bs-lys_5_detectionA
Spike_AFFX-r2-Bs-lys_3_signal8.286563
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.067676
Spike_AFFX-r2-Bs-thr_M_signal24.935341
Signal(P)230.454224
Spike_AFFX-r2-Bs-phe_3-5-ratio0.876964
Spike_AFFX-r2-Bs-thr_3_detectionA
Central-Avg:9410,Count:9
Spike_AFFX-r2-P1-cre_5_signal3815.650146
Spike_AFFX-r2-Bs-phe_M_detectionA
#A8331
Signal(M)24.475142
BackgroundAvg:77.59,Std:1.22,Min:74.7,Max:80.1
Spike_AFFX-r2-Ec-bioC_avg-signal187.367203
Spike_AFFX-r2-Bs-dap_avg-signal36.552071
Spike_AFFX-r2-Bs-dap_3-5-ratio6.305157
Spike_AFFX-r2-Ec-bioB_5_signal15.035289
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.726358
NF1.000000
HZ4
Tau0.015000

Slide: Mueller_648-6_lpr1lpr2(-)_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 ("Mueller_648-6_lpr1lpr2(-)_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: Mueller_648-6_lpr1lpr2(-)_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: lpr1lpr2
Stock Code:
Genetic Background: Col-0
Growth Conditions:
Stratification3-5 mg of seeds were stratified over night in agar solution (0,1% Agar in sterile dd. water) in an 2ml centrifugation tube at 4°C.
Sterilisation3-5 mg seeds were incubated for 35 min in an exicator containing a mixture of 6 ml HCl (37%) and 10 ml sodium hypochlorite (12%).
ProtocolAfter surface sterilization and stratification Arabidopsis seeds were germinated and grown for 4 days on 1% Phytagar medium (pH 5.6) containing 5 mM KNO3, 2.5 mM KH2PO4, 2 mM MgSO4, 2 mM Ca(NO3)2, 50 µM Fe-EDTA, 70 µM H3BO3, 14 µM MnCl2, 0.5 µM CuSO4, 1 µM ZnSO4, 0.2 µM NaMoO4, 10 µM NaCl, and 0.01 µM CoCl2. In addition, 2.5 mM Mes-KOH (pH 5.6) and 0.5% sucrose were included. This medium is referred to as high or +Pi medium. For low or -Pi medium, KH2PO4 was omitted from the above nutrient solution. To remove remnants of phosphorus from Phytagar we included washing steps using dialysis before preparing the medium. Plants were grown on long day conditions (16h light/ 8h dark) at 20°C in a growth room.
Substrate Sterilising Proceduresterilisation by autoclaving
Plant Spacingca 5 mg seeds in 3 rows on square dishes
Temperature20 °C average, 20 °C day, 20 °C night
Humidity60 % average, 60 % day, 60 % night
MediumOwn medium: 1% Phytagar medium (pH 5.6) containing 5 mM KNO3, 2.5 mM KH2PO4, 2 mM MgSO4, 2 mM Ca(NO3)2, 50 µM Fe-EDTA, 70 µM H3BO3, 14 µM MnCl2, 0.5 µM CuSO4, 1 µM ZnSO4, 0.2 µM NaMoO4, 10 µM NaCl, and 0.01 µM CoCl2. In addition, 2.5 mM Mes-KOH (pH 5.6) and 0.5% sucrose were included
Lighting
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)
Genetic Variation: T-DNA knock out mutation in AT1G23010,AT1G71040
Tissue: whole root
in vivo Treatment: Plants were germinated and grown for 4 days on medium with high phosphate (2,5mM / (+)) and subsequently transferred for 20h to either medium with no phosphate (0mM / (-)) or to medium with high phosphate (control plants).
Additional Organism Information:
Sample DescriptionSamples were derived from roots of 5 days old seedlings.
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:0.557613
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-ratio1.221554
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.954100
Spike_AFFX-r2-Bs-dap_5_signal17.102335
NoiseAvg:3.11,Std:0.07,Min:2.9,Max:3.4
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionA
Spike_AFFX-r2-Ec-bioB_3_detectionA
Spike_AFFX-r2-Bs-thr_5_signal6.826969
#P14935
Spike_AFFX-r2-Bs-phe_M_signal5.873622
Corner-Avg:10923,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal4.717744
Spike_AFFX-r2-Ec-bioB_3_signal6.545023
Spike_AFFX-r2-Bs-lys_M_signal9.069993
Spike_AFFX-r2-P1-cre_3_signal4060.847656
Spike_AFFX-r2-Bs-lys_3-5-ratio1.290064
Spike_AFFX-r2-Bs-dap_M_signal42.138252
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.322465
Spike_AFFX-r2-Ec-bioB_avg-signal6.040886
Spike_AFFX-r2-Bs-thr_avg-signal15.965878
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal577.587219
Spike_AFFX-r2-Bs-phe_5_signal8.841676
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal915.069275
RawQ2.842474
Spike_AFFX-r2-Bs-lys_5_signal7.928169
Signal(A)4.347677
%A32.924156
Signal(All)142.263535
Corner+Avg:218,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal154.198959
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal12.327195
Spike_AFFX-r2-Ec-bioD_avg-signal746.328247
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionA
%P65.475670
Spike_AFFX-r2-Bs-lys_avg-signal9.075335
Spike_AFFX-r2-P1-cre_avg-signal3692.588867
Spike_AFFX-r2-Ec-bioB_M_detectionA
Spike_AFFX-r2-Bs-lys_M_detectionA
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.600175
Spike_AFFX-r2-Bs-thr_3_signal22.682365
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionA
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal9.014164
Spike_AFFX-r2-Bs-dap_3_signal76.891922
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.584296
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal158.725342
#M365
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal10.227841
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.971483
Spike_AFFX-r2-Bs-thr_M_signal18.388300
Signal(P)214.706009
Spike_AFFX-r2-Bs-phe_3-5-ratio1.394215
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:9346,Count:9
Spike_AFFX-r2-P1-cre_5_signal3324.329834
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7510
Signal(M)15.742478
BackgroundAvg:71.41,Std:1.09,Min:68.6,Max:73.8
Spike_AFFX-r2-Ec-bioC_avg-signal156.462158
Spike_AFFX-r2-Bs-dap_avg-signal45.377502
Spike_AFFX-r2-Bs-dap_3-5-ratio4.495990
Spike_AFFX-r2-Ec-bioB_5_signal6.859892
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.557613
NF1.000000
HZ4
Tau0.015000

Slide: Mueller_648-5_pdr2(-)_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 ("Mueller_648-5_pdr2(-)_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: Mueller_648-5_pdr2(-)_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: pdr2
Stock Code:
Genetic Background: Col-0
Growth Conditions:
Stratification3-5 mg of seeds were stratified over night in agar solution (0,1% Agar in sterile dd. water) in an 2ml centrifugation tube at 4°C.
Sterilisation3-5 mg seeds were incubated for 35 min in an exicator containing a mixture of 6 ml HCl (37%) and 10 ml sodium hypochlorite (12%).
ProtocolAfter surface sterilization and stratification Arabidopsis seeds were germinated and grown for 4 days on 1% Phytagar medium (pH 5.6) containing 5 mM KNO3, 2.5 mM KH2PO4, 2 mM MgSO4, 2 mM Ca(NO3)2, 50 µM Fe-EDTA, 70 µM H3BO3, 14 µM MnCl2, 0.5 µM CuSO4, 1 µM ZnSO4, 0.2 µM NaMoO4, 10 µM NaCl, and 0.01 µM CoCl2. In addition, 2.5 mM Mes-KOH (pH 5.6) and 0.5% sucrose were included. This medium is referred to as high or +Pi medium. For low or -Pi medium, KH2PO4 was omitted from the above nutrient solution. To remove remnants of phosphorus from Phytagar we included washing steps using dialysis before preparing the medium. Plants were grown on long day conditions (16h light/ 8h dark) at 20°C in a growth room.
Substrate Sterilising Proceduresterilisation by autoclaving
Plant Spacingca 5 mg seeds in 3 rows on square dishes
Temperature20 °C average, 20 °C day, 20 °C night
Humidity60 % average, 60 % day, 60 % night
MediumOwn medium: 1% Phytagar medium (pH 5.6) containing 5 mM KNO3, 2.5 mM KH2PO4, 2 mM MgSO4, 2 mM Ca(NO3)2, 50 µM Fe-EDTA, 70 µM H3BO3, 14 µM MnCl2, 0.5 µM CuSO4, 1 µM ZnSO4, 0.2 µM NaMoO4, 10 µM NaCl, and 0.01 µM CoCl2. In addition, 2.5 mM Mes-KOH (pH 5.6) and 0.5% sucrose were included
Lighting
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)
Genetic Variation: EMS induced mutation mutation in AT5G23630
Tissue: whole root
in vivo Treatment: Plants were germinated and grown for 4 days on medium with high phosphate (2,5mM / (+)) and subsequently transferred for 20h to either medium with no phosphate (0mM / (-)) or to medium with high phosphate (control plants).
Additional Organism Information:
Sample DescriptionSamples were derived from roots of 5 days old seedlings.
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:0.735634
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-ratio1.183445
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.939870
Spike_AFFX-r2-Bs-dap_5_signal24.304157
NoiseAvg:2.68,Std:0.09,Min:2.4,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_signal7.540232
#P14896
Spike_AFFX-r2-Bs-phe_M_signal17.470213
Corner-Avg:10914,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal12.267410
Spike_AFFX-r2-Ec-bioB_3_signal11.732825
Spike_AFFX-r2-Bs-lys_M_signal16.716290
Spike_AFFX-r2-P1-cre_3_signal4920.895508
Spike_AFFX-r2-Bs-lys_3-5-ratio2.054363
Spike_AFFX-r2-Bs-dap_M_signal95.366669
Spike_AFFX-r2-Bs-thr_M_detectionA
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio7.244173
Spike_AFFX-r2-Ec-bioB_avg-signal12.161231
Spike_AFFX-r2-Bs-thr_avg-signal30.889624
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal884.593201
Spike_AFFX-r2-Bs-phe_5_signal16.265692
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1375.469360
RawQ2.504808
Spike_AFFX-r2-Bs-lys_5_signal9.337537
Signal(A)4.581127
%A32.998684
Signal(All)139.508133
Corner+Avg:185,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal204.939148
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal31.790407
Spike_AFFX-r2-Ec-bioD_avg-signal1130.031250
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P65.304688
Spike_AFFX-r2-Bs-lys_avg-signal15.078838
Spike_AFFX-r2-P1-cre_avg-signal4539.503906
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.696624
Spike_AFFX-r2-Bs-thr_3_signal54.622746
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-signal21.842104
Spike_AFFX-r2-Bs-dap_3_signal166.907120
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.554917
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal224.356461
#M387
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal19.182688
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.913453
Spike_AFFX-r2-Bs-thr_M_signal30.505892
Signal(P)210.885864
Spike_AFFX-r2-Bs-phe_3-5-ratio1.954445
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:8866,Count:9
Spike_AFFX-r2-P1-cre_5_signal4158.111816
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7527
Signal(M)16.388540
BackgroundAvg:63.14,Std:0.38,Min:62.1,Max:64.4
Spike_AFFX-r2-Ec-bioC_avg-signal214.647797
Spike_AFFX-r2-Bs-dap_avg-signal95.525993
Spike_AFFX-r2-Bs-dap_3-5-ratio6.867431
Spike_AFFX-r2-Ec-bioB_5_signal12.483455
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.735634
NF1.000000
HZ4
Tau0.015000

Slide: Mueller_648-4_Col(-)_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 ("Mueller_648-4_Col(-)_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: Mueller_648-4_Col(-)_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Columbia-0
Stock Code:
Growth Conditions:
Stratification3-5 mg of seeds were stratified over night in agar solution (0,1% Agar in sterile dd. water) in an 2ml centrifugation tube at 4°C.
Sterilisation3-5 mg seeds were incubated for 35 min in an exicator containing a mixture of 6 ml HCl (37%) and 10 ml sodium hypochlorite (12%).
ProtocolAfter surface sterilization and stratification Arabidopsis seeds were germinated and grown for 4 days on 1% Phytagar medium (pH 5.6) containing 5 mM KNO3, 2.5 mM KH2PO4, 2 mM MgSO4, 2 mM Ca(NO3)2, 50 µM Fe-EDTA, 70 µM H3BO3, 14 µM MnCl2, 0.5 µM CuSO4, 1 µM ZnSO4, 0.2 µM NaMoO4, 10 µM NaCl, and 0.01 µM CoCl2. In addition, 2.5 mM Mes-KOH (pH 5.6) and 0.5% sucrose were included. This medium is referred to as high or +Pi medium. For low or -Pi medium, KH2PO4 was omitted from the above nutrient solution. To remove remnants of phosphorus from Phytagar we included washing steps using dialysis before preparing the medium. Plants were grown on long day conditions (16h light/ 8h dark) at 20°C in a growth room.
Substrate Sterilising Proceduresterilisation by autoclaving
Plant Spacingca 5 mg seeds in 3 rows on square dishes
Temperature20 °C average, 20 °C day, 20 °C night
Humidity60 % average, 60 % day, 60 % night
MediumOwn medium: 1% Phytagar medium (pH 5.6) containing 5 mM KNO3, 2.5 mM KH2PO4, 2 mM MgSO4, 2 mM Ca(NO3)2, 50 µM Fe-EDTA, 70 µM H3BO3, 14 µM MnCl2, 0.5 µM CuSO4, 1 µM ZnSO4, 0.2 µM NaMoO4, 10 µM NaCl, and 0.01 µM CoCl2. In addition, 2.5 mM Mes-KOH (pH 5.6) and 0.5% sucrose were included
Lighting
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)
Tissue: whole root
in vivo Treatment: Plants were germinated and grown for 4 days on medium with high phosphate (2,5mM / (+)) and subsequently transferred for 20h to either medium with no phosphate (0mM / (-)) or to medium with high phosphate (control plants).
Additional Organism Information:
Sample DescriptionSamples were derived from roots of 5 days old seedlings.
Other Information:
ecotype_habitat

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:0.683236
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-ratio1.316726
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.269158
Spike_AFFX-r2-Bs-dap_5_signal13.443154
NoiseAvg:3.23,Std:0.06,Min:3.0,Max:3.4
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionA
Spike_AFFX-r2-Bs-thr_5_signal3.288729
#P14530
Spike_AFFX-r2-Bs-phe_M_signal9.532389
Corner-Avg:10491,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal14.262850
Spike_AFFX-r2-Ec-bioB_3_signal5.867195
Spike_AFFX-r2-Bs-lys_M_signal5.802975
Spike_AFFX-r2-P1-cre_3_signal5187.940430
Spike_AFFX-r2-Bs-lys_3-5-ratio3.462961
Spike_AFFX-r2-Bs-dap_M_signal49.011017
Spike_AFFX-r2-Bs-thr_M_detectionM
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio13.740445
Spike_AFFX-r2-Ec-bioB_avg-signal13.976120
Spike_AFFX-r2-Bs-thr_avg-signal24.071775
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal966.317993
Spike_AFFX-r2-Bs-phe_5_signal8.478407
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1371.135986
RawQ2.978590
Spike_AFFX-r2-Bs-lys_5_signal5.644563
Signal(A)5.260252
%A34.357738
Signal(All)141.447586
Corner+Avg:193,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal192.881744
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal26.960855
Spike_AFFX-r2-Ec-bioD_avg-signal1168.727051
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionA
%P63.700130
Spike_AFFX-r2-Bs-lys_avg-signal10.331479
Spike_AFFX-r2-P1-cre_avg-signal4563.984863
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionA
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.942131
Spike_AFFX-r2-Bs-thr_3_signal45.188606
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-signal14.990550
Spike_AFFX-r2-Bs-dap_3_signal108.563972
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.418928
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal230.380325
#M443
Spike_AFFX-r2-Bs-lys_5_detectionA
Spike_AFFX-r2-Bs-lys_3_signal19.546902
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.837232
Spike_AFFX-r2-Bs-thr_M_signal23.737993
Signal(P)218.620514
Spike_AFFX-r2-Bs-phe_3-5-ratio3.179944
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:8988,Count:9
Spike_AFFX-r2-P1-cre_5_signal3940.029541
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7837
Signal(M)19.500635
BackgroundAvg:70.88,Std:0.46,Min:69.8,Max:72.1
Spike_AFFX-r2-Ec-bioC_avg-signal211.631042
Spike_AFFX-r2-Bs-dap_avg-signal57.006046
Spike_AFFX-r2-Bs-dap_3-5-ratio8.075781
Spike_AFFX-r2-Ec-bioB_5_signal21.798313
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.683236
NF1.000000
HZ4
Tau0.015000

Slide: Mueller_648-3_lpr1lpr2(+)_Rep1_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 ("Mueller_648-3_lpr1lpr2(+)_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: Mueller_648-3_lpr1lpr2(+)_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: lpr1lpr2
Stock Code:
Genetic Background: Col-0
Growth Conditions:
Stratification3-5 mg of seeds were stratified over night in agar solution (0,1% Agar in sterile dd. water) in an 2ml centrifugation tube at 4°C.
Sterilisation3-5 mg seeds were incubated for 35 min in an exicator containing a mixture of 6 ml HCl (37%) and 10 ml sodium hypochlorite (12%).
ProtocolAfter surface sterilization and stratification Arabidopsis seeds were germinated and grown for 4 days on 1% Phytagar medium (pH 5.6) containing 5 mM KNO3, 2.5 mM KH2PO4, 2 mM MgSO4, 2 mM Ca(NO3)2, 50 µM Fe-EDTA, 70 µM H3BO3, 14 µM MnCl2, 0.5 µM CuSO4, 1 µM ZnSO4, 0.2 µM NaMoO4, 10 µM NaCl, and 0.01 µM CoCl2. In addition, 2.5 mM Mes-KOH (pH 5.6) and 0.5% sucrose were included. This medium is referred to as high or +Pi medium. For low or -Pi medium, KH2PO4 was omitted from the above nutrient solution. To remove remnants of phosphorus from Phytagar we included washing steps using dialysis before preparing the medium. Plants were grown on long day conditions (16h light/ 8h dark) at 20°C in a growth room.
Substrate Sterilising Proceduresterilisation by autoclaving
Plant Spacingca 5 mg seeds in 3 rows on square dishes
Temperature20 °C average, 20 °C day, 20 °C night
Humidity60 % average, 60 % day, 60 % night
MediumOwn medium: 1% Phytagar medium (pH 5.6) containing 5 mM KNO3, 2.5 mM KH2PO4, 2 mM MgSO4, 2 mM Ca(NO3)2, 50 µM Fe-EDTA, 70 µM H3BO3, 14 µM MnCl2, 0.5 µM CuSO4, 1 µM ZnSO4, 0.2 µM NaMoO4, 10 µM NaCl, and 0.01 µM CoCl2. In addition, 2.5 mM Mes-KOH (pH 5.6) and 0.5% sucrose were included
Lighting
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)
Genetic Variation: T-DNA knock out mutation in AT1G23010,AT1G71040
Tissue: whole root
in vivo Treatment: Plants were germinated and grown for 4 days on medium with high phosphate (2,5mM / (+)) and subsequently transferred for 20h to either medium with no phosphate (0mM / (-)) or to medium with high phosphate (control plants).
Additional Organism Information:
Sample DescriptionSamples were derived from roots of 5 days old seedlings.
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:0.512962
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-ratio1.256193
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.387643
Spike_AFFX-r2-Bs-dap_5_signal15.185452
NoiseAvg:3.17,Std:0.09,Min:2.9,Max:3.5
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionM
Spike_AFFX-r2-Ec-bioB_3_detectionA
Spike_AFFX-r2-Bs-thr_5_signal8.111259
#P14955
Spike_AFFX-r2-Bs-phe_M_signal5.171142
Corner-Avg:10858,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal6.884141
Spike_AFFX-r2-Ec-bioB_3_signal4.403281
Spike_AFFX-r2-Bs-lys_M_signal7.403142
Spike_AFFX-r2-P1-cre_3_signal4068.906006
Spike_AFFX-r2-Bs-lys_3-5-ratio2.965385
Spike_AFFX-r2-Bs-dap_M_signal39.606411
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.581600
Spike_AFFX-r2-Ec-bioB_avg-signal7.548841
Spike_AFFX-r2-Bs-thr_avg-signal17.602106
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal696.691040
Spike_AFFX-r2-Bs-phe_5_signal12.234447
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal934.738403
RawQ2.714676
Spike_AFFX-r2-Bs-lys_5_signal4.914368
Signal(A)4.607524
%A32.643578
Signal(All)138.107727
Corner+Avg:195,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal181.097397
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal19.067097
Spike_AFFX-r2-Ec-bioD_avg-signal815.714722
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionA
%P65.563347
Spike_AFFX-r2-Bs-lys_avg-signal8.963501
Spike_AFFX-r2-P1-cre_avg-signal3653.992188
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionM
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.793073
Spike_AFFX-r2-Bs-thr_3_signal29.051285
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-signal12.157562
Spike_AFFX-r2-Bs-dap_3_signal86.922752
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.341683
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal174.490601
#M409
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal14.572994
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.037863
Spike_AFFX-r2-Bs-thr_M_signal15.643778
Signal(P)207.916672
Spike_AFFX-r2-Bs-phe_3-5-ratio1.558476
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:9165,Count:9
Spike_AFFX-r2-P1-cre_5_signal3239.078125
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7446
Signal(M)15.979384
BackgroundAvg:64.17,Std:0.30,Min:63.4,Max:65.1
Spike_AFFX-r2-Ec-bioC_avg-signal177.794006
Spike_AFFX-r2-Bs-dap_avg-signal47.238205
Spike_AFFX-r2-Bs-dap_3-5-ratio5.724081
Spike_AFFX-r2-Ec-bioB_5_signal11.359102
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.512962
NF1.000000
HZ4
Tau0.015000

Slide: Mueller_648-2_pdr2(+)_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 ("Mueller_648-2_pdr2(+)_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: Mueller_648-2_pdr2(+)_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: pdr2
Stock Code:
Genetic Background: Col-0
Growth Conditions:
Stratification3-5 mg of seeds were stratified over night in agar solution (0,1% Agar in sterile dd. water) in an 2ml centrifugation tube at 4°C.
Sterilisation3-5 mg seeds were incubated for 35 min in an exicator containing a mixture of 6 ml HCl (37%) and 10 ml sodium hypochlorite (12%).
ProtocolAfter surface sterilization and stratification Arabidopsis seeds were germinated and grown for 4 days on 1% Phytagar medium (pH 5.6) containing 5 mM KNO3, 2.5 mM KH2PO4, 2 mM MgSO4, 2 mM Ca(NO3)2, 50 µM Fe-EDTA, 70 µM H3BO3, 14 µM MnCl2, 0.5 µM CuSO4, 1 µM ZnSO4, 0.2 µM NaMoO4, 10 µM NaCl, and 0.01 µM CoCl2. In addition, 2.5 mM Mes-KOH (pH 5.6) and 0.5% sucrose were included. This medium is referred to as high or +Pi medium. For low or -Pi medium, KH2PO4 was omitted from the above nutrient solution. To remove remnants of phosphorus from Phytagar we included washing steps using dialysis before preparing the medium. Plants were grown on long day conditions (16h light/ 8h dark) at 20°C in a growth room.
Substrate Sterilising Proceduresterilisation by autoclaving
Plant Spacingca 5 mg seeds in 3 rows on square dishes
Temperature20 °C average, 20 °C day, 20 °C night
Humidity60 % average, 60 % day, 60 % night
MediumOwn medium: 1% Phytagar medium (pH 5.6) containing 5 mM KNO3, 2.5 mM KH2PO4, 2 mM MgSO4, 2 mM Ca(NO3)2, 50 µM Fe-EDTA, 70 µM H3BO3, 14 µM MnCl2, 0.5 µM CuSO4, 1 µM ZnSO4, 0.2 µM NaMoO4, 10 µM NaCl, and 0.01 µM CoCl2. In addition, 2.5 mM Mes-KOH (pH 5.6) and 0.5% sucrose were included
Lighting
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)
Genetic Variation: EMS induced mutation mutation in AT5G23630
Tissue: whole root
in vivo Treatment: Plants were germinated and grown for 4 days on medium with high phosphate (2,5mM / (+)) and subsequently transferred for 20h to either medium with no phosphate (0mM / (-)) or to medium with high phosphate (control plants).
Additional Organism Information:
Sample DescriptionSamples were derived from roots of 5 days old seedlings.
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:0.460176
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-ratio1.249732
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.205508
Spike_AFFX-r2-Bs-dap_5_signal21.087723
NoiseAvg:3.16,Std:0.09,Min:3.0,Max:3.4
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionM
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal4.798570
#P15269
Spike_AFFX-r2-Bs-phe_M_signal9.310271
Corner-Avg:10270,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal8.965755
Spike_AFFX-r2-Ec-bioB_3_signal15.315457
Spike_AFFX-r2-Bs-lys_M_signal8.421760
Spike_AFFX-r2-P1-cre_3_signal4156.952148
Spike_AFFX-r2-Bs-lys_3-5-ratio1.736380
Spike_AFFX-r2-Bs-dap_M_signal60.410038
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio5.284024
Spike_AFFX-r2-Ec-bioB_avg-signal12.328593
Spike_AFFX-r2-Bs-thr_avg-signal18.026524
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal730.023254
Spike_AFFX-r2-Bs-phe_5_signal9.007162
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1007.458069
RawQ2.701396
Spike_AFFX-r2-Bs-lys_5_signal6.638732
Signal(A)3.808147
%A31.464270
Signal(All)138.635910
Corner+Avg:192,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal194.751846
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal16.968229
Spike_AFFX-r2-Ec-bioD_avg-signal868.740662
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P66.939941
Spike_AFFX-r2-Bs-lys_avg-signal8.862617
Spike_AFFX-r2-P1-cre_avg-signal3741.613281
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_signal25.355759
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-signal11.761887
Spike_AFFX-r2-Bs-dap_3_signal115.409187
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.380036
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal180.137054
#M364
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal11.527359
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.081131
Spike_AFFX-r2-Bs-thr_M_signal23.925243
Signal(P)204.951706
Spike_AFFX-r2-Bs-phe_3-5-ratio1.883860
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:9154,Count:9
Spike_AFFX-r2-P1-cre_5_signal3326.274658
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7177
Signal(M)15.236944
BackgroundAvg:62.68,Std:0.61,Min:61.1,Max:64.5
Spike_AFFX-r2-Ec-bioC_avg-signal187.444458
Spike_AFFX-r2-Bs-dap_avg-signal65.635651
Spike_AFFX-r2-Bs-dap_3-5-ratio5.472814
Spike_AFFX-r2-Ec-bioB_5_signal12.704566
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.460176
NF1.000000
HZ4
Tau0.015000

Slide: Mueller_648-1_Col(+)_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 ("Mueller_648-1_Col(+)_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: Mueller_648-1_Col(+)_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Columbia-0
Stock Code:
Growth Conditions:
Stratification3-5 mg of seeds were stratified over night in agar solution (0,1% Agar in sterile dd. water) in an 2ml centrifugation tube at 4°C.
Sterilisation3-5 mg seeds were incubated for 35 min in an exicator containing a mixture of 6 ml HCl (37%) and 10 ml sodium hypochlorite (12%).
ProtocolAfter surface sterilization and stratification Arabidopsis seeds were germinated and grown for 4 days on 1% Phytagar medium (pH 5.6) containing 5 mM KNO3, 2.5 mM KH2PO4, 2 mM MgSO4, 2 mM Ca(NO3)2, 50 µM Fe-EDTA, 70 µM H3BO3, 14 µM MnCl2, 0.5 µM CuSO4, 1 µM ZnSO4, 0.2 µM NaMoO4, 10 µM NaCl, and 0.01 µM CoCl2. In addition, 2.5 mM Mes-KOH (pH 5.6) and 0.5% sucrose were included. This medium is referred to as high or +Pi medium. For low or -Pi medium, KH2PO4 was omitted from the above nutrient solution. To remove remnants of phosphorus from Phytagar we included washing steps using dialysis before preparing the medium. Plants were grown on long day conditions (16h light/ 8h dark) at 20°C in a growth room.
Substrate Sterilising Proceduresterilisation by autoclaving
Plant Spacingca 5 mg seeds in 3 rows on square dishes
Temperature20 °C average, 20 °C day, 20 °C night
Humidity60 % average, 60 % day, 60 % night
MediumOwn medium: 1% Phytagar medium (pH 5.6) containing 5 mM KNO3, 2.5 mM KH2PO4, 2 mM MgSO4, 2 mM Ca(NO3)2, 50 µM Fe-EDTA, 70 µM H3BO3, 14 µM MnCl2, 0.5 µM CuSO4, 1 µM ZnSO4, 0.2 µM NaMoO4, 10 µM NaCl, and 0.01 µM CoCl2. In addition, 2.5 mM Mes-KOH (pH 5.6) and 0.5% sucrose were included
Lighting
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)
Tissue: whole root
in vivo Treatment: Plants were germinated and grown for 4 days on medium with high phosphate (2,5mM) and subsequently transferred for 20h to medium with no phosphate (0mM). Control plants were transferred from high phosphate to high phosphate in order to ensure that changes in expression are not induced by mechanical stress.
Additional Organism Information:
Sample DescriptionSamples were derived from roots of 5 days old seedlings.
Other Information:
ecotype_habitat

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:0.548197
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-ratio1.327236
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.536617
Spike_AFFX-r2-Bs-dap_5_signal20.683586
NoiseAvg:3.43,Std:0.06,Min:3.3,Max:3.7
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionM
Spike_AFFX-r2-Ec-bioB_3_detectionA
Spike_AFFX-r2-Bs-thr_5_signal4.607800
#P14723
Spike_AFFX-r2-Bs-phe_M_signal12.150310
Corner-Avg:11753,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal6.444217
Spike_AFFX-r2-Ec-bioB_3_signal8.661041
Spike_AFFX-r2-Bs-lys_M_signal8.474158
Spike_AFFX-r2-P1-cre_3_signal5064.752441
Spike_AFFX-r2-Bs-lys_3-5-ratio3.155712
Spike_AFFX-r2-Bs-dap_M_signal60.771065
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio8.645965
Spike_AFFX-r2-Ec-bioB_avg-signal10.415116
Spike_AFFX-r2-Bs-thr_avg-signal22.768969
Spike_AFFX-r2-Bs-thr_5_detectionA
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal912.827637
Spike_AFFX-r2-Bs-phe_5_signal6.844206
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1291.508423
RawQ2.903992
Spike_AFFX-r2-Bs-lys_5_signal8.292853
Signal(A)4.788615
%A33.586147
Signal(All)141.369278
Corner+Avg:216,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal174.590805
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal20.894825
Spike_AFFX-r2-Ec-bioD_avg-signal1102.167969
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionA
%P64.546249
Spike_AFFX-r2-Bs-lys_avg-signal14.312290
Spike_AFFX-r2-P1-cre_avg-signal4440.382813
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionA
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.867602
Spike_AFFX-r2-Bs-thr_3_signal39.838879
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionA
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal13.296448
Spike_AFFX-r2-Bs-dap_3_signal125.805862
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.414844
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal218.813126
#M426
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal26.169859
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.797899
Spike_AFFX-r2-Bs-thr_M_signal23.860226
Signal(P)215.997223
Spike_AFFX-r2-Bs-phe_3-5-ratio3.052922
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:9579,Count:9
Spike_AFFX-r2-P1-cre_5_signal3816.013672
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7661
Signal(M)18.358126
BackgroundAvg:67.76,Std:0.45,Min:66.7,Max:69.0
Spike_AFFX-r2-Ec-bioC_avg-signal196.701965
Spike_AFFX-r2-Bs-dap_avg-signal69.086845
Spike_AFFX-r2-Bs-dap_3-5-ratio6.082401
Spike_AFFX-r2-Ec-bioB_5_signal16.140089
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.548197
NF1.000000
HZ4
Tau0.015000


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