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Experiment: Global expression changes in CK2mut plants (a dominant negative mutant of protein kinase CK2) after gamma radiation

Experiment Description

NASCArrays Experiment Reference Number: NASCARRAYS-698

CK2 is an essential protein kinase involved in a wide variety of cellular processes. The aim of these experiments was to decipher the role of CK2 kinase in Arabidopsis DNA damage response. It is well reported that a rapid transcriptional burst occurs when plants are exposed to gamma radiation. For this reason, we studied the global changes of gene expression in 7-day-old Arabidopsis seedlings expressing a dominant-negative mutant of CK2 (CK2mut plants). Those plants contain a CK2-alfa inactive subunit cloned downstream of a GVG inducible promoter, which is inducible by Dexametahone (Dex)(Moreno-Romero et al. 2008). The gene expression changes were analyzed in gamma-irradiated, Dex-treated mutant seedlings, and were compared to those in irradiated, Dex-untreated seedlings.METHOD: Arabidopsis seeds were surface sterilized, cold-treated at 4ºC for 48 hours, and then sown on MS plates and grown for five days. Afterwards, plantlets were transferred to MS plates supplemented with 1uM Dex and after two days were treated with 100 Gy of gamma rays. Total RNA was isolated from frozen plantlets with Trizol (Invitrogen) and later purified using Qiagen RNA easy Plant Mini Kit columns (Qiagen, Hilden, Germany). RNA quality was checked using Experion (Bio-Rad laboratories). Three independent RNA preparations were made from CK2mut pooled samples in two different conditions: Dex-treated and irradiated, or mock-treated and irradiated. The data relative to controls necessary for this experiment (plants transformed with the empty vector, and non-irradiated plants) are deposited in NASC (ref. NASCARRAYS-642).Moreno-Romero et al. 2008. A role for protein kinase CK2 in plant development: evidence obtained using a dominant-negative mutant. The Plant Journal 55, 118-130 [2008].

About the Experimenter

Name:Dr. Jordi Moreno-Romero
Head of Lab Name:Dr. M Carmen Martínez
Lab:
Address:Departament de Bioquimica i Biologia Molecular
Facultat de Biociencies
Universitat Autonoma de Barcelona
Bellaterra, Spain
Postcode: 08193
Country: Spain
 

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

About this Experiment

Experiment Type: compound_based_treatment
Number of Slides:6
 
Experimental Parameters:
parameterirradiate
parametertimepoint
parametergenetic_modification
Quality Control Measures Taken:
References:
Reference The Plant Journal 55, 118-130 [2008].
Reference NASCArray-642, Moreno-Romero et al. 2008.
 
Other Information:

Slides in this Experiment

Hybridisation Set: Moreno-Romero: Global expression changes in CK2mut plants (a dominant negative mutant of protein kinase CK2) after gamma radiation

Slide: Moreno-Romero_698-1_CK2mut_Dex_Gamma_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 ("Moreno-Romero_698-1_CK2mut_Dex_Gamma_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: Moreno-Romero_698-1_CK2mut_Dex_Gamma_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: CK2mut
Stock Code:
Genetic Background: Col-0
Age: 7-days-old
Growth Conditions:
Stratification2 days at 4 C
Sterilisationseed surface sterilization with bleach
ProtocolSurface sterilized seeds were sown on MS plates and grown for five days. Afterwards, plantlets were transferred to MS plates supplemented with 1uM Dex and after two days were treated with 100 Gy of gamma rays.
Percentage Agrose10
Substrate Sterilising ProcedureAutoclaved MS media
Temperature22 °C average, 22 °C day, 22 °C night
Humidity- % average, - % day, - % night
MediumMurashige & Skoog basal salt mixture. Applied: N/A
Lighting
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Genetic Variation: T-DNA induced mutation mutation in at5g67380,at3g50000 ,at2g23080
Tissue: whole plant
in vivo Treatment: Surface sterilized seeds were sown on MS plates and grown for five days. Afterwards, plantlets were transferred to MS plates supplemented with 1uM Dex and after two days were treated with 100 Gy of gamma rays. Ionizing radiation (IR) was performed using a Cesium-137 source generated by a IBL 437C Irradiator (CIS Bio International) at a dose rate of 5.7-5.5 Gy/min.
Additional Organism Information:
Sample Description
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:0.667279
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-ratio1.029978
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.680728
Spike_AFFX-r2-Bs-dap_5_signal112.250603
NoiseAvg:4.84,Std:0.24,Min:4.3,Max:5.8
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal64.134262
#P13610
Spike_AFFX-r2-Bs-phe_M_signal38.892998
Corner-Avg:5443,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal115.306160
Spike_AFFX-r2-Ec-bioB_3_signal85.745476
Spike_AFFX-r2-Bs-lys_M_signal11.673183
Spike_AFFX-r2-P1-cre_3_signal3560.576416
Spike_AFFX-r2-Bs-lys_3-5-ratio1.361076
Spike_AFFX-r2-Bs-dap_M_signal160.543289
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio1.584246
Spike_AFFX-r2-Ec-bioB_avg-signal109.004356
Spike_AFFX-r2-Bs-thr_avg-signal97.061211
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal837.318970
Spike_AFFX-r2-Bs-phe_5_signal30.116812
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1058.798706
RawQ4.079949
Spike_AFFX-r2-Bs-lys_5_signal16.643141
Signal(A)6.059760
%A38.461201
Signal(All)142.510742
Corner+Avg:83,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal314.690796
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal29.355831
Spike_AFFX-r2-Ec-bioD_avg-signal948.058838
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P59.666813
Spike_AFFX-r2-Bs-lys_avg-signal16.989637
Spike_AFFX-r2-P1-cre_avg-signal3508.760742
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionM
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.871986
Spike_AFFX-r2-Bs-thr_3_signal101.604446
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-signal32.788548
Spike_AFFX-r2-Bs-dap_3_signal181.357758
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.264511
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal297.157043
#M427
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal22.652584
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.059005
Spike_AFFX-r2-Bs-thr_M_signal125.444916
Signal(P)234.316437
Spike_AFFX-r2-Bs-phe_3-5-ratio0.974732
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:5399,Count:9
Spike_AFFX-r2-P1-cre_5_signal3456.945313
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8773
Signal(M)19.815170
BackgroundAvg:108.43,Std:2.52,Min:101.4,Max:116.9
Spike_AFFX-r2-Ec-bioC_avg-signal305.923920
Spike_AFFX-r2-Bs-dap_avg-signal151.383896
Spike_AFFX-r2-Bs-dap_3-5-ratio1.615651
Spike_AFFX-r2-Ec-bioB_5_signal125.961426
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.667279
NF1.000000
HZ4
Tau0.015000

Slide: Moreno-Romero_698-2_CK2mut_Dex_Gamma_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 ("Moreno-Romero_698-2_CK2mut_Dex_Gamma_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: Moreno-Romero_698-2_CK2mut_Dex_Gamma_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: CK2mut
Stock Code:
Genetic Background: Col-0
Age: 7-days-old
Growth Conditions:
Stratification2 days at 4 C
Sterilisationseed surface sterilization with bleach
ProtocolSurface sterilized seeds were sown on MS plates and grown for five days. Afterwards, plantlets were transferred to MS plates supplemented with 1uM Dex and after two days were treated with 100 Gy of gamma rays.
Percentage Agrose10
Substrate Sterilising ProcedureAutoclaved MS media
Temperature22 °C average, 22 °C day, 22 °C night
Humidity- % average, - % day, - % night
MediumMurashige & Skoog basal salt mixture. Applied: N/A
Lighting
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Genetic Variation: T-DNA induced mutation mutation in at5g67380,at3g50000 ,at2g23080
Tissue: whole plant
in vivo Treatment: Surface sterilized seeds were sown on MS plates and grown for five days. Afterwards, plantlets were transferred to MS plates supplemented with 1uM Dex and after two days were treated with 100 Gy of gamma rays. Ionizing radiation (IR) was performed using a Cesium-137 source generated by a IBL 437C Irradiator (CIS Bio International) at a dose rate of 5.7-5.5 Gy/min.
Additional Organism Information:
Sample Description
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:0.504751
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-ratio1.297513
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.687952
Spike_AFFX-r2-Bs-dap_5_signal161.973785
NoiseAvg:5.56,Std:0.47,Min:4.7,Max:7.1
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal62.104431
#P13319
Spike_AFFX-r2-Bs-phe_M_signal35.627888
Corner-Avg:7254,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal111.800262
Spike_AFFX-r2-Ec-bioB_3_signal86.788956
Spike_AFFX-r2-Bs-lys_M_signal21.820923
Spike_AFFX-r2-P1-cre_3_signal4357.885254
Spike_AFFX-r2-Bs-lys_3-5-ratio1.595804
Spike_AFFX-r2-Bs-dap_M_signal228.812500
Spike_AFFX-r2-Bs-thr_M_detectionM
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.161149
Spike_AFFX-r2-Ec-bioB_avg-signal108.248253
Spike_AFFX-r2-Bs-thr_avg-signal102.068542
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal831.973938
Spike_AFFX-r2-Bs-phe_5_signal39.269688
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1192.137085
RawQ4.160131
Spike_AFFX-r2-Bs-lys_5_signal19.189972
Signal(A)6.804472
%A39.465145
Signal(All)142.744354
Corner+Avg:137,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal339.989929
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal25.162840
Spike_AFFX-r2-Ec-bioD_avg-signal1012.055542
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P58.391056
Spike_AFFX-r2-Bs-lys_avg-signal23.878111
Spike_AFFX-r2-P1-cre_avg-signal3858.265381
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M2.143797
Spike_AFFX-r2-Bs-thr_3_signal134.216949
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal33.353470
Spike_AFFX-r2-Bs-dap_3_signal248.416489
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.432902
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal309.245026
#M489
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal30.623436
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.099419
Spike_AFFX-r2-Bs-thr_M_signal109.884247
Signal(P)239.061630
Spike_AFFX-r2-Bs-phe_3-5-ratio0.640770
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:6886,Count:9
Spike_AFFX-r2-P1-cre_5_signal3358.645508
Spike_AFFX-r2-Bs-phe_M_detectionP
#A9002
Signal(M)21.846636
BackgroundAvg:115.72,Std:3.77,Min:110.7,Max:127.0
Spike_AFFX-r2-Ec-bioC_avg-signal324.617493
Spike_AFFX-r2-Bs-dap_avg-signal213.067581
Spike_AFFX-r2-Bs-dap_3-5-ratio1.533683
Spike_AFFX-r2-Ec-bioB_5_signal126.155518
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.504751
NF1.000000
HZ4
Tau0.015000

Slide: Moreno-Romero_698-3_CK2mut_Dex_Gamma_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 ("Moreno-Romero_698-3_CK2mut_Dex_Gamma_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: Moreno-Romero_698-3_CK2mut_Dex_Gamma_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: CK2mut
Stock Code:
Genetic Background: Col-0
Age: 7-days-old
Growth Conditions:
Stratification2 days at 4 C
Sterilisationseed surface sterilization with bleach
ProtocolSurface sterilized seeds were sown on MS plates and grown for five days. Afterwards, plantlets were transferred to MS plates supplemented with 1uM Dex and after two days were treated with 100 Gy of gamma rays.
Percentage Agrose10
Substrate Sterilising ProcedureAutoclaved MS media
Temperature22 °C average, 22 °C day, 22 °C night
Humidity- % average, - % day, - % night
MediumMurashige & Skoog basal salt mixture. Applied: N/A
Lighting
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Genetic Variation: T-DNA induced mutation mutation in at5g67380,at3g50000 ,at2g23080
Tissue: whole plant
in vivo Treatment: Surface sterilized seeds were sown on MS plates and grown for five days. Afterwards, plantlets were transferred to MS plates supplemented with 1uM Dex and after two days were treated with 100 Gy of gamma rays. Ionizing radiation (IR) was performed using a Cesium-137 source generated by a IBL 437C Irradiator (CIS Bio International) at a dose rate of 5.7-5.5 Gy/min.
Additional Organism Information:
Sample Description
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:0.901078
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0

Normalisation Information

Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
Normalisation Protocol Parameters:
Spike_AFFX-r2-P1-cre_3-5-ratio0.946253
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.901415
Spike_AFFX-r2-Bs-dap_5_signal90.003555
NoiseAvg:3.69,Std:0.08,Min:3.5,Max:3.9
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal58.889797
#P13015
Spike_AFFX-r2-Bs-phe_M_signal20.928900
Corner-Avg:15012,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal127.276123
Spike_AFFX-r2-Ec-bioB_3_signal133.382614
Spike_AFFX-r2-Bs-lys_M_signal16.955009
Spike_AFFX-r2-P1-cre_3_signal5022.171875
Spike_AFFX-r2-Bs-lys_3-5-ratio3.076698
Spike_AFFX-r2-Bs-dap_M_signal130.495468
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio1.121053
Spike_AFFX-r2-Ec-bioB_avg-signal136.209671
Spike_AFFX-r2-Bs-thr_avg-signal75.360924
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1157.725830
Spike_AFFX-r2-Bs-phe_5_signal40.769966
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1689.725220
RawQ3.531849
Spike_AFFX-r2-Bs-lys_5_signal10.068311
Signal(A)6.834501
%A40.802280
Signal(All)148.530273
Corner+Avg:145,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal491.354004
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal36.999813
Spike_AFFX-r2-Ec-bioD_avg-signal1423.725586
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P57.058308
Spike_AFFX-r2-Bs-lys_avg-signal19.333490
Spike_AFFX-r2-P1-cre_avg-signal5164.801270
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M2.139413
Spike_AFFX-r2-Bs-thr_3_signal66.018562
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-signal32.899559
Spike_AFFX-r2-Bs-dap_3_signal166.354340
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.459521
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal484.708466
#M488
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal30.977154
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.013710
Spike_AFFX-r2-Bs-thr_M_signal101.174393
Signal(P)254.612427
Spike_AFFX-r2-Bs-phe_3-5-ratio0.907526
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:12804,Count:9
Spike_AFFX-r2-P1-cre_5_signal5307.430664
Spike_AFFX-r2-Bs-phe_M_detectionP
#A9307
Signal(M)21.692913
BackgroundAvg:99.61,Std:1.23,Min:95.8,Max:103.2
Spike_AFFX-r2-Ec-bioC_avg-signal488.031250
Spike_AFFX-r2-Bs-dap_avg-signal128.951111
Spike_AFFX-r2-Bs-dap_3-5-ratio1.848309
Spike_AFFX-r2-Ec-bioB_5_signal147.970291
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.901078
NF1.000000
HZ4
Tau0.015000

Slide: Moreno-Romero_698-4_CK2mut_etOH_Gamma_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 ("Moreno-Romero_698-4_CK2mut_etOH_Gamma_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: Moreno-Romero_698-4_CK2mut_etOH_Gamma_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: CK2mut
Stock Code:
Genetic Background: Col-0
Age: 7-days-old
Growth Conditions:
Stratification2 days at 4 C
Sterilisationseed surface sterilization with bleach
ProtocolSurface sterilized seeds were sown on MS plates and grown for five days. Afterwards, plantlets were transferred to MS plates supplemented with 1uM Dex and after two days were treated with 100 Gy of gamma rays.
Percentage Agrose10
Substrate Sterilising ProcedureAutoclaved MS media
Temperature22 °C average, 22 °C day, 22 °C night
Humidity- % average, - % day, - % night
MediumMurashige & Skoog basal salt mixture. Applied: N/A
Lighting
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Genetic Variation: T-DNA induced mutation mutation in at5g67380,at3g50000 ,at2g23080
Tissue: whole plant
in vivo Treatment: Surface sterilized seeds were sown on MS plates and grown for five days. Afterwards, plantlets were transferred to MS plates supplemented with 1uM Dex and after two days were treated with 100 Gy of gamma rays. Ionizing radiation (IR) was performed using a Cesium-137 source generated by a IBL 437C Irradiator (CIS Bio International) at a dose rate of 5.7-5.5 Gy/min.
Additional Organism Information:
Sample Description
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:0.735226
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-ratio1.217830
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.893144
Spike_AFFX-r2-Bs-dap_5_signal129.934525
NoiseAvg:3.88,Std:0.17,Min:3.5,Max:4.3
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal73.791344
#P13680
Spike_AFFX-r2-Bs-phe_M_signal33.479370
Corner-Avg:5556,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal166.780960
Spike_AFFX-r2-Ec-bioB_3_signal118.077507
Spike_AFFX-r2-Bs-lys_M_signal14.442225
Spike_AFFX-r2-P1-cre_3_signal5422.401367
Spike_AFFX-r2-Bs-lys_3-5-ratio1.518411
Spike_AFFX-r2-Bs-dap_M_signal228.240387
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.109201
Spike_AFFX-r2-Ec-bioB_avg-signal139.020935
Spike_AFFX-r2-Bs-thr_avg-signal123.619232
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1271.581421
Spike_AFFX-r2-Bs-phe_5_signal41.509090
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1619.081543
RawQ3.558239
Spike_AFFX-r2-Bs-lys_5_signal22.364939
Signal(A)6.329064
%A38.005260
Signal(All)155.003036
Corner+Avg:86,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal492.972595
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal41.398331
Spike_AFFX-r2-Ec-bioD_avg-signal1445.331543
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P59.973694
Spike_AFFX-r2-Bs-lys_avg-signal23.588778
Spike_AFFX-r2-P1-cre_avg-signal4937.457031
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M2.021043
Spike_AFFX-r2-Bs-thr_3_signal155.640793
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal38.795597
Spike_AFFX-r2-Bs-dap_3_signal204.141983
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.273282
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal501.191437
#M461
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal33.959171
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.983601
Spike_AFFX-r2-Bs-thr_M_signal141.425552
Signal(P)253.679718
Spike_AFFX-r2-Bs-phe_3-5-ratio0.997332
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:4522,Count:9
Spike_AFFX-r2-P1-cre_5_signal4452.512207
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8669
Signal(M)22.590092
BackgroundAvg:96.82,Std:2.16,Min:91.4,Max:102.9
Spike_AFFX-r2-Ec-bioC_avg-signal497.082031
Spike_AFFX-r2-Bs-dap_avg-signal187.438965
Spike_AFFX-r2-Bs-dap_3-5-ratio1.571114
Spike_AFFX-r2-Ec-bioB_5_signal132.204346
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.735226
NF1.000000
HZ4
Tau0.015000

Slide: Moreno-Romero_698-5_CK2mut_etOH_Gamma_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 ("Moreno-Romero_698-5_CK2mut_etOH_Gamma_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: Moreno-Romero_698-5_CK2mut_etOH_Gamma_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: CK2mut
Stock Code:
Genetic Background: Col-0
Age: 7-days-old
Growth Conditions:
Stratification2 days at 4 C
Sterilisationseed surface sterilization with bleach
ProtocolSurface sterilized seeds were sown on MS plates and grown for five days. Afterwards, plantlets were transferred to MS plates supplemented with 1uM Dex and after two days were treated with 100 Gy of gamma rays.
Percentage Agrose10
Substrate Sterilising ProcedureAutoclaved MS media
Temperature22 °C average, 22 °C day, 22 °C night
Humidity- % average, - % day, - % night
MediumMurashige & Skoog basal salt mixture. Applied: N/A
Lighting
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Genetic Variation: T-DNA induced mutation mutation in at5g67380,at3g50000 ,at2g23080
Tissue: whole plant
in vivo Treatment: Surface sterilized seeds were sown on MS plates and grown for five days. Afterwards, plantlets were transferred to MS plates supplemented with 1uM Dex and after two days were treated with 100 Gy of gamma rays. Ionizing radiation (IR) was performed using a Cesium-137 source generated by a IBL 437C Irradiator (CIS Bio International) at a dose rate of 5.7-5.5 Gy/min.
Additional Organism Information:
Sample Description
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:0.717682
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-ratio1.281853
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.796019
Spike_AFFX-r2-Bs-dap_5_signal186.405136
NoiseAvg:3.83,Std:0.16,Min:3.5,Max:4.4
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal83.768562
#P13618
Spike_AFFX-r2-Bs-phe_M_signal54.402607
Corner-Avg:6795,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal174.610550
Spike_AFFX-r2-Ec-bioB_3_signal136.907822
Spike_AFFX-r2-Bs-lys_M_signal18.618021
Spike_AFFX-r2-P1-cre_3_signal6536.395508
Spike_AFFX-r2-Bs-lys_3-5-ratio2.202650
Spike_AFFX-r2-Bs-dap_M_signal292.757202
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.167492
Spike_AFFX-r2-Ec-bioB_avg-signal161.169662
Spike_AFFX-r2-Bs-thr_avg-signal132.586288
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1609.429443
Spike_AFFX-r2-Bs-phe_5_signal75.526672
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1976.153076
RawQ3.322878
Spike_AFFX-r2-Bs-lys_5_signal27.254625
Signal(A)6.882150
%A37.965805
Signal(All)159.268646
Corner+Avg:118,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal578.685242
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal59.314697
Spike_AFFX-r2-Ec-bioD_avg-signal1792.791260
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P59.701885
Spike_AFFX-r2-Bs-lys_avg-signal35.301682
Spike_AFFX-r2-P1-cre_avg-signal5817.786621
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M2.332310
Spike_AFFX-r2-Bs-thr_3_signal181.567657
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-signal63.081326
Spike_AFFX-r2-Bs-dap_3_signal300.736572
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.227859
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal541.415527
#M532
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal60.032398
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.068838
Spike_AFFX-r2-Bs-thr_M_signal132.422623
Signal(P)261.516327
Spike_AFFX-r2-Bs-phe_3-5-ratio0.785348
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:5760,Count:9
Spike_AFFX-r2-P1-cre_5_signal5099.177734
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8660
Signal(M)22.535809
BackgroundAvg:98.04,Std:1.78,Min:93.6,Max:102.1
Spike_AFFX-r2-Ec-bioC_avg-signal560.050415
Spike_AFFX-r2-Bs-dap_avg-signal259.966309
Spike_AFFX-r2-Bs-dap_3-5-ratio1.613349
Spike_AFFX-r2-Ec-bioB_5_signal171.990601
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.717682
NF1.000000
HZ4
Tau0.015000

Slide: Moreno-Romero_698-6_CK2mut_etOH_Gamma_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 ("Moreno-Romero_698-6_CK2mut_etOH_Gamma_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: Moreno-Romero_698-6_CK2mut_etOH_Gamma_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: CK2mut
Stock Code:
Genetic Background: Col-0
Age: 7-days-old
Growth Conditions:
Stratification2 days at 4 C
Sterilisationseed surface sterilization with bleach
ProtocolSurface sterilized seeds were sown on MS plates and grown for five days. Afterwards, plantlets were transferred to MS plates supplemented with 1uM Dex and after two days were treated with 100 Gy of gamma rays.
Percentage Agrose10
Substrate Sterilising ProcedureAutoclaved MS media
Temperature22 °C average, 22 °C day, 22 °C night
Humidity- % average, - % day, - % night
MediumMurashige & Skoog basal salt mixture. Applied: N/A
Lighting
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)1.0
Genetic Variation: T-DNA induced mutation mutation in at5g67380,at3g50000 ,at2g23080
Tissue: whole plant
in vivo Treatment: Surface sterilized seeds were sown on MS plates and grown for five days. Afterwards, plantlets were transferred to MS plates supplemented with 1uM Dex and after two days were treated with 100 Gy of gamma rays. Ionizing radiation (IR) was performed using a Cesium-137 source generated by a IBL 437C Irradiator (CIS Bio International) at a dose rate of 5.7-5.5 Gy/min.
Additional Organism Information:
Sample Description
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:0.661694
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-ratio1.241200
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.183405
Spike_AFFX-r2-Bs-dap_5_signal71.899101
NoiseAvg:4.12,Std:0.28,Min:3.7,Max:5.8
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal44.538483
#P14134
Spike_AFFX-r2-Bs-phe_M_signal25.316570
Corner-Avg:16381,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal185.977066
Spike_AFFX-r2-Ec-bioB_3_signal172.521240
Spike_AFFX-r2-Bs-lys_M_signal11.575065
Spike_AFFX-r2-P1-cre_3_signal6526.482422
Spike_AFFX-r2-Bs-lys_3-5-ratio0.675460
Spike_AFFX-r2-Bs-dap_M_signal110.063377
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio1.367047
Spike_AFFX-r2-Ec-bioB_avg-signal168.094009
Spike_AFFX-r2-Bs-thr_avg-signal60.487976
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1603.978882
Spike_AFFX-r2-Bs-phe_5_signal20.976826
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1959.417480
RawQ3.539233
Spike_AFFX-r2-Bs-lys_5_signal19.728329
Signal(A)5.247364
%A36.093819
Signal(All)153.310547
Corner+Avg:171,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal463.740295
Spike_AFFX-r2-Bs-lys_3_detectionA
Spike_AFFX-r2-Bs-phe_3_signal28.650101
Spike_AFFX-r2-Ec-bioD_avg-signal1781.698242
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P61.964050
Spike_AFFX-r2-Bs-lys_avg-signal14.876363
Spike_AFFX-r2-P1-cre_avg-signal5892.341797
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.942131
Spike_AFFX-r2-Bs-thr_3_signal60.886196
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal24.981165
Spike_AFFX-r2-Bs-dap_3_signal115.318947
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.221598
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal547.191833
#M443
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal13.325697
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.847491
Spike_AFFX-r2-Bs-thr_M_signal76.039246
Signal(P)243.748016
Spike_AFFX-r2-Bs-phe_3-5-ratio1.365798
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:14495,Count:9
Spike_AFFX-r2-P1-cre_5_signal5258.201660
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8233
Signal(M)19.588602
BackgroundAvg:99.83,Std:0.80,Min:97.0,Max:101.2
Spike_AFFX-r2-Ec-bioC_avg-signal505.466064
Spike_AFFX-r2-Bs-dap_avg-signal99.093811
Spike_AFFX-r2-Bs-dap_3-5-ratio1.603900
Spike_AFFX-r2-Ec-bioB_5_signal145.783722
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.661694
NF1.000000
HZ4
Tau0.015000


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