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Experiment: The role of ribosomes in plant development

Experiment Description

NASCArrays Experiment Reference Number: NASCARRAYS-607

Ribosome pull downs are employed to study ribosome-associated transcripts in wild type and a ribosomal mutant (pgy1)

About the Experimenter

Name:Dr Cristina Pignocchi
Head of Lab Name:Dr Robert Sablowski
Lab:
Address:Department of Cell and Developmental Biology, John Innes Centre
Norwich Research Park, Colney Lane, Norwich, Norfolk, NR4 7UH, UNITED KINGDOM
Postcode: NR4 7UH
Country: United Kingdom
 

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

About this Experiment

Experiment Type: gene_knock_out
Number of Slides:12
 
Experimental Parameters:
parametergene_knock_out
Quality Control Measures Taken:
References:
 
Other Information:

Slides in this Experiment

Hybridisation Set: Pignocchi: The role of ribosomes in plant development

Slide: Pignocchi_607-1_pgy3_FLAG-RP5A-Total_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 ("Pignocchi_607-1_pgy3_FLAG-RP5A-Total_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: Pignocchi_607-1_pgy3_FLAG-RP5A-Total_Rep1_ATH1
Organism: Arabidopsis thaliana
Stock Code:
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:0.733706
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-ratio1.272933
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.050161
Spike_AFFX-r2-Bs-dap_5_signal89.644485
NoiseAvg:2.66,Std:0.06,Min:2.4,Max:2.8
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal16.457834
#P13854
Spike_AFFX-r2-Bs-phe_M_signal89.572845
Corner-Avg:12817,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal40.006786
Spike_AFFX-r2-Ec-bioB_3_signal32.639835
Spike_AFFX-r2-Bs-lys_M_signal51.882595
Spike_AFFX-r2-P1-cre_3_signal6177.375977
Spike_AFFX-r2-Bs-lys_3-5-ratio1.471257
Spike_AFFX-r2-Bs-dap_M_signal495.834747
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio21.639683
Spike_AFFX-r2-Ec-bioB_avg-signal34.575802
Spike_AFFX-r2-Bs-thr_avg-signal162.608597
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1453.183716
Spike_AFFX-r2-Bs-phe_5_signal76.404922
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1763.794800
RawQ2.390263
Spike_AFFX-r2-Bs-lys_5_signal75.196709
Signal(A)6.235918
%A36.957474
Signal(All)152.159027
Corner+Avg:210,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal308.730621
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal182.018417
Spike_AFFX-r2-Ec-bioD_avg-signal1608.489258
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P60.736519
Spike_AFFX-r2-Bs-lys_avg-signal79.237663
Spike_AFFX-r2-P1-cre_avg-signal5515.121582
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M2.306006
Spike_AFFX-r2-Bs-thr_3_signal356.142303
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-signal115.998718
Spike_AFFX-r2-Bs-dap_3_signal851.752502
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.213745
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal328.956024
#M526
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal110.633682
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.938516
Spike_AFFX-r2-Bs-thr_M_signal115.225639
Signal(P)245.918518
Spike_AFFX-r2-Bs-phe_3-5-ratio2.382287
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:10280,Count:9
Spike_AFFX-r2-P1-cre_5_signal4852.867188
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8430
Signal(M)21.336914
BackgroundAvg:57.37,Std:0.54,Min:55.7,Max:58.6
Spike_AFFX-r2-Ec-bioC_avg-signal318.843323
Spike_AFFX-r2-Bs-dap_avg-signal479.077271
Spike_AFFX-r2-Bs-dap_3-5-ratio9.501449
Spike_AFFX-r2-Ec-bioB_5_signal31.080782
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.733706
NF1.000000
HZ4
Tau0.015000

Slide: Pignocchi_607-2_pgy3_FLAG-RP5A-Total_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 ("Pignocchi_607-2_pgy3_FLAG-RP5A-Total_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: Pignocchi_607-2_pgy3_FLAG-RP5A-Total_Rep2_ATH1
Organism: Arabidopsis thaliana
Stock Code:
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:0.722451
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-ratio1.194712
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.677956
Spike_AFFX-r2-Bs-dap_5_signal116.628197
NoiseAvg:2.62,Std:0.06,Min:2.5,Max:2.8
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal35.066269
#P14309
Spike_AFFX-r2-Bs-phe_M_signal97.593307
Corner-Avg:11934,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal46.122223
Spike_AFFX-r2-Ec-bioB_3_signal26.920420
Spike_AFFX-r2-Bs-lys_M_signal62.127644
Spike_AFFX-r2-P1-cre_3_signal5721.511719
Spike_AFFX-r2-Bs-lys_3-5-ratio1.514718
Spike_AFFX-r2-Bs-dap_M_signal519.036621
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio14.034891
Spike_AFFX-r2-Ec-bioB_avg-signal37.583622
Spike_AFFX-r2-Bs-thr_avg-signal229.260696
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1369.115479
Spike_AFFX-r2-Bs-phe_5_signal123.911362
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1737.430176
RawQ2.369270
Spike_AFFX-r2-Bs-lys_5_signal86.980972
Signal(A)5.661503
%A35.168785
Signal(All)149.790909
Corner+Avg:208,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal310.953674
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal171.673950
Spike_AFFX-r2-Ec-bioD_avg-signal1553.272827
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P62.731258
Spike_AFFX-r2-Bs-lys_avg-signal93.620094
Spike_AFFX-r2-P1-cre_avg-signal5255.270508
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M2.099956
Spike_AFFX-r2-Bs-thr_3_signal492.151276
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-signal131.059555
Spike_AFFX-r2-Bs-dap_3_signal1038.940918
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.269017
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal333.010345
#M479
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal131.751678
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.933766
Spike_AFFX-r2-Bs-thr_M_signal160.564575
Signal(P)234.933304
Spike_AFFX-r2-Bs-phe_3-5-ratio1.385458
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:8493,Count:9
Spike_AFFX-r2-P1-cre_5_signal4789.028809
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8022
Signal(M)20.153208
BackgroundAvg:57.66,Std:0.25,Min:57.1,Max:58.6
Spike_AFFX-r2-Ec-bioC_avg-signal321.981995
Spike_AFFX-r2-Bs-dap_avg-signal558.201904
Spike_AFFX-r2-Bs-dap_3-5-ratio8.908145
Spike_AFFX-r2-Ec-bioB_5_signal39.708229
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.722451
NF1.000000
HZ4
Tau0.015000

Slide: Pignocchi_607-3_pgy3_FLAG-RP5A-Total_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 ("Pignocchi_607-3_pgy3_FLAG-RP5A-Total_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: Pignocchi_607-3_pgy3_FLAG-RP5A-Total_Rep3_ATH1
Organism: Arabidopsis thaliana
Stock Code:
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:0.699538
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-ratio0.938753
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.278951
Spike_AFFX-r2-Bs-dap_5_signal107.457428
NoiseAvg:2.47,Std:0.10,Min:2.2,Max:2.8
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal30.489328
#P14622
Spike_AFFX-r2-Bs-phe_M_signal83.636269
Corner-Avg:11352,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal47.476177
Spike_AFFX-r2-Ec-bioB_3_signal36.172050
Spike_AFFX-r2-Bs-lys_M_signal46.965290
Spike_AFFX-r2-P1-cre_3_signal4144.109863
Spike_AFFX-r2-Bs-lys_3-5-ratio1.234560
Spike_AFFX-r2-Bs-dap_M_signal469.589539
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio12.643205
Spike_AFFX-r2-Ec-bioB_avg-signal37.310268
Spike_AFFX-r2-Bs-thr_avg-signal186.238876
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1176.839233
Spike_AFFX-r2-Bs-phe_5_signal112.939545
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1454.418335
RawQ2.414338
Spike_AFFX-r2-Bs-lys_5_signal82.695808
Signal(A)5.167778
%A33.849190
Signal(All)144.714813
Corner+Avg:191,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal315.879211
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal146.637390
Spike_AFFX-r2-Ec-bioD_avg-signal1315.628784
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P64.103462
Spike_AFFX-r2-Bs-lys_avg-signal77.251335
Spike_AFFX-r2-P1-cre_avg-signal4279.295898
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M2.047348
Spike_AFFX-r2-Bs-thr_3_signal385.482819
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-signal114.404396
Spike_AFFX-r2-Bs-dap_3_signal938.111267
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.235868
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal321.152344
#M467
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal102.092911
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.983581
Spike_AFFX-r2-Bs-thr_M_signal142.744492
Signal(P)222.473831
Spike_AFFX-r2-Bs-phe_3-5-ratio1.298371
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:9307,Count:9
Spike_AFFX-r2-P1-cre_5_signal4414.481445
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7721
Signal(M)17.199776
BackgroundAvg:57.23,Std:0.60,Min:55.8,Max:59.3
Spike_AFFX-r2-Ec-bioC_avg-signal318.515778
Spike_AFFX-r2-Bs-dap_avg-signal505.052734
Spike_AFFX-r2-Bs-dap_3-5-ratio8.730074
Spike_AFFX-r2-Ec-bioB_5_signal28.282587
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.699538
NF1.000000
HZ4
Tau0.015000

Slide: Pignocchi_607-4_pgy1-pgy3-FLAG-RP5A-Total_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 ("Pignocchi_607-4_pgy1-pgy3-FLAG-RP5A-Total_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: Pignocchi_607-4_pgy1-pgy3-FLAG-RP5A-Total_Rep1_ATH1
Organism: Arabidopsis thaliana
Stock Code:
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:0.510341
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-ratio1.183457
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.937976
Spike_AFFX-r2-Bs-dap_5_signal71.687637
NoiseAvg:2.89,Std:0.06,Min:2.7,Max:3.1
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal21.790592
#P15044
Spike_AFFX-r2-Bs-phe_M_signal74.515106
Corner-Avg:12988,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal39.105080
Spike_AFFX-r2-Ec-bioB_3_signal25.512947
Spike_AFFX-r2-Bs-lys_M_signal57.351269
Spike_AFFX-r2-P1-cre_3_signal4870.177734
Spike_AFFX-r2-Bs-lys_3-5-ratio1.359716
Spike_AFFX-r2-Bs-dap_M_signal394.450409
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio18.418558
Spike_AFFX-r2-Ec-bioB_avg-signal30.606009
Spike_AFFX-r2-Bs-thr_avg-signal172.357712
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1189.450684
Spike_AFFX-r2-Bs-phe_5_signal77.625389
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1403.617554
RawQ2.497729
Spike_AFFX-r2-Bs-lys_5_signal70.798180
Signal(A)4.475927
%A31.920210
Signal(All)144.765686
Corner+Avg:256,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal274.383514
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal163.634033
Spike_AFFX-r2-Ec-bioD_avg-signal1296.534180
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P65.953529
Spike_AFFX-r2-Bs-lys_avg-signal74.804939
Spike_AFFX-r2-P1-cre_avg-signal4492.696289
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M2.126261
Spike_AFFX-r2-Bs-thr_3_signal401.351288
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-signal105.258179
Spike_AFFX-r2-Bs-dap_3_signal779.658752
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.180055
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal319.210876
#M485
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal96.265388
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.859568
Spike_AFFX-r2-Bs-thr_M_signal93.931229
Signal(P)216.799576
Spike_AFFX-r2-Bs-phe_3-5-ratio2.107996
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:10348,Count:9
Spike_AFFX-r2-P1-cre_5_signal4115.214844
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7281
Signal(M)16.460278
BackgroundAvg:61.72,Std:0.54,Min:60.5,Max:63.0
Spike_AFFX-r2-Ec-bioC_avg-signal296.797180
Spike_AFFX-r2-Bs-dap_avg-signal415.265594
Spike_AFFX-r2-Bs-dap_3-5-ratio10.875777
Spike_AFFX-r2-Ec-bioB_5_signal27.199993
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.510341
NF1.000000
HZ4
Tau0.015000

Slide: Pignocchi_607-5_pgy1-pgy3-FLAG-RP5A-Total_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 ("Pignocchi_607-5_pgy1-pgy3-FLAG-RP5A-Total_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: Pignocchi_607-5_pgy1-pgy3-FLAG-RP5A-Total_Rep2_ATH1
Organism: Arabidopsis thaliana
Stock Code:
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:0.463866
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-ratio1.206861
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.818402
Spike_AFFX-r2-Bs-dap_5_signal46.070492
NoiseAvg:3.10,Std:0.07,Min:2.9,Max:3.3
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal16.113306
#P15065
Spike_AFFX-r2-Bs-phe_M_signal68.929955
Corner-Avg:13505,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal38.283234
Spike_AFFX-r2-Ec-bioB_3_signal33.298527
Spike_AFFX-r2-Bs-lys_M_signal44.508381
Spike_AFFX-r2-P1-cre_3_signal4224.270508
Spike_AFFX-r2-Bs-lys_3-5-ratio1.765752
Spike_AFFX-r2-Bs-dap_M_signal322.180328
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio22.742783
Spike_AFFX-r2-Ec-bioB_avg-signal37.423004
Spike_AFFX-r2-Bs-thr_avg-signal155.600876
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal937.655945
Spike_AFFX-r2-Bs-phe_5_signal67.382515
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1298.937500
RawQ2.714382
Spike_AFFX-r2-Bs-lys_5_signal64.056099
Signal(A)4.350523
%A31.937746
Signal(All)141.643661
Corner+Avg:248,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal273.577332
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal119.007088
Spike_AFFX-r2-Ec-bioD_avg-signal1118.296753
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P66.045593
Spike_AFFX-r2-Bs-lys_avg-signal73.890556
Spike_AFFX-r2-P1-cre_avg-signal3862.242188
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M2.016659
Spike_AFFX-r2-Bs-thr_3_signal366.461426
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-signal85.106514
Spike_AFFX-r2-Bs-dap_3_signal687.094910
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.385303
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal298.916168
#M460
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal113.107170
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.915231
Spike_AFFX-r2-Bs-thr_M_signal84.227882
Signal(P)211.851776
Spike_AFFX-r2-Bs-phe_3-5-ratio1.766142
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:11220,Count:9
Spike_AFFX-r2-P1-cre_5_signal3500.213623
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7285
Signal(M)16.633129
BackgroundAvg:68.15,Std:0.59,Min:66.6,Max:69.6
Spike_AFFX-r2-Ec-bioC_avg-signal286.246765
Spike_AFFX-r2-Bs-dap_avg-signal351.781891
Spike_AFFX-r2-Bs-dap_3-5-ratio14.913991
Spike_AFFX-r2-Ec-bioB_5_signal40.687260
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.463866
NF1.000000
HZ4
Tau0.015000

Slide: Pignocchi_607-6_pgy1-pgy3-FLAG-RP5A-Total_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 ("Pignocchi_607-6_pgy1-pgy3-FLAG-RP5A-Total_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: Pignocchi_607-6_pgy1-pgy3-FLAG-RP5A-Total_Rep3_ATH1
Organism: Arabidopsis thaliana
Stock Code:
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:0.57151
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-ratio1.208612
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.147596
Spike_AFFX-r2-Bs-dap_5_signal61.431023
NoiseAvg:3.02,Std:0.10,Min:2.8,Max:3.4
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal17.868202
#P14550
Spike_AFFX-r2-Bs-phe_M_signal71.745895
Corner-Avg:13126,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal38.799534
Spike_AFFX-r2-Ec-bioB_3_signal39.514797
Spike_AFFX-r2-Bs-lys_M_signal61.106468
Spike_AFFX-r2-P1-cre_3_signal4872.943359
Spike_AFFX-r2-Bs-lys_3-5-ratio1.003131
Spike_AFFX-r2-Bs-dap_M_signal364.406525
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio17.426512
Spike_AFFX-r2-Ec-bioB_avg-signal37.582333
Spike_AFFX-r2-Bs-thr_avg-signal138.016281
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1225.237061
Spike_AFFX-r2-Bs-phe_5_signal99.981964
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1564.135376
RawQ2.686144
Spike_AFFX-r2-Bs-lys_5_signal81.481705
Signal(A)5.279069
%A33.910564
Signal(All)145.226242
Corner+Avg:224,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal330.650085
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal143.972595
Spike_AFFX-r2-Ec-bioD_avg-signal1394.686279
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P63.787811
Spike_AFFX-r2-Bs-lys_avg-signal74.775009
Spike_AFFX-r2-P1-cre_avg-signal4452.396484
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M2.301622
Spike_AFFX-r2-Bs-thr_3_signal311.380432
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-signal105.233482
Spike_AFFX-r2-Bs-dap_3_signal594.845581
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.276598
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal339.424530
#M525
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal81.736847
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.974149
Spike_AFFX-r2-Bs-thr_M_signal84.800247
Signal(P)224.216385
Spike_AFFX-r2-Bs-phe_3-5-ratio1.439986
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:10642,Count:9
Spike_AFFX-r2-P1-cre_5_signal4031.849609
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7735
Signal(M)17.959177
BackgroundAvg:63.94,Std:0.81,Min:62.1,Max:65.6
Spike_AFFX-r2-Ec-bioC_avg-signal335.037292
Spike_AFFX-r2-Bs-dap_avg-signal340.227692
Spike_AFFX-r2-Bs-dap_3-5-ratio9.683146
Spike_AFFX-r2-Ec-bioB_5_signal34.432667
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.571510
NF1.000000
HZ4
Tau0.015000

Slide: Pignocchi_607-7_pgy3-FLAG-RPL5A_Ribosome-IP_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 ("Pignocchi_607-7_pgy3-FLAG-RPL5A_Ribosome-IP_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: Pignocchi_607-7_pgy3-FLAG-RPL5A_Ribosome-IP_Rep1_ATH1
Organism: Arabidopsis thaliana
Stock Code:
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:0.456902
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-ratio1.209436
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.590099
Spike_AFFX-r2-Bs-dap_5_signal134.455383
NoiseAvg:3.06,Std:0.09,Min:2.9,Max:3.4
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal48.551987
#P13776
Spike_AFFX-r2-Bs-phe_M_signal81.829346
Corner-Avg:15432,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal43.332909
Spike_AFFX-r2-Ec-bioB_3_signal24.953411
Spike_AFFX-r2-Bs-lys_M_signal49.913189
Spike_AFFX-r2-P1-cre_3_signal4301.667969
Spike_AFFX-r2-Bs-lys_3-5-ratio1.432385
Spike_AFFX-r2-Bs-dap_M_signal509.586395
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio5.827981
Spike_AFFX-r2-Ec-bioB_avg-signal36.857700
Spike_AFFX-r2-Bs-thr_avg-signal161.836609
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1150.081543
Spike_AFFX-r2-Bs-phe_5_signal99.202141
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1385.937378
RawQ2.408641
Spike_AFFX-r2-Bs-lys_5_signal71.539436
Signal(A)4.948459
%A37.321350
Signal(All)148.235672
Corner+Avg:320,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal289.294159
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal152.604675
Spike_AFFX-r2-Ec-bioD_avg-signal1268.009521
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P60.394566
Spike_AFFX-r2-Bs-lys_avg-signal74.641563
Spike_AFFX-r2-P1-cre_avg-signal3929.212402
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M2.284086
Spike_AFFX-r2-Bs-thr_3_signal282.960083
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-signal111.212059
Spike_AFFX-r2-Bs-dap_3_signal784.444702
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.205078
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal327.024994
#M521
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal102.472046
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.884624
Spike_AFFX-r2-Bs-thr_M_signal153.997757
Signal(P)241.731827
Spike_AFFX-r2-Bs-phe_3-5-ratio1.538320
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:12110,Count:9
Spike_AFFX-r2-P1-cre_5_signal3556.756592
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8513
Signal(M)17.335133
BackgroundAvg:56.01,Std:0.51,Min:55.2,Max:57.7
Spike_AFFX-r2-Ec-bioC_avg-signal308.159576
Spike_AFFX-r2-Bs-dap_avg-signal476.162201
Spike_AFFX-r2-Bs-dap_3-5-ratio5.834238
Spike_AFFX-r2-Ec-bioB_5_signal42.286793
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.456902
NF1.000000
HZ4
Tau0.015000

Slide: Pignocchi_607-8_pgy3-FLAG-RPL5A_Ribosome-IP_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 ("Pignocchi_607-8_pgy3-FLAG-RPL5A_Ribosome-IP_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: Pignocchi_607-8_pgy3-FLAG-RPL5A_Ribosome-IP_Rep2_ATH1
Organism: Arabidopsis thaliana
Stock Code:
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:0.528753
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-ratio1.231430
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.677126
Spike_AFFX-r2-Bs-dap_5_signal87.336861
NoiseAvg:3.30,Std:0.10,Min:3.0,Max:3.6
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal36.391819
#P13797
Spike_AFFX-r2-Bs-phe_M_signal63.463661
Corner-Avg:11249,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal35.099827
Spike_AFFX-r2-Ec-bioB_3_signal26.145288
Spike_AFFX-r2-Bs-lys_M_signal37.589500
Spike_AFFX-r2-P1-cre_3_signal4126.101074
Spike_AFFX-r2-Bs-lys_3-5-ratio1.402145
Spike_AFFX-r2-Bs-dap_M_signal370.755005
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio9.098467
Spike_AFFX-r2-Ec-bioB_avg-signal33.285751
Spike_AFFX-r2-Bs-thr_avg-signal163.016022
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal858.524658
Spike_AFFX-r2-Bs-phe_5_signal72.172394
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1177.369019
RawQ2.786691
Spike_AFFX-r2-Bs-lys_5_signal57.851707
Signal(A)5.632219
%A36.904865
Signal(All)146.766006
Corner+Avg:209,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal291.647583
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal128.364014
Spike_AFFX-r2-Ec-bioD_avg-signal1017.946838
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P60.486629
Spike_AFFX-r2-Bs-lys_avg-signal58.852558
Spike_AFFX-r2-P1-cre_avg-signal3738.379395
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M2.608505
Spike_AFFX-r2-Bs-thr_3_signal331.109772
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-signal88.000023
Spike_AFFX-r2-Bs-dap_3_signal686.597717
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.371386
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal293.554688
#M595
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal81.116463
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.993503
Spike_AFFX-r2-Bs-thr_M_signal121.546463
Signal(P)238.411484
Spike_AFFX-r2-Bs-phe_3-5-ratio1.778575
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:9561,Count:9
Spike_AFFX-r2-P1-cre_5_signal3350.657471
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8418
Signal(M)18.415625
BackgroundAvg:66.79,Std:0.87,Min:65.1,Max:69.6
Spike_AFFX-r2-Ec-bioC_avg-signal292.601135
Spike_AFFX-r2-Bs-dap_avg-signal381.563232
Spike_AFFX-r2-Bs-dap_3-5-ratio7.861488
Spike_AFFX-r2-Ec-bioB_5_signal38.612133
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.528753
NF1.000000
HZ4
Tau0.015000

Slide: Pignocchi_607-9_pgy3-FLAG-RPL5A_Ribosome-IP_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 ("Pignocchi_607-9_pgy3-FLAG-RPL5A_Ribosome-IP_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: Pignocchi_607-9_pgy3-FLAG-RPL5A_Ribosome-IP_Rep3_ATH1
Organism: Arabidopsis thaliana
Stock Code:
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:0.521447
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-ratio1.236274
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.961581
Spike_AFFX-r2-Bs-dap_5_signal132.863190
NoiseAvg:3.09,Std:0.08,Min:2.8,Max:3.3
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal43.299767
#P14040
Spike_AFFX-r2-Bs-phe_M_signal90.134857
Corner-Avg:11422,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal32.792587
Spike_AFFX-r2-Ec-bioB_3_signal25.669746
Spike_AFFX-r2-Bs-lys_M_signal39.753620
Spike_AFFX-r2-P1-cre_3_signal4176.097656
Spike_AFFX-r2-Bs-lys_3-5-ratio1.336443
Spike_AFFX-r2-Bs-dap_M_signal459.233582
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio8.499039
Spike_AFFX-r2-Ec-bioB_avg-signal28.385900
Spike_AFFX-r2-Bs-thr_avg-signal191.187332
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal906.887268
Spike_AFFX-r2-Bs-phe_5_signal99.858063
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1234.486450
RawQ2.667857
Spike_AFFX-r2-Bs-lys_5_signal66.009499
Signal(A)5.318241
%A35.918457
Signal(All)145.404816
Corner+Avg:200,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal298.276123
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal131.308640
Spike_AFFX-r2-Ec-bioD_avg-signal1070.686890
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P61.551952
Spike_AFFX-r2-Bs-lys_avg-signal64.660347
Spike_AFFX-r2-P1-cre_avg-signal3777.034180
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M2.529592
Spike_AFFX-r2-Bs-thr_3_signal368.006409
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-signal107.100525
Spike_AFFX-r2-Bs-dap_3_signal752.742249
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.361235
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal301.686615
#M577
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal88.217941
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.988695
Spike_AFFX-r2-Bs-thr_M_signal162.255859
Signal(P)232.419571
Spike_AFFX-r2-Bs-phe_3-5-ratio1.314953
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:10201,Count:9
Spike_AFFX-r2-P1-cre_5_signal3377.970459
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8193
Signal(M)17.228521
BackgroundAvg:63.01,Std:0.52,Min:61.3,Max:64.3
Spike_AFFX-r2-Ec-bioC_avg-signal299.981384
Spike_AFFX-r2-Bs-dap_avg-signal448.279663
Spike_AFFX-r2-Bs-dap_3-5-ratio5.665544
Spike_AFFX-r2-Ec-bioB_5_signal26.695362
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.521447
NF1.000000
HZ4
Tau0.015000

Slide: Pignocchi_607-10_pgy1-pgy3-FLAG-RPL5A -Ribosome-IP_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 ("Pignocchi_607-10_pgy1-pgy3-FLAG-RPL5A -Ribosome-IP_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: Pignocchi_607-10_pgy1-pgy3-FLAG-RPL5A -Ribosome-IP_Rep1_ATH1
Organism: Arabidopsis thaliana
Stock Code:
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:0.571947
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-ratio1.143441
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.871275
Spike_AFFX-r2-Bs-dap_5_signal84.253502
NoiseAvg:3.02,Std:0.07,Min:2.8,Max:3.2
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal27.819651
#P13917
Spike_AFFX-r2-Bs-phe_M_signal75.232101
Corner-Avg:12105,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal36.772453
Spike_AFFX-r2-Ec-bioB_3_signal36.447250
Spike_AFFX-r2-Bs-lys_M_signal38.610931
Spike_AFFX-r2-P1-cre_3_signal4669.253906
Spike_AFFX-r2-Bs-lys_3-5-ratio1.500911
Spike_AFFX-r2-Bs-dap_M_signal419.915436
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio11.180563
Spike_AFFX-r2-Ec-bioB_avg-signal38.350590
Spike_AFFX-r2-Bs-thr_avg-signal145.663803
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1266.762695
Spike_AFFX-r2-Bs-phe_5_signal69.379799
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1519.007813
RawQ2.681310
Spike_AFFX-r2-Bs-lys_5_signal68.515465
Signal(A)5.363917
%A36.641823
Signal(All)151.580582
Corner+Avg:203,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal312.158295
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal99.411697
Spike_AFFX-r2-Ec-bioD_avg-signal1392.885254
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P61.012714
Spike_AFFX-r2-Bs-lys_avg-signal69.987335
Spike_AFFX-r2-P1-cre_avg-signal4376.381836
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M2.345463
Spike_AFFX-r2-Bs-thr_3_signal311.039368
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-signal81.341194
Spike_AFFX-r2-Bs-dap_3_signal747.777405
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.199126
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal355.483002
#M535
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal102.835609
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.878124
Spike_AFFX-r2-Bs-thr_M_signal98.132378
Signal(P)244.506210
Spike_AFFX-r2-Bs-phe_3-5-ratio1.432862
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:10291,Count:9
Spike_AFFX-r2-P1-cre_5_signal4083.510254
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8358
Signal(M)18.558071
BackgroundAvg:64.88,Std:0.79,Min:63.1,Max:66.6
Spike_AFFX-r2-Ec-bioC_avg-signal333.820648
Spike_AFFX-r2-Bs-dap_avg-signal417.315460
Spike_AFFX-r2-Bs-dap_3-5-ratio8.875327
Spike_AFFX-r2-Ec-bioB_5_signal41.832073
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.571947
NF1.000000
HZ4
Tau0.015000

Slide: Pignocchi_607-11_pgy1-pgy3-FLAG-RPL5A -Ribosome-IP_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 ("Pignocchi_607-11_pgy1-pgy3-FLAG-RPL5A -Ribosome-IP_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: Pignocchi_607-11_pgy1-pgy3-FLAG-RPL5A -Ribosome-IP_Rep2_ATH1
Organism: Arabidopsis thaliana
Stock Code:
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:0.530926
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-ratio1.248510
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.922986
Spike_AFFX-r2-Bs-dap_5_signal80.588402
NoiseAvg:2.76,Std:0.07,Min:2.6,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_signal24.329659
#P14472
Spike_AFFX-r2-Bs-phe_M_signal59.236019
Corner-Avg:11271,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal34.544903
Spike_AFFX-r2-Ec-bioB_3_signal27.642647
Spike_AFFX-r2-Bs-lys_M_signal46.806801
Spike_AFFX-r2-P1-cre_3_signal4854.525879
Spike_AFFX-r2-Bs-lys_3-5-ratio1.275014
Spike_AFFX-r2-Bs-dap_M_signal330.205231
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio10.784683
Spike_AFFX-r2-Ec-bioB_avg-signal30.712229
Spike_AFFX-r2-Bs-thr_avg-signal125.129578
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1039.733887
Spike_AFFX-r2-Bs-phe_5_signal49.038181
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1163.417969
RawQ2.475724
Spike_AFFX-r2-Bs-lys_5_signal52.307938
Signal(A)4.488272
%A34.379658
Signal(All)148.355347
Corner+Avg:190,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal217.052780
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal106.144440
Spike_AFFX-r2-Ec-bioD_avg-signal1101.575928
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P63.445858
Spike_AFFX-r2-Bs-lys_avg-signal55.269363
Spike_AFFX-r2-P1-cre_avg-signal4371.390137
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M2.174485
Spike_AFFX-r2-Bs-thr_3_signal262.387665
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-signal71.472878
Spike_AFFX-r2-Bs-dap_3_signal699.691956
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.118957
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal258.143097
#M496
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal66.693352
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.840823
Spike_AFFX-r2-Bs-thr_M_signal88.671425
Signal(P)230.843399
Spike_AFFX-r2-Bs-phe_3-5-ratio2.164526
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:9103,Count:9
Spike_AFFX-r2-P1-cre_5_signal3888.254639
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7842
Signal(M)16.174477
BackgroundAvg:59.80,Std:0.34,Min:58.7,Max:60.7
Spike_AFFX-r2-Ec-bioC_avg-signal237.597931
Spike_AFFX-r2-Bs-dap_avg-signal370.161865
Spike_AFFX-r2-Bs-dap_3-5-ratio8.682291
Spike_AFFX-r2-Ec-bioB_5_signal29.949139
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.530926
NF1.000000
HZ4
Tau0.015000

Slide: Pignocchi_607-12_pgy1-pgy3-FLAG-RPL5A -Ribosome-IP_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 ("Pignocchi_607-12_pgy1-pgy3-FLAG-RPL5A -Ribosome-IP_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: Pignocchi_607-12_pgy1-pgy3-FLAG-RPL5A -Ribosome-IP_Rep3_ATH1
Organism: Arabidopsis thaliana
Stock Code:
Other Information:

Protocols for BioSource 1

Extraction Protocol Information

Name of Protocol: Qiagen / Trizol
Method:
ProtocolQiagen RNAeasy kit protocol
Type: total RNA
Amplification: Amplified during labelling process - see labelling protocol
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Labelling Protocol Information

Name of Protocol: Biotin Labelled cRNA using Affymetrix Enzo Kit
Amount Labelled: Unknown
Label Name: Biotin
Labelling Method: In-vitro transcription method
Other Information:
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

Slide Information

Date Hybridised:

Array Design Information

Slide Design Name: Affymetrix ATH1 Arabidopsis Genome Array
Array Type: Affymetrix Gene Chip
Number of Spots on the Array: 22810

Scanning Protocol Information

Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0

Image Analysis Information

Scaling Factor:0.530472
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-ratio1.149580
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.570559
Spike_AFFX-r2-Bs-dap_5_signal97.909470
NoiseAvg:2.78,Std:0.10,Min:2.6,Max:3.2
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal37.335442
#P14181
Spike_AFFX-r2-Bs-phe_M_signal63.973049
Corner-Avg:12486,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal37.559753
Spike_AFFX-r2-Ec-bioB_3_signal23.520409
Spike_AFFX-r2-Bs-lys_M_signal42.850597
Spike_AFFX-r2-P1-cre_3_signal4789.685059
Spike_AFFX-r2-Bs-lys_3-5-ratio1.418389
Spike_AFFX-r2-Bs-dap_M_signal367.190552
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio7.242902
Spike_AFFX-r2-Ec-bioB_avg-signal34.101208
Spike_AFFX-r2-Bs-thr_avg-signal141.037277
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1074.648438
Spike_AFFX-r2-Bs-phe_5_signal79.638062
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1388.509155
RawQ2.449154
Spike_AFFX-r2-Bs-lys_5_signal66.085686
Signal(A)4.634452
%A35.589653
Signal(All)152.455185
Corner+Avg:212,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal242.061661
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal140.462128
Spike_AFFX-r2-Ec-bioD_avg-signal1231.578857
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P62.170101
Spike_AFFX-r2-Bs-lys_avg-signal67.557167
Spike_AFFX-r2-P1-cre_avg-signal4478.074707
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M2.240246
Spike_AFFX-r2-Bs-thr_3_signal270.416962
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-signal94.691078
Spike_AFFX-r2-Bs-dap_3_signal810.822144
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.292059
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal273.567139
#M511
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal93.735222
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.884835
Spike_AFFX-r2-Bs-thr_M_signal115.359398
Signal(P)241.987961
Spike_AFFX-r2-Bs-phe_3-5-ratio1.763756
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:9932,Count:9
Spike_AFFX-r2-P1-cre_5_signal4166.464355
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8118
Signal(M)16.142916
BackgroundAvg:59.48,Std:0.43,Min:58.2,Max:60.5
Spike_AFFX-r2-Ec-bioC_avg-signal257.814392
Spike_AFFX-r2-Bs-dap_avg-signal425.307373
Spike_AFFX-r2-Bs-dap_3-5-ratio8.281345
Spike_AFFX-r2-Ec-bioB_5_signal41.223465
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.530472
NF1.000000
HZ4
Tau0.015000


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