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Experiment: SCR-LRP x Col0 comparison

Experiment Description

NASCArrays Experiment Reference Number: NASCARRAYS-541

A digenic mutant in the Col-0 was isolated. The mutant has pleiotropic effects on plant growth and development. It will be compared with it's corresponding wild-type to identify gene expression differences that contribute to the phenotypic differences.

About the Experimenter

Name:Dr Brian Jones
Head of Lab Name:Dr Brian Jones
Lab:
Address:Department of Plant Physiology, Faculty of Science and Technology, Ume� Universitet
Ume�, V�sterbottens l�n
Postcode: SE-901 87
Country: SWEDEN
 
Telephone Number: +46 90 786 6918
Fax Number: +46 90 786 8165

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

About this Experiment

Experiment Type: genetic_modification_design
Number of Slides:6
 
Experimental Parameters:
parametergenetic_variation
Quality Control Measures Taken:
References:
 
Other Information:

Slides in this Experiment

Hybridisation Set: Jones: SCR-LRP x Col0 comparison

Slide: Jones_541-1_Col-0_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 ("Jones_541-1_Col-0_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: Jones_541-1_Col-0_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Age: 6 weeks
Growth Conditions:
ProtocolSeeds were planted to 5½ cm x 5½ cm plastic pots containing ‘Plugger Custom’ (Debco) potting media (composted pine bark, mined sand, crushed stone, and coir pith) ‘Osmocote Exact Mini’ fertiliser containing 16% N, 3.5% P, 9.1% K, 1.2% Mg, and various trace elements at the rate of 1.5g/litre (w/v). Each pot contained one seedling of either the mutant or the wild-type. Twenty individual pots were placed in a 29 cm x 35 cm tray in a randomised block design, and were placed in the growth chamber, and watered as required every 2-3 days. Growth chamber conditions: 120-150 E m-2 s-1, 23oC/21oC and 16h/8h day/night.
Temperature21 °C average, 23 °C day, 21 °C night
Humidity60 % average, 55 % day, 65 % night
MediumNone
Lighting
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)6.30
Tissue: hypocotyl
Additional Organism Information:
Sample DescriptionWild-type Col-0
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:0.443371
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-ratio1.240926
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.916900
Spike_AFFX-r2-Bs-dap_5_signal69.617943
NoiseAvg:2.48,Std:0.08,Min:2.3,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_signal27.021933
#P14832
Spike_AFFX-r2-Bs-phe_M_signal34.090149
Corner-Avg:7543,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal74.019981
Spike_AFFX-r2-Ec-bioB_3_signal55.626381
Spike_AFFX-r2-Bs-lys_M_signal23.217520
Spike_AFFX-r2-P1-cre_3_signal3956.721191
Spike_AFFX-r2-Bs-lys_3-5-ratio1.428353
Spike_AFFX-r2-Bs-dap_M_signal141.456894
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio4.727562
Spike_AFFX-r2-Ec-bioB_avg-signal63.438084
Spike_AFFX-r2-Bs-thr_avg-signal75.955772
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal730.664673
Spike_AFFX-r2-Bs-phe_5_signal46.114590
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal941.634766
RawQ2.300359
Spike_AFFX-r2-Bs-lys_5_signal17.670166
Signal(A)2.627753
%A33.682594
Signal(All)136.078369
Corner+Avg:82,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal240.339050
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal37.423283
Spike_AFFX-r2-Ec-bioD_avg-signal836.149719
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P65.024109
Spike_AFFX-r2-Bs-lys_avg-signal22.042305
Spike_AFFX-r2-P1-cre_avg-signal3572.622559
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.293292
Spike_AFFX-r2-Bs-thr_3_signal127.747879
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-signal39.209339
Spike_AFFX-r2-Bs-dap_3_signal261.942810
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.288737
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal186.507156
#M295
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal25.239229
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.288632
Spike_AFFX-r2-Bs-thr_M_signal73.097511
Signal(P)207.702469
Spike_AFFX-r2-Bs-phe_3-5-ratio0.811528
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:5546,Count:9
Spike_AFFX-r2-P1-cre_5_signal3188.523926
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7683
Signal(M)10.561120
BackgroundAvg:54.30,Std:0.28,Min:53.5,Max:55.0
Spike_AFFX-r2-Ec-bioC_avg-signal213.423096
Spike_AFFX-r2-Bs-dap_avg-signal157.672562
Spike_AFFX-r2-Bs-dap_3-5-ratio3.762576
Spike_AFFX-r2-Ec-bioB_5_signal60.667896
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.443371
NF1.000000
HZ4
Tau0.015000

Slide: Jones_541-2_Col-0_Rep2_ATH1

Add to Slide Selection

Get the data!

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

Summary Information

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

  • Extract 1 ("Jones_541-2_Col-0_Rep2_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

The slide used was "Affymetrix ATH1 Arabidopsis Genome Array".

Click on the options above for more information about this slide and its preparation.

Hybridisation Protocol Information

Name of Protocol: Affymetrix Antibody Amplification Protocol
Solution:
BufferEDTA, NaCl, Tween20 according to Affymetrix protocol
Water
Blocking Agent:
Herring Sperm DNA(Source: Promega)100pg/ml
Acetylated BSA(Source: Sigma-Aldrich)0.1mg/ml
Wash Procedure:
Step 1(Source: Affymetrix)10 cycles of 2 mixes/cycle with Non-Stringent buffer
Step 2(Source: Affymetrix)4 cycles of 15 mixes/cycle with Stringent buffer
Step 3(Source: Affymetrix)Stain the probe array for 10 minutes in Streptavaidin Phycoerythrin (SAPE) solution at 25 C
Step 4(Source: Affymetrix)10 cycles of 4 mixes/cycle with Non-Stringent buffer
Step 5(Source: Affymetrix)Stain the probe array for 10 minutes in antibody solution
Step 6(Source: Affymetrix)Stain the probe array for 10 minutes in SAPE solution at 25 C
Step 7(Source: Affymetrix)15 cycles of 4mixes/cycle with Non-Stringent buffer at 30 C
Step 8(Source: Affymetrix)Hold at 25 C
Quantity Used:
Amount15 microgram Fragmented cRNA
Time: 16 hours
Concentration: 50 pg/ml
Volume: 200 microlitres
Temperature: 45 C
Other Information:
Spike(Source: Affymetrix)Control Oligo B2 to 50pM for landing lights
Spike(Source: Affymetrix)20X Eukaryotic Hybridisation Controls (bioB (1.5pM, bioC 5pM, bioD 25pM, cre 100pM)
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

BioSource 1 Information

BioSource Name: Jones_541-2_Col-0_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Age: 6 weeks
Growth Conditions:
ProtocolSeeds were planted to 5½ cm x 5½ cm plastic pots containing ‘Plugger Custom’ (Debco) potting media (composted pine bark, mined sand, crushed stone, and coir pith) ‘Osmocote Exact Mini’ fertiliser containing 16% N, 3.5% P, 9.1% K, 1.2% Mg, and various trace elements at the rate of 1.5g/litre (w/v). Each pot contained one seedling of either the mutant or the wild-type. Twenty individual pots were placed in a 29 cm x 35 cm tray in a randomised block design, and were placed in the growth chamber, and watered as required every 2-3 days. Growth chamber conditions: 120-150 E m-2 s-1, 23oC/21oC and 16h/8h day/night.
Temperature21 °C average, 23 °C day, 21 °C night
Humidity60 % average, 55 % day, 65 % night
MediumNone
Lighting
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)6.30
Tissue: hypocotyl
Additional Organism Information:
Sample DescriptionWild-type Col-0
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:0.594363
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-ratio1.347055
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.894991
Spike_AFFX-r2-Bs-dap_5_signal58.246765
NoiseAvg:2.38,Std:0.15,Min:2.1,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_signal19.845381
#P14738
Spike_AFFX-r2-Bs-phe_M_signal25.815538
Corner-Avg:6525,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal68.079063
Spike_AFFX-r2-Ec-bioB_3_signal49.353527
Spike_AFFX-r2-Bs-lys_M_signal17.542974
Spike_AFFX-r2-P1-cre_3_signal4174.993164
Spike_AFFX-r2-Bs-lys_3-5-ratio1.673169
Spike_AFFX-r2-Bs-dap_M_signal122.549301
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.967729
Spike_AFFX-r2-Ec-bioB_avg-signal57.525578
Spike_AFFX-r2-Bs-thr_avg-signal52.825237
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal696.943726
Spike_AFFX-r2-Bs-phe_5_signal27.514961
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal811.838196
RawQ2.232053
Spike_AFFX-r2-Bs-lys_5_signal13.573711
Signal(A)2.965846
%A34.125385
Signal(All)135.875580
Corner+Avg:72,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal249.353622
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal36.988411
Spike_AFFX-r2-Ec-bioD_avg-signal754.390991
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P64.612015
Spike_AFFX-r2-Bs-lys_avg-signal17.942602
Spike_AFFX-r2-P1-cre_avg-signal3637.171143
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.262604
Spike_AFFX-r2-Bs-thr_3_signal78.741096
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-signal30.106302
Spike_AFFX-r2-Bs-dap_3_signal193.355453
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.164855
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal173.687881
#M288
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal22.711121
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.435642
Spike_AFFX-r2-Bs-thr_M_signal59.889233
Signal(P)208.511658
Spike_AFFX-r2-Bs-phe_3-5-ratio1.344302
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:5190,Count:9
Spike_AFFX-r2-P1-cre_5_signal3099.349121
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7784
Signal(M)11.080673
BackgroundAvg:55.79,Std:0.64,Min:54.2,Max:57.5
Spike_AFFX-r2-Ec-bioC_avg-signal211.520752
Spike_AFFX-r2-Bs-dap_avg-signal124.717171
Spike_AFFX-r2-Bs-dap_3-5-ratio3.319591
Spike_AFFX-r2-Ec-bioB_5_signal55.144154
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.594363
NF1.000000
HZ4
Tau0.015000

Slide: Jones_541-3_Col-0_Rep3_ATH1

Add to Slide Selection

Get the data!

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

Summary Information

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

  • Extract 1 ("Jones_541-3_Col-0_Rep3_ATH1") was made from "Arabidopsis thaliana" and labelled using "Biotin Labelled cRNA using Affymetrix Enzo Kit".

The slide used was "Affymetrix ATH1 Arabidopsis Genome Array".

Click on the options above for more information about this slide and its preparation.

Hybridisation Protocol Information

Name of Protocol: Affymetrix Antibody Amplification Protocol
Solution:
BufferEDTA, NaCl, Tween20 according to Affymetrix protocol
Water
Blocking Agent:
Herring Sperm DNA(Source: Promega)100pg/ml
Acetylated BSA(Source: Sigma-Aldrich)0.1mg/ml
Wash Procedure:
Step 1(Source: Affymetrix)10 cycles of 2 mixes/cycle with Non-Stringent buffer
Step 2(Source: Affymetrix)4 cycles of 15 mixes/cycle with Stringent buffer
Step 3(Source: Affymetrix)Stain the probe array for 10 minutes in Streptavaidin Phycoerythrin (SAPE) solution at 25 C
Step 4(Source: Affymetrix)10 cycles of 4 mixes/cycle with Non-Stringent buffer
Step 5(Source: Affymetrix)Stain the probe array for 10 minutes in antibody solution
Step 6(Source: Affymetrix)Stain the probe array for 10 minutes in SAPE solution at 25 C
Step 7(Source: Affymetrix)15 cycles of 4mixes/cycle with Non-Stringent buffer at 30 C
Step 8(Source: Affymetrix)Hold at 25 C
Quantity Used:
Amount15 microgram Fragmented cRNA
Time: 16 hours
Concentration: 50 pg/ml
Volume: 200 microlitres
Temperature: 45 C
Other Information:
Spike(Source: Affymetrix)Control Oligo B2 to 50pM for landing lights
Spike(Source: Affymetrix)20X Eukaryotic Hybridisation Controls (bioB (1.5pM, bioC 5pM, bioD 25pM, cre 100pM)
ProtocolSourceAffymetrix GeneChip Technical Analysis Manual

BioSource 1 Information

BioSource Name: Jones_541-3_Col-0_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: Col-0 (Columbia)
Stock Code: N1092
Age: 6 weeks
Growth Conditions:
ProtocolSeeds were planted to 5½ cm x 5½ cm plastic pots containing ‘Plugger Custom’ (Debco) potting media (composted pine bark, mined sand, crushed stone, and coir pith) ‘Osmocote Exact Mini’ fertiliser containing 16% N, 3.5% P, 9.1% K, 1.2% Mg, and various trace elements at the rate of 1.5g/litre (w/v). Each pot contained one seedling of either the mutant or the wild-type. Twenty individual pots were placed in a 29 cm x 35 cm tray in a randomised block design, and were placed in the growth chamber, and watered as required every 2-3 days. Growth chamber conditions: 120-150 E m-2 s-1, 23oC/21oC and 16h/8h day/night.
Temperature21 °C average, 23 °C day, 21 °C night
Humidity60 % average, 55 % day, 65 % night
MediumNone
Lighting
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)6.30
Tissue: hypocotyl
Additional Organism Information:
Sample DescriptionWild-type Col-0
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:0.451221
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-ratio1.238395
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.059537
Spike_AFFX-r2-Bs-dap_5_signal86.872276
NoiseAvg:2.84,Std:0.07,Min:2.7,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_signal33.259598
#P14756
Spike_AFFX-r2-Bs-phe_M_signal43.539513
Corner-Avg:6308,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal50.141140
Spike_AFFX-r2-Ec-bioB_3_signal39.384968
Spike_AFFX-r2-Bs-lys_M_signal23.672859
Spike_AFFX-r2-P1-cre_3_signal2974.932861
Spike_AFFX-r2-Bs-lys_3-5-ratio1.674478
Spike_AFFX-r2-Bs-dap_M_signal195.618347
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio4.880317
Spike_AFFX-r2-Ec-bioB_avg-signal42.232655
Spike_AFFX-r2-Bs-thr_avg-signal95.757080
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal422.746063
Spike_AFFX-r2-Bs-phe_5_signal56.974590
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal628.830444
RawQ2.532055
Spike_AFFX-r2-Bs-lys_5_signal21.939976
Signal(A)2.949262
%A33.884262
Signal(All)134.079422
Corner+Avg:75,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal157.449936
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal58.245670
Spike_AFFX-r2-Ec-bioD_avg-signal525.788269
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P64.690926
Spike_AFFX-r2-Bs-lys_avg-signal27.450281
Spike_AFFX-r2-P1-cre_avg-signal2688.590820
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.424814
Spike_AFFX-r2-Bs-thr_3_signal162.317383
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-signal52.919926
Spike_AFFX-r2-Bs-dap_3_signal351.176666
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.487490
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal118.466286
#M325
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal36.738007
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.329070
Spike_AFFX-r2-Bs-thr_M_signal91.694237
Signal(P)205.453979
Spike_AFFX-r2-Bs-phe_3-5-ratio1.022310
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:5205,Count:9
Spike_AFFX-r2-P1-cre_5_signal2402.248535
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7729
Signal(M)11.932064
BackgroundAvg:64.28,Std:0.40,Min:62.9,Max:65.3
Spike_AFFX-r2-Ec-bioC_avg-signal137.958115
Spike_AFFX-r2-Bs-dap_avg-signal211.222427
Spike_AFFX-r2-Bs-dap_3-5-ratio4.042448
Spike_AFFX-r2-Ec-bioB_5_signal37.171864
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.451221
NF1.000000
HZ4
Tau0.015000

Slide: Jones_541-4_digenic-mutant_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 ("Jones_541-4_digenic-mutant_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: Jones_541-4_digenic-mutant_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: scr-lrp
Stock Code:
Genetic Background: Col-0
Age: 6 weeks
Growth Conditions:
ProtocolSeeds were planted to 5½ cm x 5½ cm plastic pots containing ‘Plugger Custom’ (Debco) potting media (composted pine bark, mined sand, crushed stone, and coir pith) ‘Osmocote Exact Mini’ fertiliser containing 16% N, 3.5% P, 9.1% K, 1.2% Mg, and various trace elements at the rate of 1.5g/litre (w/v). Each pot contained one seedling of either the mutant or the wild-type. Twenty individual pots were placed in a 29 cm x 35 cm tray in a randomised block design, and were placed in the growth chamber, and watered as required every 2-3 days. Growth chamber conditions: 120-150 E m-2 s-1, 23oC/21oC and 16h/8h day/night.
Temperature21 °C average, 23 °C day, 21 °C night
Humidity60 % average, 55 % day, 65 % night
MediumNone
Lighting
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)6.30
Genetic Variation: EMS induced mutation mutation
Tissue: hypocotyl
Additional Organism Information:
Sample DescriptionDigenic mutant of Col-0 accession
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:0.464866
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-ratio1.234771
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.910696
Spike_AFFX-r2-Bs-dap_5_signal70.462852
NoiseAvg:2.41,Std:0.07,Min:2.1,Max:2.6
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal24.220551
#P14721
Spike_AFFX-r2-Bs-phe_M_signal35.714996
Corner-Avg:6819,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal46.474060
Spike_AFFX-r2-Ec-bioB_3_signal47.740246
Spike_AFFX-r2-Bs-lys_M_signal24.818533
Spike_AFFX-r2-P1-cre_3_signal3708.774902
Spike_AFFX-r2-Bs-lys_3-5-ratio1.807280
Spike_AFFX-r2-Bs-dap_M_signal164.333160
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio4.655010
Spike_AFFX-r2-Ec-bioB_avg-signal48.878681
Spike_AFFX-r2-Bs-thr_avg-signal67.047142
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal569.868103
Spike_AFFX-r2-Bs-phe_5_signal44.405228
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal755.046326
RawQ2.164253
Spike_AFFX-r2-Bs-lys_5_signal18.821661
Signal(A)2.743096
%A34.033318
Signal(All)136.752945
Corner+Avg:74,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal201.108475
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal40.591846
Spike_AFFX-r2-Ec-bioD_avg-signal662.457214
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P64.537483
Spike_AFFX-r2-Bs-lys_avg-signal25.885405
Spike_AFFX-r2-P1-cre_avg-signal3356.194824
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.429198
Spike_AFFX-r2-Bs-thr_3_signal112.746910
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-signal40.237354
Spike_AFFX-r2-Bs-dap_3_signal260.836456
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.324949
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal152.519501
#M326
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal34.016018
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.318576
Spike_AFFX-r2-Bs-thr_M_signal64.173965
Signal(P)210.198944
Spike_AFFX-r2-Bs-phe_3-5-ratio0.914123
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:4922,Count:9
Spike_AFFX-r2-P1-cre_5_signal3003.614502
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7763
Signal(M)11.353583
BackgroundAvg:56.55,Std:0.41,Min:55.2,Max:57.7
Spike_AFFX-r2-Ec-bioC_avg-signal176.813995
Spike_AFFX-r2-Bs-dap_avg-signal165.210831
Spike_AFFX-r2-Bs-dap_3-5-ratio3.701758
Spike_AFFX-r2-Ec-bioB_5_signal52.421738
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.464866
NF1.000000
HZ4
Tau0.015000

Slide: Jones_541-5_digenic-mutant_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 ("Jones_541-5_digenic-mutant_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: Jones_541-5_digenic-mutant_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: scr-lrp
Stock Code:
Genetic Background: Col-0
Age: 6 weeks
Growth Conditions:
ProtocolSeeds were planted to 5½ cm x 5½ cm plastic pots containing ‘Plugger Custom’ (Debco) potting media (composted pine bark, mined sand, crushed stone, and coir pith) ‘Osmocote Exact Mini’ fertiliser containing 16% N, 3.5% P, 9.1% K, 1.2% Mg, and various trace elements at the rate of 1.5g/litre (w/v). Each pot contained one seedling of either the mutant or the wild-type. Twenty individual pots were placed in a 29 cm x 35 cm tray in a randomised block design, and were placed in the growth chamber, and watered as required every 2-3 days. Growth chamber conditions: 120-150 E m-2 s-1, 23oC/21oC and 16h/8h day/night.
Temperature21 °C average, 23 °C day, 21 °C night
Humidity60 % average, 55 % day, 65 % night
MediumNone
Lighting
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)6.30
Genetic Variation: EMS induced mutation mutation
Tissue: hypocotyl
Additional Organism Information:
Sample DescriptionDigenic mutant of Col-0 accession
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:0.721885
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-ratio1.277787
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.034659
Spike_AFFX-r2-Bs-dap_5_signal102.921600
NoiseAvg:2.05,Std:0.07,Min:1.8,Max:2.3
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal35.740803
#P14484
Spike_AFFX-r2-Bs-phe_M_signal41.320980
Corner-Avg:6480,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal91.082100
Spike_AFFX-r2-Ec-bioB_3_signal64.794067
Spike_AFFX-r2-Bs-lys_M_signal20.476381
Spike_AFFX-r2-P1-cre_3_signal5088.691406
Spike_AFFX-r2-Bs-lys_3-5-ratio1.577553
Spike_AFFX-r2-Bs-dap_M_signal171.376984
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.799159
Spike_AFFX-r2-Ec-bioB_avg-signal72.833252
Spike_AFFX-r2-Bs-thr_avg-signal91.681038
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal831.673218
Spike_AFFX-r2-Bs-phe_5_signal51.441853
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1060.700195
RawQ2.119163
Spike_AFFX-r2-Bs-lys_5_signal20.269814
Signal(A)2.980483
%A35.274002
Signal(All)138.372467
Corner+Avg:70,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal333.961578
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal51.190628
Spike_AFFX-r2-Ec-bioD_avg-signal946.186707
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P63.498466
Spike_AFFX-r2-Bs-lys_avg-signal24.240965
Spike_AFFX-r2-P1-cre_avg-signal4535.558594
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.227532
Spike_AFFX-r2-Bs-thr_3_signal135.785004
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-signal47.984486
Spike_AFFX-r2-Bs-dap_3_signal231.985855
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.275381
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal248.878738
#M280
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal31.976700
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.341865
Spike_AFFX-r2-Bs-thr_M_signal103.517296
Signal(P)216.029099
Spike_AFFX-r2-Bs-phe_3-5-ratio0.995116
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:4863,Count:9
Spike_AFFX-r2-P1-cre_5_signal3982.425537
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8046
Signal(M)11.890616
BackgroundAvg:51.20,Std:0.69,Min:49.0,Max:52.8
Spike_AFFX-r2-Ec-bioC_avg-signal291.420166
Spike_AFFX-r2-Bs-dap_avg-signal168.761490
Spike_AFFX-r2-Bs-dap_3-5-ratio2.254005
Spike_AFFX-r2-Ec-bioB_5_signal62.623600
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.721885
NF1.000000
HZ4
Tau0.015000

Slide: Jones_541-6_digenic mutant_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 ("Jones_541-6_digenic mutant_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: Jones_541-6_digenic mutant_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: scr-lrp
Stock Code:
Genetic Background: Col-0
Age: 6 weeks
Growth Conditions:
ProtocolSeeds were planted to 5½ cm x 5½ cm plastic pots containing ‘Plugger Custom’ (Debco) potting media (composted pine bark, mined sand, crushed stone, and coir pith) ‘Osmocote Exact Mini’ fertiliser containing 16% N, 3.5% P, 9.1% K, 1.2% Mg, and various trace elements at the rate of 1.5g/litre (w/v). Each pot contained one seedling of either the mutant or the wild-type. Twenty individual pots were placed in a 29 cm x 35 cm tray in a randomised block design, and were placed in the growth chamber, and watered as required every 2-3 days. Growth chamber conditions: 120-150 E m-2 s-1, 23oC/21oC and 16h/8h day/night.
Temperature21 °C average, 23 °C day, 21 °C night
Humidity60 % average, 55 % day, 65 % night
MediumNone
Lighting
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)6.30
Genetic Variation: EMS induced mutation mutation
Tissue: hypocotyl
Additional Organism Information:
Sample DescriptionDigenic mutant of Col-0 accession
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:0.871551
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-ratio1.141037
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.981479
Spike_AFFX-r2-Bs-dap_5_signal153.359009
NoiseAvg:1.88,Std:0.04,Min:1.8,Max:2.0
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal76.216309
#P14134
Spike_AFFX-r2-Bs-phe_M_signal79.707672
Corner-Avg:5746,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal99.434380
Spike_AFFX-r2-Ec-bioB_3_signal72.587563
Spike_AFFX-r2-Bs-lys_M_signal46.496502
Spike_AFFX-r2-P1-cre_3_signal5195.558105
Spike_AFFX-r2-Bs-lys_3-5-ratio1.112064
Spike_AFFX-r2-Bs-dap_M_signal351.567657
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio5.237856
Spike_AFFX-r2-Ec-bioB_avg-signal81.993103
Spike_AFFX-r2-Bs-thr_avg-signal231.837845
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal864.135864
Spike_AFFX-r2-Bs-phe_5_signal115.671051
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1206.393799
RawQ1.959165
Spike_AFFX-r2-Bs-lys_5_signal58.709064
Signal(A)3.749412
%A36.606750
Signal(All)140.920105
Corner+Avg:67,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal299.028259
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal105.656502
Spike_AFFX-r2-Ec-bioD_avg-signal1035.264893
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P61.964050
Spike_AFFX-r2-Bs-lys_avg-signal56.831272
Spike_AFFX-r2-P1-cre_avg-signal4874.461426
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.429198
Spike_AFFX-r2-Bs-thr_3_signal399.210083
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-signal100.345070
Spike_AFFX-r2-Bs-dap_3_signal559.593933
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.396070
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal261.971283
#M326
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal65.288254
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.141454
Spike_AFFX-r2-Bs-thr_M_signal220.087158
Signal(P)224.864426
Spike_AFFX-r2-Bs-phe_3-5-ratio0.913422
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:3973,Count:9
Spike_AFFX-r2-P1-cre_5_signal4553.364746
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8350
Signal(M)14.865791
BackgroundAvg:46.51,Std:0.30,Min:45.5,Max:47.3
Spike_AFFX-r2-Ec-bioC_avg-signal280.499756
Spike_AFFX-r2-Bs-dap_avg-signal354.840210
Spike_AFFX-r2-Bs-dap_3-5-ratio3.648915
Spike_AFFX-r2-Ec-bioB_5_signal73.957359
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.871551
NF1.000000
HZ4
Tau0.015000


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