NASC's International Affymetrix Service

AI logo

NASCArrays

home, selection, spot history, gene swinger, two gene scatterplot, digital northern, bulk gene download, tutorial, help, Affymetrix site, NASC

Experiment: Finlayson: Transcriptomics of Axillary Bud Outgrowth Regulation by Shade Signals in Arabidopsis.

Experiment Description

NASCArrays Experiment Reference Number: NASCARRAYS-561

Aims: To determine the changes in the Arabidopsis axillary bud transcriptome in response to changes in the red light (R) to far red light (FR) ratio (R:FR).Background: The branching habit of plants is a key determinant of overall plant form and function with great relevance to modern agriculture. Shade signals transduced by phytochromes are major regulators of axillary bud outgrowth, and in turn control branching in both natural and agricultural environments. To continue our investigations into the regulation of branching by R:FR, we have developed a system using supplemental FR LEDs to tightly control the outgrowth of Arabidopsis axillary buds. Depending on the position of the bud in the rosette, outgrowth is either repressed (uppermost bud) or rapidly promoted (bud in the axil of the third leaf down) by the transition from low to high R:FR.Treatment: Two separate experiments were conducted to evaluate the effects of R:FR on transcriptome changes in the uppermost rosette bud (bud n) and the axillary bud in the axil of the third leaf from the top (bud n-2). WT Col-60000 was used as the experimental material. Plants were grown individually in 25 by 50 mm tubes and watered and fertilized optimally. Plants were grown in a split growth chamber (providing uniform temperature and PPFD but allowing for differential R:FR) with 18 h photoperiods (185 ­Moles m-2 s-1 PPFD provided by T12 VHO CW fluorescent lamps) and 24oC/18oC day/night temperatures. One day after sowing the R:FR was reduced on both sides of the chamber from 3.5 to 0.08 using FR LEDs fixed in clear overhead arrays. Prior to anthesis the plants were matched and split into two treatment groups. In experiment 1 the FR source for one of the groups was switched off at 12:00 pm on the day of anthesis, causing the R:FR to increase to 3.5. Unelongated axillary buds in the axil of the uppermost leaves (approx. 2.5 mm long) were harvested for RNA preparation from both groups (low and transiently increased R:FR) 3 h after changing the R:FR. Each treatment was composed of three biological replicates, each containing buds from about 15-18 plants. Experiment 2 was conducted exactly the same as experiment 1, except the R:FR was altered 3 days after anthesis and the unelongated axillary buds in the axils of the third leaves down (approx. 1 mm long) were harvested for RNA preparation.

About the Experimenter

Name:Dr Scott Finlayson
Head of Lab Name:Dr Scott Finlayson
Lab:
Address:Department of Soil and Crop Sciences, College of Agriculture and Life Science, Texas A
&
M University
Heep Ctr., 370 Olsen Blvd, College Station, Texas, 77843-2474, UNITED STATES
Postcode:
Country:
 
Telephone Number: 9798479287
Fax Number: 9798450456

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: stimulus_or_stress_design
Number of Slides:12
 
Experimental Parameters:
parameterchange_light
Quality Control Measures Taken:
References:
 
Other Information:

Slides in this Experiment

Hybridisation Set: Finlayson: Transcriptomics of Axillary Bud Outgrowth Regulation by Shade Signals in Arabidopsis.

Slide: Finlayson_561-10_high-R:FR-bud-n-2_Rep1_ATH1

Add to Slide Selection

Get the data!

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

Summary Information

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

  • Extract 1 ("Finlayson_561-10_high-R:FR-bud-n-2_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:

BioSource 1 Information

BioSource Name: Finlayson_561-10_high-R:FR-bud-n-2_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Col-8 (Columbia)
Stock Code: CS60000
Genetic Background: Col-0
Age: 18
Growth Conditions:
ProtocolPlants were grown individually in 26 by 60 mm tubes and watered and fertilized optimally. Plants were grown in a split growth chamber (providing \ uniform temperature and PPFD but allowing for differential R:FR) with 18 h photoperiods (185 microMoles m-2 s-1 PPFD provided by T12 VHO CW fluorescent lamp\ s) and 24oC/18oC day/night temperatures.
stratification3 days at 4oC.
Temperature22.5°C average, 24 °C day, 18 °C night
Humidity50 % average, 50 % day, 50 % night
Lighting(Source: Fluorescent. Wavelength: White)
MediumHoagland ampapos;s No.2 basal salt mixture
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)6.00
Tissue: Rosette axillary bud n-2
Other Information:
treatment Two separate experiments were conducted to evaluate the effects of R:FR on transcriptome changes in the uppermost rosette bud (bud n) and the axillary bud in the axil of the third leaf from the top (bud n-2). WT Col-0 (CS60000) was used as the experimental material. Plants were grown individually in 26 by 60 mm tubes and watered and fertilized optimally. Plants were grown in a split growth chamber (providing uniform temperature and PPFD but\ allowing for differential R:FR) with 18 h photoperiods (185 microMoles m-2 s-1 PPFD provided by T12 VHO CW fluorescent lamps) and 24oC/18oC day/night temperatures. One day after sowing the R:FR was reduced on both sides of the chamber from 3.5 to 0.08 using FR LEDs fixed in clear overhead arrays. Prior to anthesis the plants were matched and split into two treatment groups. In experiment 1 the FR source for one of the groups was switched off at 12:00 pm on the\ day of anthesis, causing the R:FR to increase to 3.5. Unelongated axillary buds in the axil of the uppermost leaves (approx. 2.5 mm long) were harvested for RNA preparation from both groups (low and transiently increased R:FR) 3 h after changing the R:FR. Each treatment was composed of three biological replicates, each containing buds from about 15-18 plants. Experiment 2 was conducted exactly the same as experiment 1, except the R:FR was altered 3 days after \ anthesis and the unelongated axillary buds in the axils of the third leaves down (approx. 1 mm long) were harvested for RNA preparation.This sample was derived from plants grown under low R:FR from 1 day after sowing until 3 days after anthesis. At 12:00 on the third day after anthesis, the plants were exposed to high R:FR for 3 h and rosette axillary bud n-2 was harvested.

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:0.491277
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-ratio1.114554
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.346888
Spike_AFFX-r2-Bs-dap_5_signal31.795303
NoiseAvg:3.19,Std:0.09,Min:3.0,Max:3.5
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal19.037632
#P15643
Spike_AFFX-r2-Bs-phe_M_signal11.031335
Corner-Avg:11322,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal105.453651
Spike_AFFX-r2-Ec-bioB_3_signal95.885612
Spike_AFFX-r2-Bs-lys_M_signal5.791767
Spike_AFFX-r2-P1-cre_3_signal4349.863770
Spike_AFFX-r2-Bs-lys_3-5-ratio2.608389
Spike_AFFX-r2-Bs-dap_M_signal59.371960
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.330881
Spike_AFFX-r2-Ec-bioB_avg-signal90.843239
Spike_AFFX-r2-Bs-thr_avg-signal31.082901
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal932.531677
Spike_AFFX-r2-Bs-phe_5_signal13.655769
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1402.084229
RawQ2.924207
Spike_AFFX-r2-Bs-lys_5_signal9.781371
Signal(A)3.662360
%A29.912319
Signal(All)136.859192
Corner+Avg:180,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal311.661865
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal11.687796
Spike_AFFX-r2-Ec-bioD_avg-signal1167.307983
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P68.579567
Spike_AFFX-r2-Bs-lys_avg-signal13.695587
Spike_AFFX-r2-P1-cre_avg-signal4126.323730
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionA
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.508111
Spike_AFFX-r2-Bs-thr_3_signal44.374451
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal12.124967
Spike_AFFX-r2-Bs-dap_3_signal114.652809
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.503525
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal296.506195
#M344
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal25.513624
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.051114
Spike_AFFX-r2-Bs-thr_M_signal29.836618
Signal(P)197.699158
Spike_AFFX-r2-Bs-phe_3-5-ratio0.855887
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:7371,Count:9
Spike_AFFX-r2-P1-cre_5_signal3902.783936
Spike_AFFX-r2-Bs-phe_M_detectionP
#A6823
Signal(M)12.098200
BackgroundAvg:73.20,Std:0.66,Min:71.7,Max:75.0
Spike_AFFX-r2-Ec-bioC_avg-signal304.084045
Spike_AFFX-r2-Bs-dap_avg-signal68.606689
Spike_AFFX-r2-Bs-dap_3-5-ratio3.605967
Spike_AFFX-r2-Ec-bioB_5_signal71.190468
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.491277
NF1.000000
HZ4
Tau0.015000

Slide: Finlayson_561-9_low-R:FR-bud-n-2_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 ("Finlayson_561-9_low-R:FR-bud-n-2_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:

BioSource 1 Information

BioSource Name: Finlayson_561-9_low-R:FR-bud-n-2_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: Col-8 (Columbia)
Stock Code: CS60000
Genetic Background: Col-0
Age: 18
Growth Conditions:
ProtocolPlants were grown individually in 26 by 60 mm tubes and watered and fertilized optimally. Plants were grown in a split growth chamber (providing \ uniform temperature and PPFD but allowing for differential R:FR) with 18 h photoperiods (185 microMoles m-2 s-1 PPFD provided by T12 VHO CW fluorescent lamp\ s) and 24oC/18oC day/night temperatures.
stratification3 days at 4oC.
Temperature22.5°C average, 24 °C day, 18 °C night
Humidity50 % average, 50 % day, 50 % night
Lighting(Source: Fluorescent. Wavelength: White)
MediumHoagland ampapos;s No.2 basal salt mixture
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)6.00
Tissue: Rosette axillary bud n-2
Other Information:
treatment Two separate experiments were conducted to evaluate the effects of R:FR on transcriptome changes in the uppermost rosette bud (bud n) and the axillary bud in the axil of the third leaf from the top (bud n-2). WT Col-0 (CS60000) was used as the experimental material. Plants were grown individually in 26 by 60 mm tubes and watered and fertilized optimally. Plants were grown in a split growth chamber (providing uniform temperature and PPFD but\ allowing for differential R:FR) with 18 h photoperiods (185 microMoles m-2 s-1 PPFD provided by T12 VHO CW fluorescent lamps) and 24oC/18oC day/night temperatures. One day after sowing the R:FR was reduced on both sides of the chamber from 3.5 to 0.08 using FR LEDs fixed in clear overhead arrays. Prior to anthesis the plants were matched and split into two treatment groups. In experiment 1 the FR source for one of the groups was switched off at 12:00 pm on the\ day of anthesis, causing the R:FR to increase to 3.5. Unelongated axillary buds in the axil of the uppermost leaves (approx. 2.5 mm long) were harvested for RNA preparation from both groups (low and transiently increased R:FR) 3 h after changing the R:FR. Each treatment was composed of three biological replicates, each containing buds from about 15-18 plants. Experiment 2 was conducted exactly the same as experiment 1, except the R:FR was altered 3 days after \ anthesis and the unelongated axillary buds in the axils of the third leaves down (approx. 1 mm long) were harvested for RNA preparation. This sample was derived from plants maintained under low R:FR from 1 day after sowing until harvest at 3 days after anthesis

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:0.634393
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-ratio1.169359
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.105663
Spike_AFFX-r2-Bs-dap_5_signal60.761795
NoiseAvg:2.87,Std:0.08,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_signal21.381718
#P15368
Spike_AFFX-r2-Bs-phe_M_signal19.449245
Corner-Avg:11623,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal124.562393
Spike_AFFX-r2-Ec-bioB_3_signal98.235214
Spike_AFFX-r2-Bs-lys_M_signal18.725328
Spike_AFFX-r2-P1-cre_3_signal5085.875977
Spike_AFFX-r2-Bs-lys_3-5-ratio1.838871
Spike_AFFX-r2-Bs-dap_M_signal119.208008
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio3.680061
Spike_AFFX-r2-Ec-bioB_avg-signal103.881653
Spike_AFFX-r2-Bs-thr_avg-signal54.214779
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1023.677795
Spike_AFFX-r2-Bs-phe_5_signal24.681540
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1623.019775
RawQ2.731207
Spike_AFFX-r2-Bs-lys_5_signal17.083109
Signal(A)4.234803
%A30.999561
Signal(All)136.430634
Corner+Avg:177,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal321.454163
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal24.676439
Spike_AFFX-r2-Ec-bioD_avg-signal1323.348755
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P67.373962
Spike_AFFX-r2-Bs-lys_avg-signal22.407356
Spike_AFFX-r2-P1-cre_avg-signal4717.581055
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.626480
Spike_AFFX-r2-Bs-thr_3_signal78.686028
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal22.935743
Spike_AFFX-r2-Bs-dap_3_signal259.095917
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.585479
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal338.445435
#M371
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal31.413633
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.949796
Spike_AFFX-r2-Bs-thr_M_signal62.576591
Signal(P)200.218277
Spike_AFFX-r2-Bs-phe_3-5-ratio0.999793
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:6934,Count:9
Spike_AFFX-r2-P1-cre_5_signal4349.286621
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7071
Signal(M)13.703574
BackgroundAvg:65.10,Std:1.33,Min:62.7,Max:69.8
Spike_AFFX-r2-Ec-bioC_avg-signal329.949799
Spike_AFFX-r2-Bs-dap_avg-signal146.355240
Spike_AFFX-r2-Bs-dap_3-5-ratio4.264125
Spike_AFFX-r2-Ec-bioB_5_signal88.847359
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.634393
NF1.000000
HZ4
Tau0.015000

Slide: Finlayson_561-8_low-R:FR-bud-n-2_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 ("Finlayson_561-8_low-R:FR-bud-n-2_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:

BioSource 1 Information

BioSource Name: Finlayson_561-8_low-R:FR-bud-n-2_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Col-8 (Columbia)
Stock Code: CS60000
Genetic Background: Col-0
Age: 18
Growth Conditions:
ProtocolPlants were grown individually in 26 by 60 mm tubes and watered and fertilized optimally. Plants were grown in a split growth chamber (providing \ uniform temperature and PPFD but allowing for differential R:FR) with 18 h photoperiods (185 microMoles m-2 s-1 PPFD provided by T12 VHO CW fluorescent lamp\ s) and 24oC/18oC day/night temperatures.
stratification3 days at 4oC.
Temperature22.5°C average, 24 °C day, 18 °C night
Humidity50 % average, 50 % day, 50 % night
Lighting(Source: Fluorescent. Wavelength: White)
MediumHoagland ampapos;s No.2 basal salt mixture
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)6.00
Tissue: Rosette axillary bud n-2
Other Information:
treatment Two separate experiments were conducted to evaluate the effects of R:FR on transcriptome changes in the uppermost rosette bud (bud n) and the axillary bud in the axil of the third leaf from the top (bud n-2). WT Col-0 (CS60000) was used as the experimental material. Plants were grown individually in 26 by 60 mm tubes and watered and fertilized optimally. Plants were grown in a split growth chamber (providing uniform temperature and PPFD but\ allowing for differential R:FR) with 18 h photoperiods (185 microMoles m-2 s-1 PPFD provided by T12 VHO CW fluorescent lamps) and 24oC/18oC day/night temperatures. One day after sowing the R:FR was reduced on both sides of the chamber from 3.5 to 0.08 using FR LEDs fixed in clear overhead arrays. Prior to anthesis the plants were matched and split into two treatment groups. In experiment 1 the FR source for one of the groups was switched off at 12:00 pm on the\ day of anthesis, causing the R:FR to increase to 3.5. Unelongated axillary buds in the axil of the uppermost leaves (approx. 2.5 mm long) were harvested for RNA preparation from both groups (low and transiently increased R:FR) 3 h after changing the R:FR. Each treatment was composed of three biological replicates, each containing buds from about 15-18 plants. Experiment 2 was conducted exactly the same as experiment 1, except the R:FR was altered 3 days after \ anthesis and the unelongated axillary buds in the axils of the third leaves down (approx. 1 mm long) were harvested for RNA preparation. This sample was derived from plants maintained under low R:FR from 1 day after sowing until harvest at 3 days after anthesis

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:0.487264
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-ratio1.163296
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.244975
Spike_AFFX-r2-Bs-dap_5_signal36.365662
NoiseAvg:3.54,Std:0.11,Min:3.3,Max:3.9
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal12.688293
#P15520
Spike_AFFX-r2-Bs-phe_M_signal12.227137
Corner-Avg:12644,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal113.500153
Spike_AFFX-r2-Ec-bioB_3_signal105.637100
Spike_AFFX-r2-Bs-lys_M_signal8.131946
Spike_AFFX-r2-P1-cre_3_signal4808.627441
Spike_AFFX-r2-Bs-lys_3-5-ratio3.688005
Spike_AFFX-r2-Bs-dap_M_signal66.526360
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.963863
Spike_AFFX-r2-Ec-bioB_avg-signal101.329353
Spike_AFFX-r2-Bs-thr_avg-signal28.845205
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1056.863647
Spike_AFFX-r2-Bs-phe_5_signal7.423788
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1618.207031
RawQ3.190258
Spike_AFFX-r2-Bs-lys_5_signal5.280996
Signal(A)4.154329
%A30.337572
Signal(All)136.562149
Corner+Avg:204,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal393.211304
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal19.341497
Spike_AFFX-r2-Ec-bioD_avg-signal1337.535400
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P68.040337
Spike_AFFX-r2-Bs-lys_avg-signal10.963094
Spike_AFFX-r2-P1-cre_avg-signal4471.125977
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.622096
Spike_AFFX-r2-Bs-thr_3_signal37.606361
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal12.997475
Spike_AFFX-r2-Bs-dap_3_signal142.713135
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.531141
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal350.119690
#M370
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal19.476341
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.123077
Spike_AFFX-r2-Bs-thr_M_signal36.240955
Signal(P)198.538239
Spike_AFFX-r2-Bs-phe_3-5-ratio2.605341
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:9434,Count:9
Spike_AFFX-r2-P1-cre_5_signal4133.624512
Spike_AFFX-r2-Bs-phe_M_detectionP
#A6920
Signal(M)13.300485
BackgroundAvg:76.73,Std:0.50,Min:75.6,Max:78.2
Spike_AFFX-r2-Ec-bioC_avg-signal371.665497
Spike_AFFX-r2-Bs-dap_avg-signal81.868385
Spike_AFFX-r2-Bs-dap_3-5-ratio3.924393
Spike_AFFX-r2-Ec-bioB_5_signal84.850807
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.487264
NF1.000000
HZ4
Tau0.015000

Slide: Finlayson_561-7_low-R:FR-bud-n-2_Rep1_ATH1

Add to Slide Selection

Get the data!

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

Summary Information

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

  • Extract 1 ("Finlayson_561-7_low-R:FR-bud-n-2_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:

BioSource 1 Information

BioSource Name: Finlayson_561-7_low-R:FR-bud-n-2_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Col-8 (Columbia)
Stock Code: CS60000
Genetic Background: Col-0
Age: 18
Growth Conditions:
ProtocolPlants were grown individually in 26 by 60 mm tubes and watered and fertilized optimally. Plants were grown in a split growth chamber (providing \ uniform temperature and PPFD but allowing for differential R:FR) with 18 h photoperiods (185 microMoles m-2 s-1 PPFD provided by T12 VHO CW fluorescent lamp\ s) and 24oC/18oC day/night temperatures.
stratification3 days at 4oC.
Temperature22.5°C average, 24 °C day, 18 °C night
Humidity50 % average, 50 % day, 50 % night
Lighting(Source: Fluorescent. Wavelength: White)
MediumHoagland ampapos;s No.2 basal salt mixture
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)6.00
Tissue: Rosette axillary bud n-2
Other Information:
treatment Two separate experiments were conducted to evaluate the effects of R:FR on transcriptome changes in the uppermost rosette bud (bud n) and the axillary bud in the axil of the third leaf from the top (bud n-2). WT Col-0 (CS60000) was used as the experimental material. Plants were grown individually in 26 by 60 mm tubes and watered and fertilized optimally. Plants were grown in a split growth chamber (providing uniform temperature and PPFD but\ allowing for differential R:FR) with 18 h photoperiods (185 microMoles m-2 s-1 PPFD provided by T12 VHO CW fluorescent lamps) and 24oC/18oC day/night temperatures. One day after sowing the R:FR was reduced on both sides of the chamber from 3.5 to 0.08 using FR LEDs fixed in clear overhead arrays. Prior to anthesis the plants were matched and split into two treatment groups. In experiment 1 the FR source for one of the groups was switched off at 12:00 pm on the\ day of anthesis, causing the R:FR to increase to 3.5. Unelongated axillary buds in the axil of the uppermost leaves (approx. 2.5 mm long) were harvested for RNA preparation from both groups (low and transiently increased R:FR) 3 h after changing the R:FR. Each treatment was composed of three biological replicates, each containing buds from about 15-18 plants. Experiment 2 was conducted exactly the same as experiment 1, except the R:FR was altered 3 days after \ anthesis and the unelongated axillary buds in the axils of the third leaves down (approx. 1 mm long) were harvested for RNA preparation. This sample was derived from plants maintained under low R:FR from 1 day after sowing until harvest at 3 days after anthesis

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:0.343122
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-ratio1.212684
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.170562
Spike_AFFX-r2-Bs-dap_5_signal37.755222
NoiseAvg:4.11,Std:0.07,Min:3.8,Max:4.2
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal12.848756
#P15942
Spike_AFFX-r2-Bs-phe_M_signal9.432499
Corner-Avg:14738,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal85.111107
Spike_AFFX-r2-Ec-bioB_3_signal75.341324
Spike_AFFX-r2-Bs-lys_M_signal6.565071
Spike_AFFX-r2-P1-cre_3_signal3961.993652
Spike_AFFX-r2-Bs-lys_3-5-ratio2.216920
Spike_AFFX-r2-Bs-dap_M_signal80.179108
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.117789
Spike_AFFX-r2-Ec-bioB_avg-signal74.938599
Spike_AFFX-r2-Bs-thr_avg-signal24.305931
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal850.111328
Spike_AFFX-r2-Bs-phe_5_signal14.316912
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1285.270874
RawQ3.283873
Spike_AFFX-r2-Bs-lys_5_signal11.903260
Signal(A)3.976406
%A28.610258
Signal(All)134.044449
Corner+Avg:240,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal271.852844
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal16.021954
Spike_AFFX-r2-Ec-bioD_avg-signal1067.691162
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P69.890396
Spike_AFFX-r2-Bs-lys_avg-signal14.952301
Spike_AFFX-r2-P1-cre_avg-signal3614.560303
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.499342
Spike_AFFX-r2-Bs-thr_3_signal27.210949
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal13.257121
Spike_AFFX-r2-Bs-dap_3_signal125.128845
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.511885
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal238.983948
#M342
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal26.388575
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.137536
Spike_AFFX-r2-Bs-thr_M_signal32.858089
Signal(P)189.914764
Spike_AFFX-r2-Bs-phe_3-5-ratio1.119093
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:10955,Count:9
Spike_AFFX-r2-P1-cre_5_signal3267.126953
Spike_AFFX-r2-Bs-phe_M_detectionP
#A6526
Signal(M)11.644926
BackgroundAvg:83.18,Std:0.82,Min:80.9,Max:85.1
Spike_AFFX-r2-Ec-bioC_avg-signal255.418396
Spike_AFFX-r2-Bs-dap_avg-signal81.021057
Spike_AFFX-r2-Bs-dap_3-5-ratio3.314213
Spike_AFFX-r2-Ec-bioB_5_signal64.363365
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.343122
NF1.000000
HZ4
Tau0.015000

Slide: Finlayson_561-6_high-R:FR-bud-n_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 ("Finlayson_561-6_high-R:FR-bud-n_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:

BioSource 1 Information

BioSource Name: Finlayson_561-6_high-R:FR-bud-n_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: Col-8 (Columbia)
Stock Code: CS60000
Genetic Background: Col-0
Age: 16 days after sowing
Growth Conditions:
ProtocolPlants were grown individually in 26 by 60 mm tubes and watered and fertilized optimally. Plants were grown in a split growth chamber (providing \ uniform temperature and PPFD but allowing for differential R:FR) with 18 h photoperiods (185 microMoles m-2 s-1 PPFD provided by T12 VHO CW fluorescent lamp\ s) and 24oC/18oC day/night temperatures.
stratification3 days at 4oC.
Temperature22.5°C average, 24 °C day, 18 °C night
Humidity50 % average, 50 % day, 50 % night
Lighting(Source: Fluorescent. Wavelength: White)
MediumHoagland ampapos;s No.2 basal salt mixture
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)6.00
Tissue: Rosette axillary bud n
Other Information:
treatment Two separate experiments were conducted to evaluate the effects of R:FR on transcriptome changes in the uppermost rosette bud (bud n) and the axillary bud in the axil of the third leaf from the top (bud n-2). WT Col-0 (CS60000) was used as the experimental material. Plants were grown individually in 26 by 60 mm tubes and watered and fertilized optimally. Plants were grown in a split growth chamber (providing uniform temperature and PPFD but\ allowing for differential R:FR) with 18 h photoperiods (185 microMoles m-2 s-1 PPFD provided by T12 VHO CW fluorescent lamps) and 24oC/18oC day/night temperatures. One day after sowing the R:FR was reduced on both sides of the chamber from 3.5 to 0.08 using FR LEDs fixed in clear overhead arrays. Prior to anthesis the plants were matched and split into two treatment groups. In experiment 1 the FR source for one of the groups was switched off at 12:00 pm on the\ day of anthesis, causing the R:FR to increase to 3.5. Unelongated axillary buds in the axil of the uppermost leaves (approx. 2.5 mm long) were harvested for RNA preparation from both groups (low and transiently increased R:FR) 3 h after changing the R:FR. Each treatment was composed of three biological replicates, each containing buds from about 15-18 plants. Experiment 2 was conducted exactly the same as experiment 1, except the R:FR was altered 3 days after \ anthesis and the unelongated axillary buds in the axils of the third leaves down (approx. 1 mm long) were harvested for RNA preparation. This sample was derived from plants grown under low R:FR from 1 day after sowing until the first day of anthesis. At 12:00 on the day of anthesis, the plants were exposed to high R:FR for 3 h and rosette axillary bud n was harvested.

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:0.361189
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-ratio0.952009
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.945331
Spike_AFFX-r2-Bs-dap_5_signal28.504683
NoiseAvg:3.94,Std:0.15,Min:3.5,Max:4.4
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal12.677217
#P14888
Spike_AFFX-r2-Bs-phe_M_signal9.034296
Corner-Avg:11926,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal70.978943
Spike_AFFX-r2-Ec-bioB_3_signal61.294857
Spike_AFFX-r2-Bs-lys_M_signal6.022498
Spike_AFFX-r2-P1-cre_3_signal2897.578125
Spike_AFFX-r2-Bs-lys_3-5-ratio2.684257
Spike_AFFX-r2-Bs-dap_M_signal59.670555
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.749388
Spike_AFFX-r2-Ec-bioB_avg-signal65.704468
Spike_AFFX-r2-Bs-thr_avg-signal24.175476
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal641.993835
Spike_AFFX-r2-Bs-phe_5_signal10.891598
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1108.291016
RawQ3.356192
Spike_AFFX-r2-Bs-lys_5_signal7.788874
Signal(A)3.211091
%A33.226654
Signal(All)138.185333
Corner+Avg:194,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal226.668869
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal11.410454
Spike_AFFX-r2-Ec-bioD_avg-signal875.142456
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P65.269615
Spike_AFFX-r2-Bs-lys_avg-signal11.572906
Spike_AFFX-r2-P1-cre_avg-signal2970.612305
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.503726
Spike_AFFX-r2-Bs-thr_3_signal34.854591
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionM
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal10.445449
Spike_AFFX-r2-Bs-dap_3_signal99.932159
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.726327
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal223.475632
#M343
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal20.907341
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.014289
Spike_AFFX-r2-Bs-thr_M_signal24.994619
Signal(P)209.796494
Spike_AFFX-r2-Bs-phe_3-5-ratio1.047638
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:8358,Count:9
Spike_AFFX-r2-P1-cre_5_signal3043.646729
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7579
Signal(M)12.303746
BackgroundAvg:83.45,Std:0.66,Min:81.7,Max:85.5
Spike_AFFX-r2-Ec-bioC_avg-signal225.072250
Spike_AFFX-r2-Bs-dap_avg-signal62.702469
Spike_AFFX-r2-Bs-dap_3-5-ratio3.505816
Spike_AFFX-r2-Ec-bioB_5_signal64.839592
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.361189
NF1.000000
HZ4
Tau0.015000

Slide: Finlayson_561-5_high-R:FR-bud-n_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 ("Finlayson_561-5_high-R:FR-bud-n_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:

BioSource 1 Information

BioSource Name: Finlayson_561-5_high-R:FR-bud-n_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Col-8 (Columbia)
Stock Code: CS60000
Genetic Background: Col-0
Age: 16 days after sowing
Growth Conditions:
ProtocolPlants were grown individually in 26 by 60 mm tubes and watered and fertilized optimally. Plants were grown in a split growth chamber (providing \ uniform temperature and PPFD but allowing for differential R:FR) with 18 h photoperiods (185 microMoles m-2 s-1 PPFD provided by T12 VHO CW fluorescent lamp\ s) and 24oC/18oC day/night temperatures.
stratification3 days at 4oC.
Temperature22.5°C average, 24 °C day, 18 °C night
Humidity50 % average, 50 % day, 50 % night
Lighting(Source: Fluorescent. Wavelength: White)
MediumHoagland ampapos;s No.2 basal salt mixture
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)6.00
Tissue: Rosette axillary bud n
Other Information:
treatment Two separate experiments were conducted to evaluate the effects of R:FR on transcriptome changes in the uppermost rosette bud (bud n) and the axillary bud in the axil of the third leaf from the top (bud n-2). WT Col-0 (CS60000) was used as the experimental material. Plants were grown individually in 26 by 60 mm tubes and watered and fertilized optimally. Plants were grown in a split growth chamber (providing uniform temperature and PPFD but\ allowing for differential R:FR) with 18 h photoperiods (185 microMoles m-2 s-1 PPFD provided by T12 VHO CW fluorescent lamps) and 24oC/18oC day/night temperatures. One day after sowing the R:FR was reduced on both sides of the chamber from 3.5 to 0.08 using FR LEDs fixed in clear overhead arrays. Prior to anthesis the plants were matched and split into two treatment groups. In experiment 1 the FR source for one of the groups was switched off at 12:00 pm on the\ day of anthesis, causing the R:FR to increase to 3.5. Unelongated axillary buds in the axil of the uppermost leaves (approx. 2.5 mm long) were harvested for RNA preparation from both groups (low and transiently increased R:FR) 3 h after changing the R:FR. Each treatment was composed of three biological replicates, each containing buds from about 15-18 plants. Experiment 2 was conducted exactly the same as experiment 1, except the R:FR was altered 3 days after \ anthesis and the unelongated axillary buds in the axils of the third leaves down (approx. 1 mm long) were harvested for RNA preparation. This sample was derived from plants grown under low R:FR from 1 day after sowing until the first day of anthesis. At 12:00 on the day of anthesis, the plants were exposed to high R:FR for 3 h and rosette axillary bud n was harvested.

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:0.446726
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-ratio1.152928
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.108949
Spike_AFFX-r2-Bs-dap_5_signal46.121670
NoiseAvg:3.57,Std:0.11,Min:3.3,Max:4.0
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal13.801003
#P14920
Spike_AFFX-r2-Bs-phe_M_signal10.661151
Corner-Avg:12453,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal102.319412
Spike_AFFX-r2-Ec-bioB_3_signal87.205872
Spike_AFFX-r2-Bs-lys_M_signal8.670321
Spike_AFFX-r2-P1-cre_3_signal3989.741211
Spike_AFFX-r2-Bs-lys_3-5-ratio1.267504
Spike_AFFX-r2-Bs-dap_M_signal80.940346
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio1.882154
Spike_AFFX-r2-Ec-bioB_avg-signal89.387871
Spike_AFFX-r2-Bs-thr_avg-signal25.264702
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal854.299622
Spike_AFFX-r2-Bs-phe_5_signal21.069307
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1236.538452
RawQ3.151998
Spike_AFFX-r2-Bs-lys_5_signal11.046636
Signal(A)3.402426
%A33.187199
Signal(All)139.830429
Corner+Avg:199,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal301.520477
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal22.724257
Spike_AFFX-r2-Ec-bioD_avg-signal1045.419067
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P65.409904
Spike_AFFX-r2-Bs-lys_avg-signal11.239537
Spike_AFFX-r2-P1-cre_avg-signal3725.135498
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.402893
Spike_AFFX-r2-Bs-thr_3_signal25.975618
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal18.151571
Spike_AFFX-r2-Bs-dap_3_signal137.846039
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.447429
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal248.748367
#M320
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal14.001657
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.212151
Spike_AFFX-r2-Bs-thr_M_signal36.017487
Signal(P)211.773270
Spike_AFFX-r2-Bs-phe_3-5-ratio1.078548
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:9709,Count:9
Spike_AFFX-r2-P1-cre_5_signal3460.529785
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7570
Signal(M)12.869947
BackgroundAvg:75.98,Std:0.69,Min:73.9,Max:78.5
Spike_AFFX-r2-Ec-bioC_avg-signal275.134430
Spike_AFFX-r2-Bs-dap_avg-signal88.302681
Spike_AFFX-r2-Bs-dap_3-5-ratio2.988748
Spike_AFFX-r2-Ec-bioB_5_signal78.638321
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.446726
NF1.000000
HZ4
Tau0.015000

Slide: Finlayson_561-4_high-R:FR-bud-n_Rep1_ATH1

Add to Slide Selection

Get the data!

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

Summary Information

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

  • Extract 1 ("Finlayson_561-4_high-R:FR-bud-n_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:

BioSource 1 Information

BioSource Name: Finlayson_561-4_high-R:FR-bud-n_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Col-8 (Columbia)
Stock Code: CS60000
Genetic Background: Col-0
Age: 16 days after sowing
Growth Conditions:
ProtocolPlants were grown individually in 26 by 60 mm tubes and watered and fertilized optimally. Plants were grown in a split growth chamber (providing \ uniform temperature and PPFD but allowing for differential R:FR) with 18 h photoperiods (185 microMoles m-2 s-1 PPFD provided by T12 VHO CW fluorescent lamp\ s) and 24oC/18oC day/night temperatures.
stratification3 days at 4oC.
Temperature22.5°C average, 24 °C day, 18 °C night
Humidity50 % average, 50 % day, 50 % night
Lighting(Source: Fluorescent. Wavelength: White)
MediumHoagland ampapos;s No.2 basal salt mixture
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)6.00
Tissue: Rosette axillary bud n
Other Information:
treatment Two separate experiments were conducted to evaluate the effects of R:FR on transcriptome changes in the uppermost rosette bud (bud n) and the axillary bud in the axil of the third leaf from the top (bud n-2). WT Col-0 (CS60000) was used as the experimental material. Plants were grown individually in 26 by 60 mm tubes and watered and fertilized optimally. Plants were grown in a split growth chamber (providing uniform temperature and PPFD but\ allowing for differential R:FR) with 18 h photoperiods (185 microMoles m-2 s-1 PPFD provided by T12 VHO CW fluorescent lamps) and 24oC/18oC day/night temperatures. One day after sowing the R:FR was reduced on both sides of the chamber from 3.5 to 0.08 using FR LEDs fixed in clear overhead arrays. Prior to anthesis the plants were matched and split into two treatment groups. In experiment 1 the FR source for one of the groups was switched off at 12:00 pm on the\ day of anthesis, causing the R:FR to increase to 3.5. Unelongated axillary buds in the axil of the uppermost leaves (approx. 2.5 mm long) were harvested for RNA preparation from both groups (low and transiently increased R:FR) 3 h after changing the R:FR. Each treatment was composed of three biological replicates, each containing buds from about 15-18 plants. Experiment 2 was conducted exactly the same as experiment 1, except the R:FR was altered 3 days after \ anthesis and the unelongated axillary buds in the axils of the third leaves down (approx. 1 mm long) were harvested for RNA preparation. This sample was derived from plants grown under low R:FR from 1 day after sowing until the first day of anthesis. At 12:00 on the day of anthesis, the plants were exposed to high R:FR for 3 h and rosette axillary bud n was harvested.

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:0.701203
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-ratio1.095407
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.956827
Spike_AFFX-r2-Bs-dap_5_signal32.681782
NoiseAvg:3.41,Std:0.14,Min:3.1,Max:4.0
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal19.016106
#P14206
Spike_AFFX-r2-Bs-phe_M_signal10.210974
Corner-Avg:11303,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal110.207657
Spike_AFFX-r2-Ec-bioB_3_signal103.880638
Spike_AFFX-r2-Bs-lys_M_signal7.338941
Spike_AFFX-r2-P1-cre_3_signal4927.938477
Spike_AFFX-r2-Bs-lys_3-5-ratio0.458661
Spike_AFFX-r2-Bs-dap_M_signal52.073540
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio1.619974
Spike_AFFX-r2-Ec-bioB_avg-signal107.552063
Spike_AFFX-r2-Bs-thr_avg-signal24.328346
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal964.743530
Spike_AFFX-r2-Bs-phe_5_signal14.671048
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1663.734741
RawQ3.067341
Spike_AFFX-r2-Bs-lys_5_signal12.377646
Signal(A)4.959124
%A36.085049
Signal(All)143.600739
Corner+Avg:177,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal334.096069
Spike_AFFX-r2-Bs-lys_3_detectionA
Spike_AFFX-r2-Bs-phe_3_signal14.954337
Spike_AFFX-r2-Ec-bioD_avg-signal1314.239136
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionM
%P62.279701
Spike_AFFX-r2-Bs-lys_avg-signal8.464577
Spike_AFFX-r2-P1-cre_avg-signal4713.333984
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionA
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.635248
Spike_AFFX-r2-Bs-thr_3_signal30.805605
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionM
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal13.278786
Spike_AFFX-r2-Bs-dap_3_signal85.154839
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.724536
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal360.891998
#M373
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal5.677142
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio0.925751
Spike_AFFX-r2-Bs-thr_M_signal23.163328
Signal(P)227.198227
Spike_AFFX-r2-Bs-phe_3-5-ratio1.019309
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:7183,Count:9
Spike_AFFX-r2-P1-cre_5_signal4498.729004
Spike_AFFX-r2-Bs-phe_M_detectionP
#A8231
Signal(M)19.132307
BackgroundAvg:74.89,Std:0.46,Min:74.0,Max:76.3
Spike_AFFX-r2-Ec-bioC_avg-signal347.494019
Spike_AFFX-r2-Bs-dap_avg-signal56.636719
Spike_AFFX-r2-Bs-dap_3-5-ratio2.605575
Spike_AFFX-r2-Ec-bioB_5_signal108.567894
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.701203
NF1.000000
HZ4
Tau0.015000

Slide: Finlayson_561-3_low-R:FR-bud-n_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 ("Finlayson_561-3_low-R:FR-bud-n_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:

BioSource 1 Information

BioSource Name: Finlayson_561-3_low-R:FR-bud-n_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: Col-8 (Columbia)
Stock Code: CS60000
Genetic Background: Col-0
Age: 16 days after sowing
Growth Conditions:
ProtocolPlants were grown individually in 26 by 60 mm tubes and watered and fertilized optimally. Plants were grown in a split growth chamber (providing \ uniform temperature and PPFD but allowing for differential R:FR) with 18 h photoperiods (185 microMoles m-2 s-1 PPFD provided by T12 VHO CW fluorescent lamp\ s) and 24oC/18oC day/night temperatures.
stratification3 days at 4oC.
Temperature22.5°C average, 24 °C day, 18 °C night
Humidity50 % average, 50 % day, 50 % night
Lighting(Source: Fluorescent. Wavelength: White)
MediumHoagland ampapos;s No.2 basal salt mixture
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)6.00
Tissue: Rosette axillary bud n
Other Information:
treatment Two separate experiments were conducted to evaluate the effects of R:FR on transcriptome changes in the uppermost rosette bud (bud n) and the axillary bud in the axil of the third leaf from the top (bud n-2). WT Col-0 (CS60000) was used as the experimental material. Plants were grown individually in 26 by 60 mm tubes and watered and fertilized optimally. Plants were grown in a split growth chamber (providing uniform temperature and PPFD but allowing for differential R:FR) with 18 h photoperiods (185 microMoles m-2 s-1 PPFD provided by T12 VHO CW fluorescent lamps) and 24oC/18oC day/night temperatures. One day after sowing the R:FR was reduced on both sides of the chamber from 3.5 to 0.08 using FR LEDs fixed in clear overhead arrays. Prior to anthesis the plants were matched and split into two treatment groups. In experiment 1 the FR source for one of the groups was switched off at 12:00 pm on the\ day of anthesis, causing the R:FR to increase to 3.5. Unelongated axillary buds in the axil of the uppermost leaves (approx. 2.5 mm long) were harvested for RNA preparation from both groups (low and transiently increased R:FR) 3 h after changing the R:FR. Each treatment was composed of three biological replicates, each containing buds from about 15-18 plants. Experiment 2 was conducted exactly the same as experiment 1, except the R:FR was altered 3 days after \ anthesis and the unelongated axillary buds in the axils of the third leaves down (approx. 1 mm long) were harvested for RNA preparation.This sample was derived from plants maintained under low R:FR from 1 day after sowing until harvest.

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:0.4119
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-ratio1.158773
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.151236
Spike_AFFX-r2-Bs-dap_5_signal43.570808
NoiseAvg:3.55,Std:0.08,Min:3.3,Max:3.8
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal16.381029
#P15008
Spike_AFFX-r2-Bs-phe_M_signal11.624488
Corner-Avg:13231,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal103.682701
Spike_AFFX-r2-Ec-bioB_3_signal90.854820
Spike_AFFX-r2-Bs-lys_M_signal7.520740
Spike_AFFX-r2-P1-cre_3_signal4355.300781
Spike_AFFX-r2-Bs-lys_3-5-ratio1.178997
Spike_AFFX-r2-Bs-dap_M_signal84.187904
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.359752
Spike_AFFX-r2-Ec-bioB_avg-signal91.152290
Spike_AFFX-r2-Bs-thr_avg-signal30.044149
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal875.555481
Spike_AFFX-r2-Bs-phe_5_signal14.786072
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1320.569702
RawQ3.051411
Spike_AFFX-r2-Bs-lys_5_signal12.213363
Signal(A)3.101057
%A32.889084
Signal(All)140.008896
Corner+Avg:214,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal304.805176
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal16.673134
Spike_AFFX-r2-Ec-bioD_avg-signal1098.062622
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P65.795700
Spike_AFFX-r2-Bs-lys_avg-signal11.377875
Spike_AFFX-r2-P1-cre_avg-signal4056.923340
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.315213
Spike_AFFX-r2-Bs-thr_3_signal38.655174
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal14.361232
Spike_AFFX-r2-Bs-dap_3_signal140.291016
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.508265
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal295.952576
#M300
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal14.399521
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.029912
Spike_AFFX-r2-Bs-thr_M_signal35.096249
Signal(P)211.009201
Spike_AFFX-r2-Bs-phe_3-5-ratio1.127624
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:8797,Count:9
Spike_AFFX-r2-P1-cre_5_signal3758.545654
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7502
Signal(M)11.709030
BackgroundAvg:76.23,Std:0.49,Min:74.9,Max:77.8
Spike_AFFX-r2-Ec-bioC_avg-signal300.378876
Spike_AFFX-r2-Bs-dap_avg-signal89.349907
Spike_AFFX-r2-Bs-dap_3-5-ratio3.219840
Spike_AFFX-r2-Ec-bioB_5_signal78.919365
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.411900
NF1.000000
HZ4
Tau0.015000

Slide: Finlayson_561-2_low-R:FR-bud-n_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 ("Finlayson_561-2_low-R:FR-bud-n_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:

BioSource 1 Information

BioSource Name: Finlayson_561-2_low-R:FR-bud-n_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Col-8 (Columbia)
Stock Code: CS60000
Genetic Background: Col-0
Age: 16 days after sowing
Growth Conditions:
ProtocolPlants were grown individually in 26 by 60 mm tubes and watered and fertilized optimally. Plants were grown in a split growth chamber (providing \ uniform temperature and PPFD but allowing for differential R:FR) with 18 h photoperiods (185 microMoles m-2 s-1 PPFD provided by T12 VHO CW fluorescent lamp\ s) and 24oC/18oC day/night temperatures.
stratification3 days at 4oC.
Temperature22.5°C average, 24 °C day, 18 °C night
Humidity50 % average, 50 % day, 50 % night
Lighting(Source: Fluorescent. Wavelength: White)
MediumHoagland ampapos;s No.2 basal salt mixture
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)6.00
Tissue: Rosette axillary bud n
Other Information:
treatment Two separate experiments were conducted to evaluate the effects of R:FR on transcriptome changes in the uppermost rosette bud (bud n) and the axillary bud in the axil of the third leaf from the top (bud n-2). WT Col-0 (CS60000) was used as the experimental material. Plants were grown individually in 26 by 60 mm tubes and watered and fertilized optimally. Plants were grown in a split growth chamber (providing uniform temperature and PPFD but allowing for differential R:FR) with 18 h photoperiods (185 microMoles m-2 s-1 PPFD provided by T12 VHO CW fluorescent lamps) and 24oC/18oC day/night temperatures. One day after sowing the R:FR was reduced on both sides of the chamber from 3.5 to 0.08 using FR LEDs fixed in clear overhead arrays. Prior to anthesis the plants were matched and split into two treatment groups. In experiment 1 the FR source for one of the groups was switched off at 12:00 pm on the\ day of anthesis, causing the R:FR to increase to 3.5. Unelongated axillary buds in the axil of the uppermost leaves (approx. 2.5 mm long) were harvested for RNA preparation from both groups (low and transiently increased R:FR) 3 h after changing the R:FR. Each treatment was composed of three biological replicates, each containing buds from about 15-18 plants. Experiment 2 was conducted exactly the same as experiment 1, except the R:FR was altered 3 days after \ anthesis and the unelongated axillary buds in the axils of the third leaves down (approx. 1 mm long) were harvested for RNA preparation.This sample was derived from plants maintained under low R:FR from 1 day after sowing until harvest.

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:0.63089
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-ratio1.195114
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.880745
Spike_AFFX-r2-Bs-dap_5_signal60.784771
NoiseAvg:2.99,Std:0.09,Min:2.8,Max:3.2
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal14.525399
#P14474
Spike_AFFX-r2-Bs-phe_M_signal16.520651
Corner-Avg:11272,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal132.738739
Spike_AFFX-r2-Ec-bioB_3_signal90.921951
Spike_AFFX-r2-Bs-lys_M_signal13.541375
Spike_AFFX-r2-P1-cre_3_signal4835.410156
Spike_AFFX-r2-Bs-lys_3-5-ratio1.235845
Spike_AFFX-r2-Bs-dap_M_signal86.945061
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio5.602851
Spike_AFFX-r2-Ec-bioB_avg-signal108.964561
Spike_AFFX-r2-Bs-thr_avg-signal47.763241
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal1011.550049
Spike_AFFX-r2-Bs-phe_5_signal17.926924
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1633.491333
RawQ2.786513
Spike_AFFX-r2-Bs-lys_5_signal14.365692
Signal(A)4.051756
%A35.037266
Signal(All)142.922729
Corner+Avg:189,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal363.334473
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal15.849328
Spike_AFFX-r2-Ec-bioD_avg-signal1322.520752
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P63.454624
Spike_AFFX-r2-Bs-lys_avg-signal15.220279
Spike_AFFX-r2-P1-cre_avg-signal4440.695313
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.508111
Spike_AFFX-r2-Bs-thr_3_signal81.383644
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal16.765635
Spike_AFFX-r2-Bs-dap_3_signal165.757278
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.614840
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal358.568909
#M344
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal17.753767
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.013291
Spike_AFFX-r2-Bs-thr_M_signal47.380672
Signal(P)222.635452
Spike_AFFX-r2-Bs-phe_3-5-ratio0.884108
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:7905,Count:9
Spike_AFFX-r2-P1-cre_5_signal4045.980713
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7992
Signal(M)15.291998
BackgroundAvg:65.54,Std:0.36,Min:64.6,Max:66.7
Spike_AFFX-r2-Ec-bioC_avg-signal360.951691
Spike_AFFX-r2-Bs-dap_avg-signal104.495697
Spike_AFFX-r2-Bs-dap_3-5-ratio2.726954
Spike_AFFX-r2-Ec-bioB_5_signal103.232994
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.630890
NF1.000000
HZ4
Tau0.015000

Slide: Finlayson_561-1_low-R:FR-bud-n_Rep1_ATH1

Add to Slide Selection

Get the data!

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

Summary Information

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

  • Extract 1 ("Finlayson_561-1_low-R:FR-bud-n_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:

BioSource 1 Information

BioSource Name: Finlayson_561-1_low-R:FR-bud-n_Rep1_ATH1
Organism: Arabidopsis thaliana
Alias: Col-8 (Columbia)
Stock Code: CS60000
Genetic Background: Col-0
Age: 16 days after sowing
Growth Conditions:
ProtocolPlants were grown individually in 26 by 60 mm tubes and watered and fertilized optimally. Plants were grown in a split growth chamber (providing \ uniform temperature and PPFD but allowing for differential R:FR) with 18 h photoperiods (185 microMoles m-2 s-1 PPFD provided by T12 VHO CW fluorescent lamp\ s) and 24oC/18oC day/night temperatures.
stratification3 days at 4oC.
Temperature22.5°C average, 24 °C day, 18 °C night
Humidity50 % average, 50 % day, 50 % night
Lighting(Source: Fluorescent. Wavelength: White)
MediumHoagland ampapos;s No.2 basal salt mixture
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)6.00
Tissue: Rosette axillary bud n
Additional Organism Information:
Sample DescriptionThe sample was derived from Col-0 plants differentially treated and harvested on the day of anthesis
Other Information:
treatment Two separate experiments were conducted to evaluate the effects of R:FR on transcriptome changes in the uppermost rosette bud (bud n) and the axillary bud in the axil of the third leaf from the top (bud n-2). WT Col-0 (CS60000) was used as the experimental material. Plants were grown individually in 26 by 60 mm tubes and watered and fertilized optimally. Plants were grown in a split growth chamber (providing uniform temperature and PPFD but allowing for differential R:FR) with 18 h photoperiods (185 microMoles m-2 s-1 PPFD provided by T12 VHO CW fluorescent lamps) and 24oC/18oC day/night temperatures. One day after sowing the R:FR was reduced on both sides of the chamber from 3.5 to 0.08 using FR LEDs fixed in clear overhead arrays. Prior to anthesis the plants were matched and split into two treatment groups. In experiment 1 the FR source for one of the groups was switched off at 12:00 pm on the day of anthesis, causing the R:FR to increase to 3.5. Unelongated axillary buds in the axil of the uppermost leaves (approx. 2.5 mm long) were harvested for RNA preparation from both groups (low and transiently increased R:FR) 3 h after changing the R:FR. Each treatment was composed of three biological replicates, each containing buds from about 15-18 plants. Experiment 2 was conducted exactly the same as experiment 1, except the R:FR was altered 3 days after anthesis and the unelongated axillary buds in the axils of the third leaves down (approx. 1 mm long) were harvested for RNA preparation.

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:0.443142
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-ratio1.209704
Spike_AFFX-r2-Ec-bioB_3-5-ratio1.233043
Spike_AFFX-r2-Bs-dap_5_signal52.489933
NoiseAvg:3.80,Std:0.35,Min:3.2,Max:5.5
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal13.145200
#P14838
Spike_AFFX-r2-Bs-phe_M_signal25.626610
Corner-Avg:14124,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal106.639542
Spike_AFFX-r2-Ec-bioB_3_signal91.657166
Spike_AFFX-r2-Bs-lys_M_signal15.228526
Spike_AFFX-r2-P1-cre_3_signal3837.126221
Spike_AFFX-r2-Bs-lys_3-5-ratio2.969074
Spike_AFFX-r2-Bs-dap_M_signal109.290176
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio4.677653
Spike_AFFX-r2-Ec-bioB_avg-signal90.876945
Spike_AFFX-r2-Bs-thr_avg-signal37.367847
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal834.994995
Spike_AFFX-r2-Bs-phe_5_signal20.578751
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1318.730591
RawQ3.044265
Spike_AFFX-r2-Bs-lys_5_signal9.181778
Signal(A)3.390856
%A33.437088
Signal(All)140.045868
Corner+Avg:232,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal296.905426
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal16.148338
Spike_AFFX-r2-Ec-bioD_avg-signal1076.862793
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P65.050415
Spike_AFFX-r2-Bs-lys_avg-signal17.223894
Spike_AFFX-r2-P1-cre_avg-signal3504.540039
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.512495
Spike_AFFX-r2-Bs-thr_3_signal61.488682
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal20.784567
Spike_AFFX-r2-Bs-dap_3_signal164.035309
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.579328
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal291.149933
#M345
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal27.261377
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.019768
Spike_AFFX-r2-Bs-thr_M_signal37.469654
Signal(P)213.247147
Spike_AFFX-r2-Bs-phe_3-5-ratio0.784709
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:9345,Count:9
Spike_AFFX-r2-P1-cre_5_signal3171.953857
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7627
Signal(M)12.819895
BackgroundAvg:72.72,Std:0.84,Min:70.4,Max:75.0
Spike_AFFX-r2-Ec-bioC_avg-signal294.027679
Spike_AFFX-r2-Bs-dap_avg-signal108.605141
Spike_AFFX-r2-Bs-dap_3-5-ratio3.125081
Spike_AFFX-r2-Ec-bioB_5_signal74.334114
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.443142
NF1.000000
HZ4
Tau0.015000

Slide: Finlayson_561-11_high-R:FR-bud-n-2_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 ("Finlayson_561-11_high-R:FR-bud-n-2_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:

BioSource 1 Information

BioSource Name: Finlayson_561-11_high-R:FR-bud-n-2_Rep2_ATH1
Organism: Arabidopsis thaliana
Alias: Col-8 (Columbia)
Stock Code: CS60000
Genetic Background: Col-0
Age: 18
Growth Conditions:
ProtocolPlants were grown individually in 26 by 60 mm tubes and watered and fertilized optimally. Plants were grown in a split growth chamber (providing \ uniform temperature and PPFD but allowing for differential R:FR) with 18 h photoperiods (185 microMoles m-2 s-1 PPFD provided by T12 VHO CW fluorescent lamp\ s) and 24oC/18oC day/night temperatures.
stratification3 days at 4oC.
Temperature22.5°C average, 24 °C day, 18 °C night
Humidity50 % average, 50 % day, 50 % night
Lighting(Source: Fluorescent. Wavelength: White)
MediumHoagland ampapos;s No.2 basal salt mixture
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)6.00
Tissue: Rosette axillary bud n-2
Other Information:
treatment Two separate experiments were conducted to evaluate the effects of R:FR on transcriptome changes in the uppermost rosette bud (bud n) and the axillary bud in the axil of the third leaf from the top (bud n-2). WT Col-0 (CS60000) was used as the experimental material. Plants were grown individually in 26 by 60 mm tubes and watered and fertilized optimally. Plants were grown in a split growth chamber (providing uniform temperature and PPFD but\ allowing for differential R:FR) with 18 h photoperiods (185 microMoles m-2 s-1 PPFD provided by T12 VHO CW fluorescent lamps) and 24oC/18oC day/night temperatures. One day after sowing the R:FR was reduced on both sides of the chamber from 3.5 to 0.08 using FR LEDs fixed in clear overhead arrays. Prior to anthesis the plants were matched and split into two treatment groups. In experiment 1 the FR source for one of the groups was switched off at 12:00 pm on the\ day of anthesis, causing the R:FR to increase to 3.5. Unelongated axillary buds in the axil of the uppermost leaves (approx. 2.5 mm long) were harvested for RNA preparation from both groups (low and transiently increased R:FR) 3 h after changing the R:FR. Each treatment was composed of three biological replicates, each containing buds from about 15-18 plants. Experiment 2 was conducted exactly the same as experiment 1, except the R:FR was altered 3 days after \ anthesis and the unelongated axillary buds in the axils of the third leaves down (approx. 1 mm long) were harvested for RNA preparation.This sample was derived from plants grown under low R:FR from 1 day after sowing until 3 days after anthesis. At 12:00 on the third day after anthesis, the plants were exposed to high R:FR for 3 h and rosette axillary bud n-2 was harvested.

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:0.738066
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-ratio1.302028
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.954751
Spike_AFFX-r2-Bs-dap_5_signal37.757343
NoiseAvg:2.95,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_signal17.657232
#P14709
Spike_AFFX-r2-Bs-phe_M_signal15.318616
Corner-Avg:15110,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal112.790161
Spike_AFFX-r2-Ec-bioB_3_signal82.534096
Spike_AFFX-r2-Bs-lys_M_signal6.613433
Spike_AFFX-r2-P1-cre_3_signal5899.037598
Spike_AFFX-r2-Bs-lys_3-5-ratio1.242545
Spike_AFFX-r2-Bs-dap_M_signal63.963490
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio2.145540
Spike_AFFX-r2-Ec-bioB_avg-signal93.923302
Spike_AFFX-r2-Bs-thr_avg-signal26.154505
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal917.005493
Spike_AFFX-r2-Bs-phe_5_signal21.171436
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1373.442505
RawQ2.684576
Spike_AFFX-r2-Bs-lys_5_signal14.772696
Signal(A)5.364212
%A33.761509
Signal(All)142.946518
Corner+Avg:235,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal288.692383
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal14.890243
Spike_AFFX-r2-Ec-bioD_avg-signal1145.223999
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P64.484879
Spike_AFFX-r2-Bs-lys_avg-signal13.247292
Spike_AFFX-r2-P1-cre_avg-signal5214.845703
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionA
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.753617
Spike_AFFX-r2-Bs-thr_3_signal37.884296
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal17.126764
Spike_AFFX-r2-Bs-dap_3_signal116.453255
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.497747
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal237.153717
#M400
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal18.355745
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.217322
Spike_AFFX-r2-Bs-thr_M_signal22.921989
Signal(P)218.372131
Spike_AFFX-r2-Bs-phe_3-5-ratio0.703318
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:12464,Count:9
Spike_AFFX-r2-P1-cre_5_signal4530.654297
Spike_AFFX-r2-Bs-phe_M_detectionP
#A7701
Signal(M)18.161486
BackgroundAvg:64.12,Std:0.41,Min:63.1,Max:65.6
Spike_AFFX-r2-Ec-bioC_avg-signal262.923035
Spike_AFFX-r2-Bs-dap_avg-signal72.724693
Spike_AFFX-r2-Bs-dap_3-5-ratio3.084255
Spike_AFFX-r2-Ec-bioB_5_signal86.445641
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.738066
NF1.000000
HZ4
Tau0.015000

Slide: Finlayson_561-12_high-R:FR-bud-n-2_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 ("Finlayson_561-12_high-R:FR-bud-n-2_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:

BioSource 1 Information

BioSource Name: Finlayson_561-12_high-R:FR-bud-n-2_Rep3_ATH1
Organism: Arabidopsis thaliana
Alias: Col-8 (Columbia)
Stock Code: CS60000
Genetic Background: Col-0
Age: 18
Growth Conditions:
ProtocolPlants were grown individually in 26 by 60 mm tubes and watered and fertilized optimally. Plants were grown in a split growth chamber (providing \ uniform temperature and PPFD but allowing for differential R:FR) with 18 h photoperiods (185 microMoles m-2 s-1 PPFD provided by T12 VHO CW fluorescent lamp\ s) and 24oC/18oC day/night temperatures.
stratification3 days at 4oC.
Temperature22.5°C average, 24 °C day, 18 °C night
Humidity50 % average, 50 % day, 50 % night
Lighting(Source: Fluorescent. Wavelength: White)
MediumHoagland ampapos;s No.2 basal salt mixture
Developmental Stage:
Growth Stage(Source: Paradigm Genetics)6.00
Tissue: Rosette axillary bud n-2
Other Information:
treatment Two separate experiments were conducted to evaluate the effects of R:FR on transcriptome changes in the uppermost rosette bud (bud n) and the axillary bud in the axil of the third leaf from the top (bud n-2). WT Col-0 (CS60000) was used as the experimental material. Plants were grown individually in 26 by 60 mm tubes and watered and fertilized optimally. Plants were grown in a split growth chamber (providing uniform temperature and PPFD but\ allowing for differential R:FR) with 18 h photoperiods (185 microMoles m-2 s-1 PPFD provided by T12 VHO CW fluorescent lamps) and 24oC/18oC day/night temperatures. One day after sowing the R:FR was reduced on both sides of the chamber from 3.5 to 0.08 using FR LEDs fixed in clear overhead arrays. Prior to anthesis the plants were matched and split into two treatment groups. In experiment 1 the FR source for one of the groups was switched off at 12:00 pm on the\ day of anthesis, causing the R:FR to increase to 3.5. Unelongated axillary buds in the axil of the uppermost leaves (approx. 2.5 mm long) were harvested for RNA preparation from both groups (low and transiently increased R:FR) 3 h after changing the R:FR. Each treatment was composed of three biological replicates, each containing buds from about 15-18 plants. Experiment 2 was conducted exactly the same as experiment 1, except the R:FR was altered 3 days after \ anthesis and the unelongated axillary buds in the axils of the third leaves down (approx. 1 mm long) were harvested for RNA preparation.This sample was derived from plants grown under low R:FR from 1 day after sowing until 3 days after anthesis. At 12:00 on the third day after anthesis, the plants were exposed to high R:FR for 3 h and rosette axillary bud n-2 was harvested.

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:0.369161
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-ratio1.064155
Spike_AFFX-r2-Ec-bioB_3-5-ratio0.888292
Spike_AFFX-r2-Bs-dap_5_signal28.280630
NoiseAvg:3.84,Std:0.14,Min:3.4,Max:4.3
Control DirectionAntisense
Spike_AFFX-r2-Ec-bioB_5_detectionP
Spike_AFFX-r2-Ec-bioB_3_detectionP
Spike_AFFX-r2-Bs-thr_5_signal12.673808
#P15727
Spike_AFFX-r2-Bs-phe_M_signal10.255529
Corner-Avg:13753,Count:32
Spike_AFFX-r2-P1-cre_3_detectionP
Spike_AFFX-r2-Ec-bioB_M_signal78.636467
Spike_AFFX-r2-Ec-bioB_3_signal58.945560
Spike_AFFX-r2-Bs-lys_M_signal7.132310
Spike_AFFX-r2-P1-cre_3_signal3225.378418
Spike_AFFX-r2-Bs-lys_3-5-ratio1.787849
Spike_AFFX-r2-Bs-dap_M_signal67.741280
Spike_AFFX-r2-Bs-thr_M_detectionP
Probe Pair Threshold1
Spike_AFFX-r2-Bs-thr_3-5-ratio1.605033
Spike_AFFX-r2-Ec-bioB_avg-signal67.980110
Spike_AFFX-r2-Bs-thr_avg-signal18.444124
Spike_AFFX-r2-Bs-thr_5_detectionP
Spike_AFFX-r2-Bs-dap_3_detectionP
Spike_AFFX-r2-Ec-bioD_5_signal696.524414
Spike_AFFX-r2-Bs-phe_5_signal13.646887
Spike_AFFX-r2-P1-cre_5_detectionP
Spike_AFFX-r2-Ec-bioD_3_signal1064.609619
RawQ3.182576
Spike_AFFX-r2-Bs-lys_5_signal10.276057
Signal(A)3.355514
%A29.535292
Signal(All)134.336334
Corner+Avg:221,Count:32
Spike_AFFX-r2-Ec-bioD_5_detectionP
Spike_AFFX-r2-Ec-bioC_3_signal228.720474
Spike_AFFX-r2-Bs-lys_3_detectionP
Spike_AFFX-r2-Bs-phe_3_signal18.475399
Spike_AFFX-r2-Ec-bioD_avg-signal880.567017
Spike_AFFX-r2-Bs-dap_5_detectionP
Spike_AFFX-r2-Bs-phe_5_detectionP
%P68.947830
Spike_AFFX-r2-Bs-lys_avg-signal11.926804
Spike_AFFX-r2-P1-cre_avg-signal3128.153809
Spike_AFFX-r2-Ec-bioB_M_detectionP
Spike_AFFX-r2-Bs-lys_M_detectionP
#Probe Sets Exceeding Probe Pair Threshold22810
%M1.516879
Spike_AFFX-r2-Bs-thr_3_signal20.341879
Spike_AFFX-r2-Ec-bioC_5_detectionP
Spike_AFFX-r2-Bs-phe_3_detectionP
Spike_AFFX-r2-Ec-bioC_3_detectionP
Spike_AFFX-r2-Bs-phe_avg-signal14.125938
Spike_AFFX-r2-Bs-dap_3_signal114.195404
Spike_AFFX-r2-Ec-bioD_3-5-ratio1.528460
Spike_AFFX-r2-Ec-bioD_3_detectionP
Spike_AFFX-r2-Ec-bioC_5_signal207.798950
#M346
Spike_AFFX-r2-Bs-lys_5_detectionP
Spike_AFFX-r2-Bs-lys_3_signal18.372044
Spike_AFFX-r2-Bs-dap_M_detectionP
Spike_AFFX-r2-Ec-bioC_3-5-ratio1.100682
Spike_AFFX-r2-Bs-thr_M_signal22.316687
Signal(P)193.149994
Spike_AFFX-r2-Bs-phe_3-5-ratio1.353818
Spike_AFFX-r2-Bs-thr_3_detectionP
Central-Avg:10728,Count:9
Spike_AFFX-r2-P1-cre_5_signal3030.929443
Spike_AFFX-r2-Bs-phe_M_detectionP
#A6737
Signal(M)11.375132
BackgroundAvg:81.74,Std:0.81,Min:79.9,Max:84.0
Spike_AFFX-r2-Ec-bioC_avg-signal218.259705
Spike_AFFX-r2-Bs-dap_avg-signal70.072433
Spike_AFFX-r2-Bs-dap_3-5-ratio4.037937
Spike_AFFX-r2-Ec-bioB_5_signal66.358292
ScaleMaskAll
BG2
VZ4
TGT100
Alpha10.040000
Alpha20.060000
SF0.369161
NF1.000000
HZ4
Tau0.015000


Problems? Comments? Suggestions? Contact the Affymetrix Team