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Sample GSM261021 Query DataSets for GSM261021
Status Public on Apr 29, 2009
Title ABA-Control-rep1
Sample type RNA
 
Source name ABA-C1
Organism Hordeum vulgare
Characteristics ABA-Control
Treatment protocol Plants were grown at 20ºC for seven days and subject to 10 mol ABA treatment
Growth protocol Barley cv. Morex plants were grown in steam-sterilized soil in a growth chamber (Model GC-15, EGC Chagrin Falls, OH) with 12 h photopheriod (148 µmol m-2 s-1 average photosynthetic active radiation) at 23ºC, 12 h dark at 20ºC and 70% relative humidity.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated using TRIzol reagent (Invitrogen) from frozen crown samples taken from above soil tissue excluding most fully extended lamina. The protocol is available on the Arabidopsis Information Resource website at http://www.arabidopsis.org/info/2010_projects/comp_proj/AFGC/RevisedAFGC/site2RnaL.htm. RNA was purified using Qiagen RNeasy spin columns with DNase treatment. Quality was assessed by running 25-250 ng on a RNA Lab-On-A-Chip (Caliper Technologies) using an Agilent Bioanalyzer 2100 (Agilent Technologies).
Label biotin
Label protocol The BioArray High-Yield RNA Transcript Labeling Kit (Enzo Diagnostics) was then used to synthesize biotin-labeled cRNA from template cDNA by in vitro transcription.
 
Hybridization protocol 10 µg labeled, fragmented cRNA was hybridized at 45°C with rotation for 16 hours in an Affymetrix GeneChip Hybridization Oven 320 on Affymetrix Barley1 Genechip arrays. The arrays were washed and stained using streptavidin phycoerythrin on an Affymetrix Fluidics Station 400.
Scan protocol The arrays were scanned on a Hewlett-Packard GeneArray scanner.
Description ABA-Control
Data processing GCOS MAS 5
 
Submission date Jan 30, 2008
Last update date Apr 28, 2009
Contact name Livia Tommasini
E-mail(s) liviat@ucr.edu
Phone 951 827 3808
Fax 951 827 4437
URL http://plantbiology.ucr.edu/research_areas/?genomics
Organization name University of California, Riverside
Department Botany and Plant Science
Lab Tim Close
Street address 2150 Batchelor Hall
City Riverside
State/province CA
ZIP/Postal code 92521-0124
Country USA
 
Platform ID GPL1340
Series (1)
GSE10328 ABA experiment

Data table header descriptions
ID_REF
VALUE Signal
ABS_CALL indicating whether the transcript was present (P), absent (A), or marginal (M)
DETECTION P-VALUE

Data table
ID_REF VALUE ABS_CALL DETECTION P-VALUE
AFFX-BioB-5_at 115.988 M 0.050229
AFFX-BioB-M_at 87.339 P 0.0464816
AFFX-BioB-3_at 82.5344 P 0.0336773
AFFX-BioC-5_at 254.557 P 0.00141043
AFFX-BioC-3_at 205.142 P 0.00359458
AFFX-BioDn-5_at 205.616 P 0.00179591
AFFX-BioDn-3_at 1725.54 P 0.000389797
AFFX-CreX-5_at 2407.18 P 4.42873e-05
AFFX-CreX-3_at 4164.71 P 4.42873e-05
AFFX-DapX-5_at 4.95911 A 0.559354
AFFX-DapX-M_at 33.3174 A 0.0780018
AFFX-DapX-3_at 15.2303 A 0.760937
AFFX-LysX-5_at 9.82455 A 0.368438
AFFX-LysX-M_at 29.9199 A 0.686277
AFFX-LysX-3_at 14.3465 A 0.440646
AFFX-PheX-5_at 4.21681 A 0.814869
AFFX-PheX-M_at 2.45023 A 0.876428
AFFX-PheX-3_at 10.8296 A 0.910522
AFFX-ThrX-5_at 6.21186 A 0.953518
AFFX-ThrX-M_at 22.0275 A 0.313723

Total number of rows: 22840

Table truncated, full table size 788 Kbytes.




Supplementary file Size Download File type/resource
GSM261021.CEL.gz 3.7 Mb (ftp)(http) CEL
GSM261021.CHP.gz 6.5 Mb (ftp)(http) CHP
Raw data provided as supplementary file
Processed data included within Sample table
Processed data provided as supplementary file

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