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Sample GSM261024 Query DataSets for GSM261024
Status Public on Apr 29, 2009
Title ABA-Early-rep1
Sample type RNA
 
Source name ABA-E1
Organism Hordeum vulgare
Characteristics ABA-Early
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-Early
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 153.662 P 0.0396608
AFFX-BioB-M_at 90.6581 P 0.036569
AFFX-BioB-3_at 84.4108 P 0.0200219
AFFX-BioC-5_at 257.695 P 0.00110197
AFFX-BioC-3_at 203.872 P 0.00359458
AFFX-BioDn-5_at 216.892 P 0.00141043
AFFX-BioDn-3_at 1871.69 P 0.000195116
AFFX-CreX-5_at 2687.6 P 4.42873e-05
AFFX-CreX-3_at 5263.56 P 4.42873e-05
AFFX-DapX-5_at 1.99081 A 0.672921
AFFX-DapX-M_at 37.5002 A 0.108979
AFFX-DapX-3_at 12.9563 A 0.804734
AFFX-LysX-5_at 19.1506 A 0.175328
AFFX-LysX-M_at 39.9926 A 0.60308
AFFX-LysX-3_at 22.5204 A 0.455413
AFFX-PheX-5_at 4.7151 A 0.814869
AFFX-PheX-M_at 2.76146 A 0.860518
AFFX-PheX-3_at 10.658 A 0.904333
AFFX-ThrX-5_at 5.8152 A 0.932322
AFFX-ThrX-M_at 30.6233 A 0.340661

Total number of rows: 22840

Table truncated, full table size 788 Kbytes.




Supplementary file Size Download File type/resource
GSM261024.CEL.gz 3.6 Mb (ftp)(http) CEL
GSM261024.CHP.gz 6.4 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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