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Sample GSM261026 Query DataSets for GSM261026
Status Public on Apr 29, 2009
Title ABA-Early-rep3
Sample type RNA
Source name 11-ABA-E3
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 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
Phone 951 827 3808
Fax 951 827 4437
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
VALUE Signal
ABS_CALL indicating whether the transcript was present (P), absent (A), or marginal (M)

Data table
AFFX-BioB-5_at 184.152 P 0.026111
AFFX-BioB-M_at 123.029 P 0.00359458
AFFX-BioB-3_at 136.37 P 0.00401721
AFFX-BioC-5_at 321.753 P 0.000972149
AFFX-BioC-3_at 228.908 P 0.000581214
AFFX-BioDn-5_at 282.633 P 0.000581214
AFFX-BioDn-3_at 2170.44 P 0.000224668
AFFX-CreX-5_at 3169.64 P 4.42873e-05
AFFX-CreX-3_at 7505.28 P 4.42873e-05
AFFX-DapX-5_at 15.5318 A 0.58862
AFFX-DapX-M_at 6.18139 A 0.48511
AFFX-DapX-3_at 13.5674 A 0.824672
AFFX-LysX-5_at 3.74116 A 0.737173
AFFX-LysX-M_at 17.3526 A 0.672921
AFFX-LysX-3_at 29.3955 A 0.131361
AFFX-PheX-5_at 2.64339 A 0.883887
AFFX-PheX-M_at 2.34622 A 0.945787
AFFX-PheX-3_at 11.1468 A 0.834139
AFFX-ThrX-5_at 5.65654 A 0.904333
AFFX-ThrX-M_at 23.7885 A 0.300606

Total number of rows: 22840

Table truncated, full table size 789 Kbytes.

Supplementary file Size Download File type/resource
GSM261026.CEL.gz 3.5 Mb (ftp)(http) CEL
GSM261026.CHP.gz 6.2 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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