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Sample GSM261041 Query DataSets for GSM261041
Status Public on Apr 29, 2009
Title Dicktoo-deacclimation-rep3
Sample type RNA
Source name JS37
Organism Hordeum vulgare
Characteristics Dicktoo-deacclimation
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 Dicktoo-deacclimation
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)
GSE10329 Low temperature stress in cv. Dicktoo

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 169.366 P 0.0336773
AFFX-BioB-M_at 120.272 P 0.00844047
AFFX-BioB-3_at 134.024 P 0.0151826
AFFX-BioC-5_at 292.375 P 0.000753643
AFFX-BioC-3_at 224.561 P 0.00255552
AFFX-BioDn-5_at 271.022 P 0.00110197
AFFX-BioDn-3_at 2191.7 P 0.000224668
AFFX-CreX-5_at 2930.15 P 4.42873e-05
AFFX-CreX-3_at 5052.18 P 4.42873e-05
AFFX-DapX-5_at 26.4094 A 0.382599
AFFX-DapX-M_at 44.4967 A 0.102165
AFFX-DapX-3_at 8.80367 A 0.897835
AFFX-LysX-5_at 3.33081 A 0.783476
AFFX-LysX-M_at 56.9197 A 0.544587
AFFX-LysX-3_at 12.586 A 0.574038
AFFX-PheX-5_at 7.50688 A 0.699394
AFFX-PheX-M_at 3.37297 A 0.876428
AFFX-PheX-3_at 14.9692 A 0.794268
AFFX-ThrX-5_at 6.37786 A 0.941556
AFFX-ThrX-M_at 38.6251 A 0.313723

Total number of rows: 22840

Table truncated, full table size 788 Kbytes.

Supplementary file Size Download File type/resource
GSM261041.CEL.gz 3.6 Mb (ftp)(http) CEL
GSM261041.CHP.gz 6.3 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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