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Sample GSM261060 Query DataSets for GSM261060
Status Public on Apr 29, 2009
Title Xantha b-12 Hardened rep2
Sample type RNA
Source name 10
Organism Hordeum vulgare
Characteristics Xantha b-12 Hardened
Treatment protocol When the first leaf was fully emerged the plants were treated for 6 d at 3 C, 12-h light (150 mmol m22 s21)/1 C, 12-h dark. Control plants were harvested after 8 d at 20 C. All samples were collected in the middle of the light period. This experiment was conducted three times to yield three independent biological replicates. To analyze the involvement of the photooxidative stress, seeds of wild type and mutants were imbibed for 3 h in water containing 0 (control) or 50 mM norfluorazon. The hydrated seeds were grown in a growth-controlled environment chamber as above except that light intensity was 10 mmol m22 s21 for the first 8 d and 200 mmol m22 s21 for the next 6 d. During the growth, treated plants were watered two times with 50 mM norfluorazon.For analysis of Cbf expression, treated samples were collected after 4, 8, and 24 h of cold treatment in the light.
Growth protocol Wild type and mutants were germinated in peat pots and grown in a controlled-environment chamber for 8 d at 20 C with 12-h photoperiod (300 mmol m22 s21).
Extracted molecule total RNA
Extraction protocol For RNA isolation, two methods were applied: RNA from embryo and endosperm collected during seed development was isolated by Trizol (Gibco BRL Life Technologies, Rockville, MD) and passed through an RNeasy spin column (Qiagen, Hilden, Germany) for further clean up as recommended by Affymetrix, Inc. (Affymetrix GeneChip Expression Analysis Technical Manual, Affymetric, Inc., Santa Clara, CA). For embryo and endosperm collected after imbibition, PURESCRIPT® RNA isolation kits (Gentra Systems, Inc., Minneapolis, MN) and RNeasy spin column (Qiagen, Hilden, Germany) were used. Quality of RNA was assessed on an Agilent Bioanalyzer 2100 (Agilent Technologies, Palo Alto, CA).
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 Xantha b-12 Hardened
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)
GSE10332 Transcriptome Analysis of Cold Acclimation in Barley Albina and Xantha Mutants1

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 318.139 P 0.0020226
AFFX-BioB-M_at 400.013 P 0.000126798
AFFX-BioB-3_at 212.923 P 0.00141043
AFFX-BioC-5_at 744.064 P 0.000581214
AFFX-BioC-3_at 449.364 P 0.000169227
AFFX-BioDn-5_at 562.775 P 8.14279e-05
AFFX-BioDn-3_at 4579.19 P 9.4506e-05
AFFX-CreX-5_at 8087.47 P 4.42873e-05
AFFX-CreX-3_at 13958.4 P 4.42873e-05
AFFX-DapX-5_at 29.0633 A 0.327079
AFFX-DapX-M_at 37.3722 A 0.340661
AFFX-DapX-3_at 23.3513 A 0.834139
AFFX-LysX-5_at 7.38171 A 0.631562
AFFX-LysX-M_at 24.8606 A 0.686277
AFFX-LysX-3_at 30.8968 M 0.0584438
AFFX-PheX-5_at 4.51227 A 0.966323
AFFX-PheX-M_at 20.7905 A 0.574038
AFFX-PheX-3_at 12.6851 A 0.9273
AFFX-ThrX-5_at 12.1185 A 0.852061
AFFX-ThrX-M_at 53.3783 A 0.39692

Total number of rows: 22840

Table truncated, full table size 781 Kbytes.

Supplementary file Size Download File type/resource
GSM261060.CEL.gz 3.4 Mb (ftp)(http) CEL
GSM261060.CHP.gz 6.0 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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