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Sample GSM261051 Query DataSets for GSM261051
Status Public on Apr 29, 2009
Title Bonus Control rep2
Sample type RNA
 
Source name 1
Organism Hordeum vulgare
Characteristics Bonus Control
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 Bonus 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)
GSE10332 Transcriptome Analysis of Cold Acclimation in Barley Albina and Xantha Mutants1

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 547.241 P 0.00762003
AFFX-BioB-M_at 705.744 P 0.000126798
AFFX-BioB-3_at 352.252 P 0.00141043
AFFX-BioC-5_at 1289 P 0.000340305
AFFX-BioC-3_at 810.922 P 0.000258358
AFFX-BioDn-5_at 989.216 P 0.000509415
AFFX-BioDn-3_at 7191.51 P 9.4506e-05
AFFX-CreX-5_at 12416.4 P 4.42873e-05
AFFX-CreX-3_at 25136.3 P 4.42873e-05
AFFX-DapX-5_at 37.927 A 0.368438
AFFX-DapX-M_at 55.3317 A 0.227636
AFFX-DapX-3_at 19.9404 A 0.749204
AFFX-LysX-5_at 3.36643 A 0.876428
AFFX-LysX-M_at 77.5701 A 0.5
AFFX-LysX-3_at 7.48804 A 0.686277
AFFX-PheX-5_at 20.5998 A 0.645547
AFFX-PheX-M_at 12.2077 A 0.804734
AFFX-PheX-3_at 23.7164 A 0.910522
AFFX-ThrX-5_at 9.66373 A 0.941556
AFFX-ThrX-M_at 67.7928 A 0.227636

Total number of rows: 22840

Table truncated, full table size 776 Kbytes.




Supplementary file Size Download File type/resource
GSM261051.CEL.gz 3.4 Mb (ftp)(http) CEL
GSM261051.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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