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Sample GSM161200 Query DataSets for GSM161200
Status Public on Feb 02, 2008
Title cold treatment rep1
Sample type RNA
Source name crown
Organism Hordeum vulgare
Characteristics cold treatment
Treatment protocol Plants were grown at 20ºC for seven days and subject to a symmetrical cycle of acclimation, cold, freeze-thaw, and deacclimation. Chilling began by decreasing the temperature overnight from 20ºC to 4ºC at a rate of 1.3ºC•h-1 and maintaining temperatures of 4 ºC in the day and 2ºC at night for 5 days. Freeze-thaw cycling lasted 12 days with day temperatures of 4ºC and night temperatures gradually decreasing from -2ºC the first night to -4ºC for three nights and -10ºC for four nights, then recovering to -4ºC for three nights and -2ºC for one night. This treatment was designed to allow daily freeze-thaw cycling and protein synthesis. Chilling conditions (4ºC day, 2ºC night) were resumed for five days, followed by deacclimation with increasing temperature to 20ºC overnight and maintaining for three days. Sampling was done at four different times, each at the 11th hour of light to avoid circadian effects: 1) before chilling treatment, 2) five days after initiation of chilling treatment, 3) eight days into freeze-thaw treatment and 4) three days into de-acclimation.
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 cold treatment
Data processing MAS files from the GCOS software were used for determining the ‘present’ gene list. Probe set intensity values above the level set by the gcRMA normalization processor were imported into GeneSpring GX 7.3 software (Silicon Genetics, CA, USA), which was used for the rest of the analysis.
Submission date Feb 08, 2007
Last update date Jul 13, 2007
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)
GSE6993 Barley low temperature stress

Data table header descriptions
VALUE GeneSpring-calculated Signal intensity
ABS_CALL the call in an absolute analysis that indicates if the transcript was present (P), absent (A), marginal (M)
DETECTION P-VALUE 'detection p-value', p-value that indicates the significance level of the detection call

Data table
Contig1198_at 1.223 P 0.254
Contig1198_x_at 1.117 P 0.509
Contig897_s_at 1.189 P 0.317
Contig149_at 1.023 P 0.896
Contig1281_at 1.306 A 0.156
Contig333_3_x_at 1.174 P 0.35
Contig333_5_at 1.182 P 0.332
Contig333_5_x_at 1.204 P 0.287
Contig333_M_at 1.151 P 0.408
Contig397_x_at 1.321 P 0.142
Contig1204_s_at 0.634 P 0.201
Contig1536_at 1.43 P 0.0818
Contig1406_at 1.093 A 0.601
Contig1483_at 0.578 P 0.175
Contig680_at 0.746 P 0.294
Contig459_s_at 0.967 P 0.853
Contig1672_s_at 0.737 P 0.283
Contig1747_at 0.979 P 0.907
Contig917_s_at 2.102 P 0.00987
Contig888_at 1.1 P 0.57

Total number of rows: 22840

Table truncated, full table size 646 Kbytes.

Supplementary file Size Download File type/resource
GSM161200.CEL.gz 3.6 Mb (ftp)(http) CEL
GSM161200.CHP.gz 6.3 Mb (ftp)(http) CHP
Raw data not provided for this record
Processed data included within Sample table

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