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Sample GSM160826 Query DataSets for GSM160826
Status Public on Feb 02, 2008
Title 19% SWC rep3
Sample type RNA
 
Source name crown
Organism Hordeum vulgare
Characteristics drought treatment
Treatment protocol Drought treatment began seven days after sowing and lasted for 21 days. Soil Water Content (SWC) was calculated relative to the field capacity of the soil by weighing at regular intervals. Control (91 % SWC) and stressed samples were collected at soil water contents of approximately 68%, 38%, 20%, 11% and 9% SWC.
Growth protocol Barley (Hordeum vulgare) 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 http://www.arabidopsis.org/info/2010_projects/comp_proj/AFGC/RevisedAFGC/site2RnaL.htm. 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 drought 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 07, 2007
Last update date Jul 13, 2007
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)
GSE6990 Barley drought stress

Data table header descriptions
ID_REF
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
ID_REF VALUE ABS_CALL DETECTION P-VALUE
Contig1198_at 0.889 P 0.646
Contig1198_x_at 0.791 P 0.44
Contig897_s_at 0.76 P 0.396
Contig149_at 1.991 P 0.02
Contig1281_at 0.974 A 0.906
Contig333_3_x_at 0.938 P 0.788
Contig333_5_at 0.933 P 0.77
Contig333_5_x_at 0.96 P 0.858
Contig333_M_at 0.846 P 0.543
Contig397_x_at 1 P 1
Contig1204_s_at 2.043 P 0.0177
Contig1536_at 0.834 P 0.517
Contig1406_at 0.959 A 0.855
Contig1483_at 1.089 P 0.683
Contig680_at 0.977 P 0.917
Contig459_s_at 0.988 P 0.957
Contig1672_s_at 1.148 P 0.505
Contig1747_at 1.202 P 0.376
Contig917_s_at 1.167 P 0.454
Contig888_at 0.657 P 0.289

Total number of rows: 22840

Table truncated, full table size 646 Kbytes.




Supplementary file Size Download File type/resource
GSM160826.CEL.gz 3.5 Mb (ftp)(http) CEL
GSM160826.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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