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Sample GSM398256 Query DataSets for GSM398256
Status Public on May 13, 2009
Title Martin_3d_rep2
Sample type RNA
 
Source name Flag leaves, harvested at 3 d after drought stress
Organism Hordeum vulgare
Characteristics genotype: Martin
trait for drought tolerance: drought tolerance
tissue: flag leaves
treatment: 3 d after drought stress
Extracted molecule total RNA
Extraction protocol Seven flag leaves of a replication for each genotype were harvested at 3 d after reach 10% of AWC in the soil to constitute a single biological replicate. These flag leaves were employed for RNA isolation by using Trizol reagent following the manufacturer’s protocol (Invitrogen, Karlsruhe, Germany). The RNA was further purified using RNeasy Kit (Qiagen, Hilden, Germany). RNA yield and quality were determined by using an Agilent 2100 Bioanalyzer (Agilent Techologies, Boblingen, Germany).
Label Biotin
Label protocol 5 µg of high quality total RNA were reverse transcribed using the One-Cycle cDNA Synthesis Kit (Affymetrix, Santa Clara, CA, USA). The resulting double-stranded cDNA was used as a template to generate biotin-tagged cRNA from an in vitro transcription reaction (IVT), using Affymetrix IVT Labeling Kit as Expression Analysis Technical Manual (2001, Affymetrix)
 
Hybridization protocol Biotin-tagged cRNA was fragmented to strands of 35 to 200 bases in length, and 15 µg of fragmented cRNA was used for each hybridization. Barley 1 GeneChips were hybridized for 16 h at 45°C with rotation in a GeneChip® Hybridization Oven 640 (Affymetrix, Santa Clara, CA, USA). The arrays were washed and stained with R-phycoerythrin streptavidin in a Fluidics Station.
Scan protocol The Arrays were subsequently scanned with Affymetrix GeneChip® Scanner 3000
Description All scanned data from barley 1 GeneChips were processed by robust multiarray average (RMA) (Irizarry et al., 2003) using ArrayAssist software version 3.4 (Stratagene, La Jolla, CA, UAS)
Data processing Normalized expression values were computed from raw CEL files by first applying the RMA model of probe-specific correction of perfect match probes. The algorithm consists of three steps—a model-based background correction stage neutralizes the effects of background noise and the processing artifacts, a subsequent quantile normalization stage aligns expression values to a common scale, and finally, an iterative median polishing procedure summarizes the data and generates a single expression value for each probe set. Resulting RMA expression values were log2-transformed. Average log signal intensity values of three biological replicates for each sample were then computed and these were used for further analysis. To identify differentially expressed genes, student's t-test was applied with a maximal FDR (false discovery rate) of 5% (Benjamini-Hochberg algorithm).
RMA data for each individual Affymetrix chip not available. Thus the Sample data tables instead report MAS5.0-processed data. A table of the average, log2 RMA signal intensity values of three biological replicates for each sample is linked as a supplementary file on the GSE15970 record.
 
Submission date Apr 28, 2009
Last update date May 15, 2009
Contact name Michael Baum
E-mail(s) m.baum@cgiar.org
Phone +963 (21) 2213433
Fax +963 (21) 2213490
URL http://www.icarda.cgiar.org
Organization name ICARDA
Department BIGMP
Street address ICARDA
City Aleppo
State/province Aleppo
ZIP/Postal code 5466
Country Syria
 
Platform ID GPL1340
Series (1)
GSE15970 Differentially Expressed Genes between Drought-tolerant and Drought-sensitive Barley Genotypes

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 40.7661 P 0.0012475
AFFX-BioB-M_at 31.0527 P 5.16732e-05
AFFX-BioB-3_at 21.0863 P 0.000258358
AFFX-BioC-5_at 93.5256 P 4.42873e-05
AFFX-BioC-3_at 95.9561 P 6.02111e-05
AFFX-BioDn-5_at 207.061 P 4.42873e-05
AFFX-BioDn-3_at 520.318 P 0.00010954
AFFX-CreX-5_at 1143.04 P 4.42873e-05
AFFX-CreX-3_at 1712.71 P 5.16732e-05
AFFX-DapX-5_at 58.2868 P 7.00668e-05
AFFX-DapX-M_at 157.485 P 0.000445901
AFFX-DapX-3_at 255.414 P 8.14279e-05
AFFX-LysX-5_at 9.63877 P 0.00141043
AFFX-LysX-M_at 22.3614 A 0.0780018
AFFX-LysX-3_at 46.4726 P 0.000195116
AFFX-PheX-5_at 14.7018 P 0.000581214
AFFX-PheX-M_at 15.9573 P 0.026111
AFFX-PheX-3_at 27.0302 P 0.0020226
AFFX-ThrX-5_at 22.3212 P 0.0012475
AFFX-ThrX-M_at 36.5052 P 0.000296708

Total number of rows: 22840

Table truncated, full table size 793 Kbytes.




Supplementary file Size Download File type/resource
GSM398256.CEL.gz 2.1 Mb (ftp)(http) CEL
GSM398256.CHP.gz 123.4 Kb (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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