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Sample GSM432479 Query DataSets for GSM432479
Status Public on Jan 12, 2010
Title spleen-baclofen-5day-rep 4
Sample type RNA
 
Source name spleen-baclofen-5day
Organism Mus musculus
Characteristics strain: B6C3F1
tissue: Spleen
treatment: Baclofen
time: 5 day
Extracted molecule total RNA
Extraction protocol RNA from bone marrow was isolated using Paxgene Bone Marrow as described by the manufacturere (Qiagen). RNA from the liver and spleen was isolated using Qiagen mini columns as recomemended by the manufacturer.
Label biotin
Label protocol The Affymetrix GeneChip One-Cycle labeling kit was used for labeling according to the manufacturer's protocol.
 
Hybridization protocol Hybridization was performed according to the standard Affymetrix protocol.
Scan protocol The microarrays were scanned on a GeneChip Scanner 3000 according to standard procedures.
Description n/a
Data processing RNA expression data were analyzed using the “affy” and “limma” packages of the Bioconductor suite of microarray analysis tools available for the R statistical environment (Gentleman, 2005; Gentleman et al., 2004; Irizarry et al., 2003; R Development Core Team, 2007). Robust Microarray Analysis (RMA) background correction and quantile normalization were used to generate microarray expression values. An overall linear model was fit to the data for all sample groups and specific contrasts of interest were evaluated to generate raw p-values for each probe set on the expression array (Smyth, 2004). The Benjamini-Hochberg False Discovery Rate (FDR) method was then used to correct for multiple testing effects. Probe sets were considered to have changed qualitatively in a specific comparison if an adjusted p-value of 0.05 was obtained, their average expression intensity was above 150 in either treatment group, and they had an absolute fold change greater than 1.3.
 
Submission date Jul 22, 2009
Last update date Jan 12, 2010
Contact name Petra Koza-Taylor
E-mail(s) petra.h.koza-taylor@pfizer.com
Organization name Pfizer
Street address Eastern Point Road
City groton
State/province CT
ZIP/Postal code 06340
Country USA
 
Platform ID GPL1261
Series (1)
GSE17266 Expression data from B6C3F1 mice treated with baclofen

Data table header descriptions
ID_REF
VALUE Abundance levels generated using RMA

Data table
ID_REF VALUE
1415670_at 484.9039999
1415671_at 1247.758823
1415672_at 2395.473469
1415673_at 223.6964168
1415674_a_at 707.3660402
1415675_at 511.4521624
1415676_a_at 1486.224496
1415677_at 689.2385747
1415678_at 837.2462789
1415679_at 2336.34614
1415680_at 724.2869152
1415681_at 946.2193101
1415682_at 414.6526934
1415683_at 1353.605983
1415684_at 310.8229525
1415685_at 386.0894747
1415686_at 606.1355945
1415687_a_at 8924.80952
1415688_at 900.4268952
1415689_s_at 557.9710718

Total number of rows: 45101

Table truncated, full table size 1025 Kbytes.




Supplementary file Size Download File type/resource
GSM432479_152203mp430a11.cel.gz 3.9 Mb (ftp)(http) CEL
Processed data included within Sample table

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