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Sample GSM2242065 Query DataSets for GSM2242065
Status Public on Jun 12, 2017
Title ML06_PFC-Ctrl6
Sample type RNA
 
Source name Home caged animal
Organism Mus musculus
Characteristics tissue: prefrontal cortex
genotype/variation: wild type
protocol: Home caged animal
Treatment protocol Mice were socialy defeated or home caged.
Growth protocol NA
Extracted molecule total RNA
Extraction protocol Trizol (Invitrogen) and RNaseazy (Qiagen) kits were used to extract total RNA according to the manufacturer's instructions.
Label Biotin
Label protocol Labeling was performed on a sample-by-sample basis according to manufacturer’s guidelines for use with the Affymetrix Mouse MoGene-1_0-st-v1 GeneChips (Affymetrix, Inc). Bioanalyzer nanochip (Agilent, Inc) and NanoDrop (ThermoFisher, Inc) were used to validate and quantitate the RNA prior to cRNA synthesis and labeling. 200 ng of total RNA was used for labeling with the Ambion WT Expression Kit (cat#4411974) and Affymetrix kit (Cat # 900652). After hybridization, the probe arrays were stained with streptavidin-phycoerythrin solution (Molecular Probes) and enhanced using an antibody solution containing 0.5 mg/mL of biotinylated anti-streptavidin (Vector Laboratories).
 
Hybridization protocol The hybridization cocktail containing the fragmented and labeled cDNAs were hybridized to Affymetrix Mouse GeneChip 1.0 ST microarrays. The microarrays were washed and stained in an Affymetrix Fluidics Station using standard Affymetrix protocols.
Scan protocol Genechips were scanned using an Affymetrix Gene Chip Scanner 3000.
Data processing Gene expression intensities were calculated using GeneChip Command Console Software (AGCC). .cel files generated by the Affymetrix AGCC program were imported in the Affymetrix Expression Console software and RMA (Robust Multichip Analysis) normalization was performed to generate the .chp files. The .chp files were normalized, log2 transformed, and summarized.
 
Submission date Jul 19, 2016
Last update date Jun 12, 2017
Contact name abdel elkahloun
E-mail(s) abdel@mail.nih.gov
Organization name nih
Street address 50 south dr
City bethesda
State/province MD
ZIP/Postal code 20892
Country USA
 
Platform ID GPL6246
Series (1)
GSE84572 Social defeat effect on mice prefrontal cortex

Data table header descriptions
ID_REF
VALUE RMA signal

Data table
ID_REF VALUE
10338001 10.2311
10338002 6.23823
10338003 8.20253
10338004 7.63463
10338005 3.62773
10338006 3.8204
10338007 4.11566
10338008 4.49333
10338009 7.50205
10338010 3.64443
10338011 5.85655
10338012 3.76991
10338013 3.40137
10338014 3.51028
10338015 3.47011
10338016 7.32764
10338017 11.7134
10338018 6.71893
10338019 5.64017
10338020 7.72298

Total number of rows: 35556

Table truncated, full table size 586 Kbytes.




Supplementary file Size Download File type/resource
GSM2242065_ML06_PFC-Ctrl6_MoGene-1_0-st-v1_.CEL.gz 4.3 Mb (ftp)(http) CEL
GSM2242065_ML06_PFC-Ctrl6_MoGene-1_0-st-v1_.rma-gene-default.chp.gz 270.9 Kb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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