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Sample GSM2242070 Query DataSets for GSM2242070
Status Public on Jun 12, 2017
Title ML11_PFC-SD9
Sample type RNA
 
Source name Social defeat animal
Organism Mus musculus
Characteristics tissue: prefrontal cortex
genotype/variation: wild type
protocol: Social defeat 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 10.4032
10338002 6.58266
10338003 8.39782
10338004 7.89562
10338005 3.52186
10338006 3.7273
10338007 4.06248
10338008 4.58832
10338009 7.73391
10338010 3.53299
10338011 6.12803
10338012 3.64905
10338013 3.33889
10338014 3.44253
10338015 3.41552
10338016 7.62475
10338017 11.9928
10338018 7.07988
10338019 5.93913
10338020 7.95063

Total number of rows: 35556

Table truncated, full table size 586 Kbytes.




Supplementary file Size Download File type/resource
GSM2242070_ML11_PFC-SD9_MoGene-1_0-st-v1_.CEL.gz 4.5 Mb (ftp)(http) CEL
GSM2242070_ML11_PFC-SD9_MoGene-1_0-st-v1_.rma-gene-default.chp.gz 270.8 Kb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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