NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM2242062 Query DataSets for GSM2242062
Status Public on Jun 12, 2017
Title ML03_PFC-Ctrl3
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 10.2951
10338002 6.51271
10338003 8.24732
10338004 7.80733
10338005 3.5267
10338006 3.75333
10338007 4.07485
10338008 4.58848
10338009 7.60967
10338010 3.57426
10338011 6.05524
10338012 3.67869
10338013 3.36823
10338014 3.47989
10338015 3.44609
10338016 7.54706
10338017 11.7201
10338018 7.00744
10338019 5.83062
10338020 7.86212

Total number of rows: 35556

Table truncated, full table size 586 Kbytes.




Supplementary file Size Download File type/resource
GSM2242062_ML03_PFC-Ctrl3_MoGene-1_0-st-v1_.CEL.gz 4.4 Mb (ftp)(http) CEL
GSM2242062_ML03_PFC-Ctrl3_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

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap