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Status |
Public on Jun 12, 2017 |
Title |
ML06_PFC-Ctrl6 |
Sample type |
RNA |
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Source name |
Home caged animal
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Organism |
Mus musculus |
Characteristics |
tissue: prefrontal cortex genotype/variation: wild type protocol: Home caged animal
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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).
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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.
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Scan protocol |
Genechips were scanned using an Affymetrix Gene Chip Scanner 3000.
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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.
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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 |
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