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Sample GSM2751042 Query DataSets for GSM2751042
Status Public on Aug 23, 2017
Title PFC CTRL female 5
Sample type SRA
 
Source name prefrontal cortex (PFC)
Organism Mus musculus
Characteristics tissue: prefrontal cortex (PFC)
gender: Female
Cause of death: NA
age: NA
pmi: NA
ph: NA
phenotype: CTRL
alcool: NA
drugs: NA
drug type: NA
medication: NA
medication type: NA
smoking: NA
rin: 8.9
Extracted molecule total RNA
Extraction protocol RNA was extracted using Trizol Reagents from flash frozen mouse brain samples. 300ng of RNA for mouse samples was used, every samples got spike-in ERCC control 1. Libraries were created using the Epicenter (Illumina) Gold Kit with ribosomal depletion
Libraries for RNAseq were created using the Epicenter (Illumina) Gold Kit with a ribosomal depletion.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Data processing FASTQ and FASTX-toolkit were used to examine the sequencing quality and trim reads. Paired-end reads for the mouse data were aligned to the MM10 and GENCODE vM2 version of the human genome and annotation using TopHat, using the comprehensive gene annotation on the reference chromosome only.
Reads were counted using HTSeq. A gene was considered the union of all its exons in any known isoforms. Any reads that fell in multiple genes were excluded from the analysis. Threshold for filtering out low expressed genes was set to >5 reads in at least 80% of the samples.
Differentially expressed genes (DEGs) between groups of samples were determined using linear models implemented in the ‘limma’ package of Bioconductor.
Genome_build: mm10
Supplementary_files_format_and_content: text file of fpkm matrix
 
Submission date Aug 22, 2017
Last update date May 15, 2019
Contact name Eddie Loh
Organization name Icahn School of Medicine at Mount Sinai
Department Department of Neuroscience
Street address 1425 Madison Avenue
City New York
ZIP/Postal code 10029
Country USA
 
Platform ID GPL13112
Series (1)
GSE102556 Sex-specific Transcriptional Signatures in Human Depression
Relations
BioSample SAMN07537475
SRA SRX3114737

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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