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Sample GSM2740638 Query DataSets for GSM2740638
Status Public on Aug 12, 2017
Title 129: Orbitofrontal (OFC; BA11)
Sample type SRA
 
Source name postmortem brain
Organism Homo sapiens
Characteristics tissue: Orbitofrontal (OFC; BA11)
gender: Female
Cause of death: Suicide
age: 32
pmi: 41
ph: 6.89
phenotype: MDD
alcool: NA
drugs: NA
drug type: NA
medication: yes
medication type: AD
smoking: yes (heavy)
rin: 8.2
Extracted molecule total RNA
Extraction protocol RNA was extracted using Trizol Reagents from human postmortem flash-frozen samples. 2.5ug of RNA for human 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 human data were aligned to the HG19 and GENCODE 2014 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: hg19
Supplementary_files_format_and_content: text file of fpkm matrix
 
Submission date Aug 11, 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 GPL11154
Series (1)
GSE102556 Sex-specific Transcriptional Signatures in Human Depression
Relations
BioSample SAMN07499832
SRA SRX3119919

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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