|
Status |
Public on Aug 12, 2017 |
Title |
205: Cingulate gyrus 25 (Cg25) |
Sample type |
SRA |
|
|
Source name |
postmortem brain
|
Organism |
Homo sapiens |
Characteristics |
tissue: Cingulate gyrus 25 (Cg25) gender: Female Cause of death: Suicide age: 48 pmi: 17.5 ph: 6.50 phenotype: MDD alcool: NA drugs: NA drug type: NA medication: NA medication type: NA smoking: yes (heavy) rin: 6.8
|
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 |
SAMN07500043 |
SRA |
SRX3120022 |