|
Status |
Public on Aug 23, 2017 |
Title |
PFC CUS male 3 |
Sample type |
SRA |
|
|
Source name |
prefrontal cortex (PFC)
|
Organism |
Mus musculus |
Characteristics |
tissue: prefrontal cortex (PFC) gender: Male Cause of death: NA age: NA pmi: NA ph: NA phenotype: Stress alcool: NA drugs: NA drug type: NA medication: NA medication type: NA smoking: NA rin: 8.7
|
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 |
SAMN07537451 |
SRA |
SRX3114706 |