|
Status |
Public on Jul 31, 2015 |
Title |
Subject 1 Hippocampus |
Sample type |
SRA |
|
|
Source name |
Brain
|
Organism |
Macaca mulatta |
Characteristics |
brain region: hippocampus age: 4 years gender: male
|
Extracted molecule |
total RNA |
Extraction protocol |
Forty brain region specific micropunches are collected from each brain region directly into 350 μL of Qiazol Lysis Reagent before total RNA isolation using the miRNeasy Mini Kit. Sequencing libraries were prepared using the standard Illumina TruSeq RNA v2 protocol
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina Genome Analyzer IIx |
|
|
Data processing |
Basecalls performed using CASAVA version 1.8.2 Reads were mapped to the Macaca mulatta reference genome using TopHat version 2.0.10 with Bowtie2 version 2.1.0 Cufflinks was utilized to quantify the expression level in FPKM Non-default parameters upper quartile normalization (-N), bias detection and correction (-b), and rRNA/tRNA mask (-M) were utilized. Genome_build: Mmul_1 Supplementary_files_format_and_content: fpkm_tracking files were generated from Cufflink version 2.1.1
|
|
|
Submission date |
Jan 08, 2015 |
Last update date |
May 15, 2019 |
Contact name |
Clifton Lee Dalgard |
E-mail(s) |
cdalgard@usuhs.edu
|
Organization name |
Uniformed Services University
|
Department |
Anatomy Physiology & Genetics
|
Lab |
Dalgard
|
Street address |
4301 Jones Bridge Road B2038
|
City |
Bethesda |
State/province |
Maryland |
ZIP/Postal code |
20814 |
Country |
USA |
|
|
Platform ID |
GPL13766 |
Series (1) |
GSE64797 |
A novel analytical brain block tool to enable functional annotation of discriminatory transcript biomarkers among discrete regions of the fronto-limbic circuit in primate brain |
|
Relations |
BioSample |
SAMN03278598 |
SRA |
SRX834486 |