NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM1580666 Query DataSets for GSM1580666
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

Supplementary file Size Download File type/resource
GSM1580666_sub1_hip_genes.fpkm_tracking.gz 968.8 Kb (ftp)(http) FPKM_TRACKING
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap