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Sample GSM2420247 Query DataSets for GSM2420247
Status Public on Mar 09, 2017
Title Chinese origin rep 3 STR
Sample type SRA
 
Source name Chinese origin_striatum
Organism Macaca mulatta
Characteristics rhesus monkey origin: Chinese origin
age (years): 11
tissue: Brain
tissue region: striatum
Growth protocol Rhesus monkeys were fed a standard stock diet plus a variety of supplemental seasonal fruits and vegetables 2 times/week throughout the course of their lifespan at the Oregon National Primate Research Center
Extracted molecule total RNA
Extraction protocol Brain regions were removed, frozen on dry ice and stored at -80⁰C. RNA was extracted using the Qiagen Rneasy Lipid Tissue Mini kit (Cat. no. 74804) Illumina TruSeq RNA Sample Prep Kit (Cat. no. RS-122-2001) was used with 1-2 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Description processed data file:
STR_Indian_vs_Chinese_origin_Cuffdiff_differential_gene_expression.xlsx
Data processing Quality of sequenced reads was determined using FastQC. Reads for all samples were of acceptable quality (PHRED score ≥ 30)
High-quality reads were mapped to mmul_1 whole genome using Tophat for illumina v1.5.0 (default settings)
Fragments Per Kilobase Of Exon Per Million Mapped Reads (FPKM) were calculated using Cuffdiff v0.0.5. Cuffdiff automatically calculates log2 transformed fold change
Fold change for each gene was manually calculated by dividing FPKM Chinese origin by FPKM Indian origin in Excel
Genome_build: mmul_1
Supplementary_files_format_and_content: excel files include average FPKM expression values for Indian-origin group and Chinese-origin group, log2 fold change, fold change, as well as statistics for differential gene expression (test statistic, unadjusted p-value, Benjamini Hochberg flase discovery rate q-value)
 
Submission date Dec 08, 2016
Last update date May 15, 2019
Contact name Emily S Mohn
Organization name Tufts University
Department Jean Mayer USDA Human Nutrition Research Center on Aging
Lab Antioxidants Research Laboratory
Street address 711 Washington Street
City Boston
State/province MA
ZIP/Postal code 02111
Country USA
 
Platform ID GPL19129
Series (1)
GSE91059 Brain Xanthophyll Content and Exploratory Gene Expression Analysis: Subspecies Differences in Rhesus Macaque
Relations
BioSample SAMN06124885
SRA SRX2405728

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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