|
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
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|
|
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)
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|
|
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 |