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Sample GSM842200 Query DataSets for GSM842200
Status Public on Feb 01, 2012
Title RZd7
Sample type SRA
 
Source name PBMC_low ranking individual
Organism Macaca mulatta
Characteristics rank: 5
gender: female
age: adult
cell type: peripheral blood mononuclear cells
Extracted molecule genomic DNA
Extraction protocol PBMCs were purified using a standard Ficoll gradient and DNA was extracted using the Gentra PureGene kit. Standard Illumina protocol for constructing DNA libraries
 
Library strategy Bisulfite-Seq
Library source genomic
Library selection RANDOM
Instrument model Illumina HiSeq 2000
 
Data processing Reads were mapped to the rhesus macaque genome (rhemac2) using the software bismark (http://www.bioinformatics.bbsrc.ac.uk/projects/bismark/) and methylation status at each CpG site was obtained using the bismark methylation_extractor function (masking data from the first three base pairs).
Columns for the bed file represent, respectively: 1) chromosome; 2) base pair coordinate; 3) base pair coordinate + 1; 4) methylated CpGs for individual REm6; 5) total coverage for REm6; 6) methylated CpGs for RGs6; 7) total coverage for RGs6; 8) methylated CpGs for RNf4; 9) total coverage for RNf4; 10) methylated CpGs for RNf6; 11) total coverage for RNf6; 12) methylated CpGs for RZd7; 13) total coverage for RZd7; 14) methylated CpGs for RZp6; 15) total coverage for RZp6.
Note also that coverage for each CpG site integrates both forward reads of that site and reverse reads for the same site.
 
Submission date Dec 03, 2011
Last update date May 15, 2019
Contact name Jenny Tung
Organization name Duke University
Street address 125 Science Drive
City Durham
State/province NC
ZIP/Postal code 27708
Country USA
 
Platform ID GPL14954
Series (2)
GSE34128 Dramatic effects of social behavior on gene regulation in rhesus macaques [Bisulfite seq]
GSE34129 Dramatic effects of social behavior on gene regulation in rhesus macaques
Relations
SRA SRX110331
BioSample SAMN00761811

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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