|
| Status |
Public on Feb 01, 2012 |
| Title |
RNf4 |
| 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 |
SRX110329 |
| BioSample |
SAMN00761809 |
