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| Status |
Public on May 30, 2018 |
| Title |
Rhesus_WGBS |
| Sample type |
SRA |
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| Source name |
Blood
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| Organism |
Macaca mulatta |
| Characteristics |
cell type: White blood cells
age: adult
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
White-blood cells were isolated using Ficoll gradient on fresh blood received in a heparin tube.
Genomic DNA was extracted from opportunistic whole blood samples from one gibbon individual and one rhesus individual and fragmented (Fragmentase Reaction Buffer v2, Fragmentase (New England Biolab)), end-repaired (T4 DNA Ligase Buffer, dNTP, T4 DNA polymerase, T4 PNK), A-tailed (NEB buffer 2, 1mM dATP, Klenow exo-) and ligated to 30mM methylated forked Illumina adaptors (Quick Ligase Reaction Buffer, Quick Ligase). Ligated fragments were size-selected (250-500bp) and bisulfite converted using the Qiagen EpiTect bisulfite kit.
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
Rhesus macaque
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| Data processing |
Adapters and low quality reads were removed using trim_galore v0.4.0.
Trimmed reads were mapped to the respective genome using Bismark v0.12.5 and CpG methylation was calculated at each cytosine genome-wide.
Genome_build: Nleu3.0, RheMac8 (Mmul_8.0.1)
Supplementary_files_format_and_content: *-WGBS-methylation.bedgraph: bedGraph files
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| Submission date |
May 29, 2018 |
| Last update date |
May 30, 2018 |
| Contact name |
Lucia Carbone |
| E-mail(s) |
carbone@ohsu.edu
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| Organization name |
Oregon Health & Science University
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| Street address |
3303 SW Bond Ave.
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| City |
Portland |
| State/province |
Oregon |
| ZIP/Postal code |
97239 |
| Country |
USA |
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| Platform ID |
GPL14954 |
| Series (2) |
| GSE115063 |
Epigenetic maintenance of topological domains in the rearranged gibbon genome [WBGS] |
| GSE115065 |
Epigenetic maintenance of topological domains in the rearranged gibbon genome |
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| Relations |
| BioSample |
SAMN09279531 |
| SRA |
SRX4138632 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3164320_Rhesus_WGBS-methylation.bedgraph.gz |
214.3 Mb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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