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Sample GSM3164319 Query DataSets for GSM3164319
Status Public on May 30, 2018
Title Gibbon_WGBS
Sample type SRA
Source name Blood
Organism Nomascus leucogenys
Characteristics cell type: White blood cells
age: adult
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.
Library strategy Bisulfite-Seq
Library source genomic
Library selection RANDOM
Instrument model Illumina HiSeq 2000
Description Gibbon
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
Submission date May 29, 2018
Last update date May 30, 2018
Contact name Lucia Carbone
Organization name Oregon Health & Science University
Street address 3303 SW Bond Ave.
City Portland
State/province Oregon
ZIP/Postal code 97239
Country USA
Platform ID GPL25056
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
BioSample SAMN09279532
SRA SRX4138631

Supplementary file Size Download File type/resource
GSM3164319_Gibbon_WGBS-methylation.bedgraph.gz 175.1 Mb (ftp)(http) BEDGRAPH
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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