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Sample GSM3184740

Query DataSets for GSM3184740

Status

Public on Sep 25, 2018

Title

C1H1 [BS-seq]

Sample type

SRA

Source name

post mortem frozen tissue

Organism

Pan troglodytes

Characteristics

individual: 4x0519
tissue: heart
Sex: male

Treatment protocol

Tissues were received postmortem.

Extracted molecule

genomic DNA

Extraction protocol

We prepared a total of 48 whole-genome bisulfite sequencing libraries (BS-seq) from extracted DNA as previously described (Tung et al. 2012, Banovich et al. 2014).
For each sample, we prepared at least two libraries, with independent PCR amplifications to minimize PCR duplication rates. The BS-seq libraries were sequenced on 111 lanes on 17 flow-cells on an Illumina HiSeq 2500 sequencer in the Gilad lab or at the University of Chicago Genomics Facility

Library strategy

Bisulfite-Seq

Library source

genomic

Library selection

RANDOM

Instrument model

Illumina HiSeq 2500

Description

Subspecies/admixture- hybrid between Central and Western

Data processing

50 bp single-end RNA-seq reads from each species were trimmed and mapped to the appropriate genome (hg19, panTro3, rheMac2) using the Bismark aligner (version 0.8.1) (Krueger et al. 2011). We permitted one mismatch in the seed of the alignment, and by default Bismark reports only uniquely mapped reads. We applied the Bismark deduplication script to each technical replicate to remove reads mapped to the same starting genomic position, which likely arise through PCR amplification of the same DNA fragments during library preparation (Bock 2012).
We estimated the percentage of methylation at an individual cytosine site by the ratio of the number of cytosines (unconverted) found in mapped reads at this position, to the total number of reads covering this position (sequenced as cytosine or thymine, i.e., converted or unconverted). We calculated methylation estimates genome-wide at CpG sites using the methylation extractor tool from Bismark (version 0.8.1). We additionally collapsed information from both DNA strands (because CpG methylation status is highly symmetrical on opposite strands (Lister et al. 2009) to achieve better precision in methylation estimates across the genome.
To obtain CpGs that mapped to multiple species, the chimpanzee and rhesus macaque CpG sites were mapped to human coordinates (hg19) using chain files from ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/liftOver/ and the LiftOver tool from the UCSC genome browser [35]. These files had previously been filtered for paralogous regions and repeats, but we also removed positions that were not remapped to their original position when we mapped from human back to their original genome. Chimpanzee and rhesus macaque CpG sites were mapped to human, even if their orthologous positions was not a CpG site in human.
Genome_build: hg19, panTro3, rheMac2
Supplementary_files_format_and_content: Per CpG methylation level and coverage for all individuals (hg19 coordinates). Object of type 'BSseq' (Hansen et al. 2012).

Submission date

Jun 11, 2018

Last update date

Sep 25, 2018

Contact name

Lauren Elizabeth Blake

E-mail(s)

leblake@uchicago.edu

Organization name

University of Chicago

Department

Human Genetics