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Sample GSM4094999

Query DataSets for GSM4094999

Status

Public on Apr 07, 2020

Title

Sample type

SRA

Source name

Skin

Organism

Heterocephalus glaber

Characteristics

tissue: Skin
age (weeks): 43.33333333
individual id: F046

Extracted molecule

genomic DNA

Extraction protocol

DNA was extracted from tissues using the PureLink™ Genomic DNA kit (Thermo Fisher, Cat. K182002), as per the manufacturer’s instructions. Tissues were digested overnight at 55 °C using 180 µl PK buffer and 20 µl PK enzyme from the kit. DNA concentration was quantified using a High Sensitivity DNA Qubit® assay (Life Technologies, Cat. Q32851).
DNA from tissues was diluted to a concentration of 11 ng/µl and 45 µl of each sample was used for generation of targeted bisulfite sequencing data by the Genome Centre Facility at the Blizard Institute, Queen Mary University of London. DNA was bisulfite converted in a 96 well plate format using the EZ-96 DNA Methylation™ Kit (Zymo, Cat. D5003). Target amplification was performed using the FastStart High Fidelity PCR System, dNTPack (Sigma-Aldrich, Cat. 4738284001) in the 48.48 layout on the Fluidigm® C1 system (Fluidigm®, USA), a microfluidics platform. Library preparation was performed using the same kit including 4 μl of Access Array Barcode Library Primer and 1 μl of PCR product diluted 1:100. Libraries were sequenced with Illumina MiSeq sequencing using v2 chemistry (150 bp, paired-end).

Library strategy

Bisulfite-Seq

Library source

genomic

Library selection

RANDOM

Instrument model

Illumina MiSeq

Description

BisPCRSeq_methylation_levels.csv

Data processing

Raw FASTQ files were mapped to the reference hetGla2 using BISMARK (v0.16.3) and Bowtie2 (v2.2.8).
Reads that mapped outside of the targeted regions were discarded from analyses, and methylated and unmethylated counts for each CpG were calculated using the custom C++ program (https://bitbucket.org/lowelabq- mul/methylation-extractor). Those CpGs with a coverage < 50× were also discarded from analyses
Genome_build: hetGla2
Supplementary_files_format_and_content: csv file containing the fractional methylation level at each contig and position within included aDMP primers for each sample.

Submission date

Sep 24, 2019

Last update date

Apr 07, 2020

Contact name

Amy Frances Danson

E-mail(s)

a.f.danson@qmul.ac.uk

Organization name

The Blizard Institute

Department

Centre for Genomics and Child Health