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Sample GSM1866005

Query DataSets for GSM1866005

Status

Public on Sep 10, 2015

Title

5_After

Sample type

SRA

Source name

Sperm

Organism

Homo sapiens

Characteristics

time point: After folic acid supplementation

Extracted molecule

genomic DNA

Extraction protocol

Sperm DNA was extracted using the QIAamp DNA Mini kit (QIAGEN, Mississauga, ON, Canada) according to the manufacturer’s protocols with minor modifications.
Full details can be found in Aarabi et al. (Hum. Mol. Genet. 2015). Briefly, ~500 ng of genomic DNA was digested with MspI, size selected, end-repaired, 3'-terminal A extended and ligated to Illumina adapters containing methylated cytosines, bilsufite converted using the EpiTect Bisulfite Kit (QIAGEN), PCR amplified with 20-25 cycles and sequenced.

Library strategy

Bisulfite-Seq

Library source

genomic

Library selection

Reduced Representation

Instrument model

Illumina HiSeq 2000

Data processing

Full details can be found in Aarabi et al. (Hum. Mol. Genet. 2015). Briefly, eight samples of sperm DNA libraries were multiplexed for paired end sequencing in one lane of a HiSeq 2000 sequencer (Illumina) followed by initial data processing and alignment of reads by the software pipeline bsmap version 2.6. Analysis was based on 100 bp step-wise tiling windows, ≥2 CpG per tile as well as ≥10× CpG coverage of each tile per sample.
Genome_build: GRCh37
Supplementary_files_format_and_content: csv files include coordinates and normalized methylation values of differentially methylated tiles after folic acid supplementation with >2 CpGs and >10x sequencing coverage

Submission date

Sep 01, 2015

Last update date

May 15, 2019

Contact name

Mahmoud Aarabi

Organization name

McGill University

Department

Human Genetics

Street address

1001 Boulevard Décarie