GEO Accession viewer

NCBI > GEO > Accession Display

Not logged in | Login

GEO help: Mouse over screen elements for information.

Sample GSM3356348

Query DataSets for GSM3356348

Status

Public on May 31, 2021

Title

S15N

Sample type

SRA

Source name

Buccal Mucosa

Organism

Homo sapiens

Characteristics

tissue: Adjacent Normal Tissue

Extracted molecule

genomic DNA

Extraction protocol

Qiagen Tissue DNA kit was used to isolate DNA from the tissue samples as per the manufacturer’s protocol
As per the protocol provided by Chatterjee A et al (PMID: 23193365). Briefly, 2.5µg of DNA was digested with 80U of MspI followed by end repair and A-tailing with clean up step. After ligation to methylated adapters, small fragments of DNA were removed by AMPure XP beads. Fragments of size 160-340bps (i.e. 40-220bps DNA + 120bp adapters) were extracted from 3% Nusieve gel using Qiaquick gel extraction kit. DNA samples were then treated for bisulfite conversion and clean-up. Libraries were prepared by13 cycles of PCR followed by size selection (160-340bps) from gel and, finally, assessed for quality using a Bioanalyzer and Kapa Kit.

Library strategy

Bisulfite-Seq

Library source

genomic

Library selection

RANDOM

Instrument model

Illumina HiSeq 2500

Description

S15_sig_mirna.txt

Data processing

Basecalls performed using CASAVA version 1.4
RRBS reads were aligned to the hg38 genome assembly using DMAP pipeline.
Data were filtered using the following specifications- Adapter removal and end trimming of last two bases were performed with Trim Galore program (Phred Score≥28).
Good quality reads, checked by FASTQC, were mapped to the human reference genome (hg38) using Bismark (with default setting of 2 mismatches in a seed region of 28 nucleotides).
Diffmeth program of the DMAP package [with fragments with at least 2 CpG sites, covered by ≥10 reads, was used. MspI fragments were used as the unit of differential methylation analysis. Proportion of methylation was calculated from the ratio of total number of methylated CpGs in all reads divided by the total number of CpGs in a read. Pair-wise Fisher’s exact test, followed by Benjamini-Hochberg correction, was performed for each fragment from each pair of tissues to get differentially methylated regions (DMR) for each sample pair.
Genome_build: hg38
Supplementary_files_format_and_content: identgeneloc files generated where each row is a DMR or differentially methylated region in that particular sample,column with label "R" represents methylation frequency in normal and column with label "S" represents methylation frequency in cancer followed by genomic location and name of the annotated gene for that DMR

Submission date

Aug 23, 2018

Last update date

May 31, 2021

Contact name

BIDYUT ROY

E-mail(s)

bidyutroy8933@gmail.com

Phone

9432076069

Organization name

indian statistical institute