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Series GSE186383 Query DataSets for GSE186383
Status Public on Oct 26, 2021
Title The SEQC2 epigenomics quality control (EpiQC) study
Organism Homo sapiens
Experiment type Methylation profiling by high throughput sequencing
Summary We present a multi-platform assessment and a global resource for epigenetics research from the FDA's Epigenomics Quality Control (EpiQC) Group. The study design leverages seven human cell lines that are designated as reference materials and publicly available from the National Institute of Standards and Technology (NIST) and Genome in a Bottle (GIAB) consortium. These samples were subject to a variety of genome-wide methylation interrogation approaches across six independent laboratories, with a primary focus on 5-methylcytosine modifications.
 
Overall design Each sample was processed in two or more technical replicates by three whole-genome bisulfite sequencing (WGBS) protocols (TruSeq DNA methylation, Accel-NGS MethylSeq, and SPLAT), oxidative bisulfite sequencing (TrueMethyl), enzymatic deamination method (EMseq), targeted methylation sequencing (Illumina Methyl Capture EPIC). All libraries were aligned to the human reference genome (build GRCh38) using bwa-meth followed by MethylDackel for DNA methylation estimation.

Please note that the methylation array data is available in the GSE230132 records.
 
Contributor(s) Jonathan F, Jessica N, Claudia L, Ting G, Michelle L, Christopher M, Youping D
Citation(s) 34872606
BioProject PRJNA200694
Submission date Oct 22, 2021
Last update date Apr 20, 2023
Contact name Jessica Nordlund
Organization name Uppsala University
Department Department of Medical Sciences
Lab Molecular Precision Medicine
Street address Box 1432, BMC
City Uppsala
ZIP/Postal code SE-75144
Country Sweden
 
Platforms (1)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Samples (106)
GSM5649418 Methylome capture of HG001 using TrueMethyl oxidative bisulite sequencing, mockBS [TrueMethylBS_HG001_LAB01_REP02]
GSM5649420 Methylome capture of HG001 using TrueMethyl oxidative bisulite sequencing, mockBS [TrueMethylBS_HG001_LAB01_REP01]
GSM5649421 Methylome capture of HG007 using TruSeq [TruSeq_HG007_LAB01_REP02]

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE186383_RAW.tar 20.2 Gb (http)(custom) TAR (of BEDGRAPH)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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