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Sample GSM2793720 Query DataSets for GSM2793720
Status Public on Dec 30, 2021
Title YY1 rep2
Sample type SRA
 
Source name HepG2 cell
Organism Homo sapiens
Characteristics cell line: HepG2
chip antibody: YY1
Growth protocol HepG2 were grown according to the approved ENCODE cell culture protocols (http://hgwdev.cse.ucsc.edu/ENCODE/protocols/cell)
Extracted molecule genomic DNA
Extraction protocol Cross-linked chromatin was immunoprecipitated with an antibody. The Protein:DNA crosslinks were then reversed and the DNA fragments were recovered and sequenced. Please see protocol notes below and go to http://hudsonalpha.org/myers-lab/protocols for the most current version of the protocol. The eluted DNA was followed by bisulfite conversion using the EZ DNA Methylation-Gold Kit from Zymo according to manufacturer’s instructions.
Illumina Single End for ChIPBS
 
Library strategy Bisulfite-Seq
Library source genomic
Library selection RANDOM
Instrument model Illumina HiSeq 2500
 
Description SL88937
ChIPBS (ChIP followed by bisulfite sequencing)
Data processing Reads were trimmed (2-3 bp from ends) using trim galore (version 0.3.7), powered by cutadapt to trim adaptor sequences for QC purpose
ChIPBS reads were processed with Bismark(bismark-0.11.1) pipeline using Bowtie2(bowtie-2-2.1.0) aligner
Deduplication and PCR duplicates removal was performed using deduplicate_bismark program
Methylation extraction from deduplicated bam files, in CpG context, was performed using bismark_methylation_extractor program
Genome_build: hg19
Supplementary_files_format_and_content: .bedGraph - [Chromosome number, start position, stop position, dataValue], .cov - [Chromosome number, start position, stop position, methylation percent, methylated reads, unmethylated reads]
 
Submission date Sep 26, 2017
Last update date Dec 30, 2021
Contact name Eric M Mendenhall
E-mail(s) emendenhall@hudsonalpha.org
Organization name HudsonAlpha Institute
Lab Mendenhall Lab
Street address 601 Genome Way Northwest
City Huntsville
State/province AL
ZIP/Postal code 35806
Country USA
 
Platform ID GPL16791
Series (2)
GSE104246 DNA methylation profiling of TF bound sites using ChIPBS (ChIP Bisulfite Sequencing)
GSE104248 Towards an integrative map of a single cell type's transcription factor landscape
Relations
BioSample SAMN07702237
SRA SRX3216482

Supplementary file Size Download File type/resource
GSM2793720_SL88937_CpG_context_deduplicated.bedGraph.gz 39.8 Mb (ftp)(http) BEDGRAPH
GSM2793720_SL88937_CpG_context_deduplicated.bismark.cov.gz 36.1 Mb (ftp)(http) COV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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