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Status |
Public on Dec 30, 2021 |
Title |
YY1 rep2 |
Sample type |
SRA |
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Source name |
HepG2 cell
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Organism |
Homo sapiens |
Characteristics |
cell line: HepG2 chip antibody: YY1
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Growth protocol |
HepG2 were grown according to the approved ENCODE cell culture protocols (http://hgwdev.cse.ucsc.edu/ENCODE/protocols/cell)
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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
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Library strategy |
Bisulfite-Seq |
Library source |
genomic |
Library selection |
RANDOM |
Instrument model |
Illumina HiSeq 2500 |
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Description |
SL88937 ChIPBS (ChIP followed by bisulfite sequencing)
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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]
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Submission date |
Sep 26, 2017 |
Last update date |
Dec 30, 2021 |
Contact name |
Eric M Mendenhall |
E-mail(s) |
emendenhall@hudsonalpha.org
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Organization name |
HudsonAlpha Institute
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Lab |
Mendenhall Lab
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Street address |
601 Genome Way Northwest
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City |
Huntsville |
State/province |
AL |
ZIP/Postal code |
35806 |
Country |
USA |
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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 |
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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 Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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