Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K4me1

Cell type

Cell type Class
Liver
Cell type
Hepatocytes
MeSH Description
The main structural component of the LIVER. They are specialized EPITHELIAL CELLS that are organized into interconnected plates called lobules.

Attributes by original data submitter

Sample

source_name
Commercially available hepatocytes (BioreclamationIVT: lot DSX)
individual
d3
cell type
Primary human hepatocytes
chip antibody
H3K4me1 (Cell Signaling Technologies, catalog# 5326BF, lot# 2)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Nuclear lysates were sonicated and histone-DNA complexes were isolated with antibody. After performing reverse cross linking on sheared chromatin the following steps were performed: end-repair, addition of A base to 3' end of DNA fragments, ligation of adapters to ends of DNA fragments, enrichment by PCR, and gel purification of PCR products.

Sequencing Platform

instrument_model
NextSeq 500

hg38

Number of total reads
35961059
Reads aligned (%)
97.4
Duplicates removed (%)
16.5
Number of peaks
62054 (qval < 1E-05)

hg19

Number of total reads
35961059
Reads aligned (%)
97.1
Duplicates removed (%)
16.6
Number of peaks
61936 (qval < 1E-05)

Base call quality data from DBCLS SRA