Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H4K12ac

Cell type

Cell type Class
Breast
Cell type
MCF 10A
Primary Tissue
Breast
Tissue Diagnosis
Fibrocystic Disease

Attributes by original data submitter

Sample

source_name
MCF10A breast epithelial cells
cell type
Breast epithelial cells
chip-seq antibody
Anti-acetyl-histone H4 (Lys12) (07-595; EMD Millipore) (1µg used)
cell line
MCF10A

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were crosslinked with 1% Formaldehyde for 10 minutes and quenched with 1.25 M Glycine. The nuclear pellets were sonicated to the fragment range of 200-400 bp. Sonicated extracts were incubated with specific antibodies at 4˚C overnight and ChIP-immune complexes were pulled down using Protein A sepharose. Library preparations were done using NEBnext Ultra DNA library preparation kit according to the manufacturer’s instructions.

Sequencing Platform

instrument_model
NextSeq 500

hg38

Number of total reads
56484192
Reads aligned (%)
93.4
Duplicates removed (%)
3.9
Number of peaks
5240 (qval < 1E-05)

hg19

Number of total reads
56484192
Reads aligned (%)
93.0
Duplicates removed (%)
5.2
Number of peaks
5070 (qval < 1E-05)

Base call quality data from DBCLS SRA