Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H4K12ac

Cell type

Cell type Class
Breast
Cell type
MCF-7
Primary Tissue
Breast
Site of Extraction
Pleura
Tissue Diagnosis
Adenocarcinoma

Attributes by original data submitter

Sample

source_name
MCF7 breast cancer cells
cell type
Human breast adenocarcinoma cell line
passages
20-30
chip-seq antibody
Anti-acetyl-histone H4 (Lys12) (07-595; EMD Millipore) (1µg used)
cell line
MCF7

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
48994401
Reads aligned (%)
87.1
Duplicates removed (%)
11.6
Number of peaks
10204 (qval < 1E-05)

hg19

Number of total reads
48994401
Reads aligned (%)
86.6
Duplicates removed (%)
13.1
Number of peaks
10206 (qval < 1E-05)

Base call quality data from DBCLS SRA