Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K4me3

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 Cell Line
cell line
MCF10A
cell type
Human mammary epithelial cell line
chip-antibody
H3K4me3 Abcam/Millipore ab

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Histone-DNA complexes were isolated using antibodies described from Control and UBR7-shRNA sonicated nuclei. Libraries for Illumina sequencing were generated following the New England BioLabs NEBNext Ultra DNA Library Prep Kit protocol. A total of 10x cycles were used during PCR amplification for the generation of all ChIP-seq libraries. Amplified ChIP DNA was purified using double-sided AMPure XP to retain fragments ~200 to 500bp and quantified using the Qubit 2000 and Bioanalyzer 1000 before multiplexing.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg38

Number of total reads
25750865
Reads aligned (%)
80.6
Duplicates removed (%)
2.9
Number of peaks
14983 (qval < 1E-05)

hg19

Number of total reads
25750865
Reads aligned (%)
79.7
Duplicates removed (%)
5.1
Number of peaks
14976 (qval < 1E-05)

Base call quality data from DBCLS SRA