Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

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 non-transformed mammary cells
cell line
MCF10A
cell type
breast cancer cell line
chip antibody
none (input)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were fixed with 1% formaldehyde for 15 min and quenched with 0.125 M glycine. Lysates were sonicated with a microtip sonicator to shear the DNA. Genomic DNA (Input) was prepared by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking, followed by ethanol precipitation. Starting with 50 ug of chromatin, genomic DNA regions of interest were isolated using Flag-M2 affinity beads. Immune complexes were washed, eluted from the beads with SDS buffer, and subjected to RNase and proteinase K treatment. Crosslinks were reversed by incubation overnight at 65 C, and ChIP DNA was purified by phenol-chloroform extraction and ethanol precipitation. Illumina sequencing libraries were prepared from the ChIP and Input DNAs by the standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation. After a final PCR amplification step, the resulting DNA libraries were quantified and sequenced on HiSeq 2500.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg38

Number of total reads
35578374
Reads aligned (%)
99.2
Duplicates removed (%)
75.4
Number of peaks
750 (qval < 1E-05)

hg19

Number of total reads
35578374
Reads aligned (%)
98.5
Duplicates removed (%)
76.9
Number of peaks
516 (qval < 1E-05)

Base call quality data from DBCLS SRA