Antigen

Antigen Class

Unclassified

Antigen

Unclassified

Cell type

Cell type Class

Breast

Cell type

Breast cells

NA

NA

Sample

source_name

Human Mammary Epithelial Cells

cell type

Mammary epithelial cells

sample type

crosslinked

passages

second or third

Sequenced DNA Library

library_strategy

ChIP-Seq

library_source

GENOMIC

library_selection

ChIP

library_construction_protocol

Nuclei were extracted after the crosslinking step (1% formaldehyde in PBS) of intact cells, followed by re-suspension in SDS lysis buffer before sonication. FAIRE DNA samples were purified by phenol/chloroform extraction. Input DNA was also purified by phenol/chloroform extraction after the crosslinking was reversed. Libraries were prepared according to Illumina's instructions (refer to http://epigenome.usc.edu/services/nextgen/making_libraries.html)

Sequencing Platform

instrument_model

Illumina HiSeq 2000

hg38

Number of total reads

19728010

Reads aligned (%)

90.8

Duplicates removed (%)

42.3

Number of peaks

5220 (qval < 1E-05)

hg19

Number of total reads

19728010

Reads aligned (%)

90.2

Duplicates removed (%)

43.7

Number of peaks

5224 (qval < 1E-05)