Antigen

Antigen Class

Histone

Antigen

H3K4me3

Cell type

Cell type Class

Breast

Cell type

MDA-MB-231

Primary Tissue

Breast

Site of Extraction

Effusion, Pleural

Tissue Diagnosis

Adenocarcinoma

Sample

source_name

MDAMB231

cell line

MDAMB231

chip antibody

H3K4me3

Sequenced DNA Library

library_strategy

ChIP-Seq

library_source

GENOMIC

library_selection

ChIP

library_construction_protocol

For FAIRE, 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. ChIP assays were performed in MDAMB231 as previously described (Jia et al, 2009). 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 1000

hg38

Number of total reads

32069455

Reads aligned (%)

85.2

Duplicates removed (%)

48.4

Number of peaks

20448 (qval < 1E-05)

hg19

Number of total reads

32069455

Reads aligned (%)

85.0

Duplicates removed (%)

48.8

Number of peaks

20441 (qval < 1E-05)