Antigen

Antigen Class

Histone

Antigen

H3K4me3

Cell type

Cell type Class

Breast

Cell type

MCF-7

Primary Tissue

Breast

Site of Extraction

Pleura

Tissue Diagnosis

Adenocarcinoma

Sample

source_name

Breast cancer cells

cell line

MCF7

tissue

breast

chip antibody

H3K4me3 (Abcam ab8580)

Sequenced DNA Library

library_strategy

ChIP-Seq

library_source

GENOMIC

library_selection

ChIP

library_construction_protocol

For ChIP samples,unfixed cells were clarified after enzymmatically digesting and lysing cells, then histone-DNA complexes were isolated with antibody. For TCL samples, cells were permeablized and treated with restriction enzymes to fragment chromatin, then diluted with lysis buffer. Antibody-adapter complexes were added to chromatin fragment solution, then a ligation mix was added to facilitate proximity ligation of the antibody bound adapter. DNA was puried and ligated DNA was amplified prior to library construction. Libraries were prepared with Illumina's NEXTERA DNA prep kit (FC-121-1031)

Sequencing Platform

instrument_model

NextSeq 500

hg38

Number of total reads

41131324

Reads aligned (%)

89.7

Duplicates removed (%)

19.8

Number of peaks

22146 (qval < 1E-05)

hg19

Number of total reads

41131324

Reads aligned (%)

89.0

Duplicates removed (%)

21.2

Number of peaks

21959 (qval < 1E-05)