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
mammary gland/breast epithelial cell
cell line
MCF-10A
antibody
H3K4me3
tissue
breast
cell type
luminal ductal cells
atcc id
ATCC CRL-10317

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIP was performed on subconfluent cells as previously described (Lee et al., 2006) with the following modification: after sonication, buffer C was exchanged for FA buffer (50 mM HEPES-KOH, pH 7.5, 140 mM sodium chloride, 1 mM EDTA, 1% v/v Triton X-100, 0.1% w/v sodium deoxycholate, 0.1% w/v SDS, 1X Roche Complete EDTA-free protease inhibitor cocktail, 25 nM MG132 in nuclease-free water) prior to antibody pulldown using Amicon columns (10,000 kDa MWCO). The following antibodies were used for ChIP-Seq: H3K4me3 (mouse monoclonal, abcam ab1012), H3K27me3 (rabbit polyclonal, Millipore 07-449), H3K9me2 (mouse monoclonal, abcam ab1220). Two replicates were processed, normalized and the data combined for further analyses. After genomic DNA was isolated for both specific IPs and input DNA, libraries were prepared for paired-end multiplexed tag Solexa/Illumina sequencing using the Illumina DNA Sample Prep Kit v2.0 according to manufacturer instructions.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg38

Number of total reads
9624285
Reads aligned (%)
36.6
Duplicates removed (%)
3.1
Number of peaks
15449 (qval < 1E-05)

hg19

Number of total reads
9624285
Reads aligned (%)
36.5
Duplicates removed (%)
3.1
Number of peaks
15428 (qval < 1E-05)

Base call quality data from DBCLS SRA