Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K4me3

Cell type

Cell type Class
Breast
Cell type
MCF10A-Er-Src
Tissue
breast
Lineage
ectoderm
Description
mammary gland, non-tumorigenic epithelial, inducible cell line, derived from the MCF-10A parental cells and contain ER-Src, a derivative of the Src kinase oncoprotein (v-Src) that is fused to the ligand-binding domain of the estrogen receptor (ER)

Attributes by original data submitter

Sample

source_name
Breast epithelial cell
cell type
MCF10A-ER-Src
antibody
H3K4me3
time point
12hr

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were treated with ethanol or tamoxifen (1 µM) for 24 hours and then cross-linked using ethylene glycol bis (succinimidyl succinate) (EGS), disuccinimidyl glutarate (DSG) and disuccinimidyl suberate (DSS) mixture (2.5 µM each) for 45 minutes at room temperature. After this initial crosslinking, cells were further fixed using 1% formaldehyde for 20 minutes at room temperature and then quenched by glycine (0.125 M). Chromatin in sonication buffer (50 mM HEPES, pH7.5, 140 mM NaCl, 2mM EDTA, 2mM EGTA, 1% Triton-100 and 0.4% SDS) was sheared using Branson Microtip Sonifier 450 (12 cycles of 15 second at a sonication setting of output 4 and duty cycle 60%) to a size mostly between 100-150 bp. The sonicated chromatin solution was diluted to 0.085% SDS and immunoprecipitated with antibodies against H3K4me3 (ab8580), H3K27ac (ab4729), H3K4me1 (ab8895), H3K36me3 (ab9050), H3K27me3 (ab6002) and H3K9me3 (ab8898). Immunoprecipitated chromatin was decrosslinked using RNase Cocktail (Ambion, AM2286) and Pronase (Roche, 10165921001). ChIP DNA was end repaired, addition of “A” and adapters ligation and PCR amplification to produce ChIP-seq libraries. The DNA concentration was measured by Bioanalyzer before sequencing using Hiseq 2000 at the Bauer Core Facility, Harvard.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg38

Number of total reads
15501396
Reads aligned (%)
96.7
Duplicates removed (%)
1.6
Number of peaks
379 (qval < 1E-05)

hg19

Number of total reads
15501396
Reads aligned (%)
95.4
Duplicates removed (%)
4.0
Number of peaks
266 (qval < 1E-05)

Base call quality data from DBCLS SRA