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
MCF10A_H3K4ME3
cell line
MCF10A
tissue source
breast
cell type
mammary gland/breast epithelial cell; luminal ductal cells
neoplasia type
fibrocystic disease
atcc id
ATCC CRL-10317
chip antibody
anti-H3K4me3 (Abcam, ab1012 lot#GR80367-1)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Nuclei were isolated using a modification of the Dignam method (Dignam et al Nucleic Acids Res. 1983) and pellets were sonicated using a Covaris S-220 Ultrasonic Processor to obtain sheared chromatin ranging from 200-800 bp with an average peak size of 500 bp. For immunoprecipitation, 30 μg of sheared chromatin was incubated with 10 ug of anti-H3K4me3 (Abcam, ab1012 lot#GR80367-1) or H3K27me3 (Millipore -07-449 lot#1764447 or 2475696) overnight at 4°C and then incubated with 50 μl Protein-G Dynabeads (Life Technologies 10004D lot#123085320) for 4 h at 4°C. Briefly, end-repair, A-tailing and paired-end adapter ligation were performed using 8 ug of ChIP-DNA at 150 pg/ul using the TruSeq ChIP sample preparation kit (Illumina cat#9235121 lot #15027084) following manufacture’s instructions. Excess adapters were removed by sequential Ampure XP (Beckman Coulter A63881 lot #1348300) purifications and recovered, ligated fragments were the amplified by PCR on a Biorad thermal cycler. Libraries were then run on a 2% agarose/TAE gel to select for fragments in the 350-400 bp range. Barcoded libraries (Illumina TruSeq) were then loaded onto an Illumina HiSeq 1500 and single-end 100-base (SE100) sequencing was performed at the Advanced Genome Technologies Core Massively Parallel Sequencing Facility at UVM.

Sequencing Platform

instrument_model
Illumina HiSeq 1500

hg38

Number of total reads
35301997
Reads aligned (%)
91.8
Duplicates removed (%)
23.8
Number of peaks
15088 (qval < 1E-05)

hg19

Number of total reads
35301997
Reads aligned (%)
90.9
Duplicates removed (%)
24.6
Number of peaks
14832 (qval < 1E-05)

Base call quality data from DBCLS SRA