Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Breast
Cell type
MCF-7
Primary Tissue
Breast
Site of Extraction
Pleura
Tissue Diagnosis
Adenocarcinoma

Attributes by original data submitter

Sample

source_name
MCF7_input
cell line
MCF7
tissue source
breast
cell type
mammary gland/breast epithelial cell; metastatic site derived
neoplasia type
adenocarcinoma
atcc id
ATCC HTB-22
chip antibody
none (input DNA control)

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
35412448
Reads aligned (%)
97.4
Duplicates removed (%)
2.7
Number of peaks
1198 (qval < 1E-05)

hg19

Number of total reads
35412448
Reads aligned (%)
96.5
Duplicates removed (%)
3.7
Number of peaks
894 (qval < 1E-05)

Base call quality data from DBCLS SRA