Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

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
MCF10A
cell type
mammary gland/breast epithelial cell
neoplasia type
luminal ductal cells
atcc id
fibrocystic disease;ATCC CRL-10317
treatment
e2bza
antibody
none

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Nuclei extraction was performed using a protocol modified from Dignam et al (Dignam, et al. Nucleic Acids Res 1983). Isolated nuclei were sonicated using a Covaris S-220 Ultrasonic Processor to obtain sheared chromatin with an average peak size of 500 bp. A total of 20 g of sheared chromatin was used for ChIP immunoprecipitation with either 6.5 ug of anti-H3K4me3 anti-H3K27ac, or anti-H3K4ac (Abcam, ab1012 lot#GR80367-1) or 8 ug of anti-H3K27me3 (Millipore -07-449 lot#1764447 or 2475696 ) used at a ratio of 3:1 or 2.5:1 chromatin to antibody, respectively. Immunoprecipitated complexes were purified using Protein-G Dynabeads (Life Technologies 10004D lot#123085320). DNA fragments were isolated by uncross-linking the protein-DNA complex overnight at 65°C. The eluted ChIP-DNA were treated with RNase A (0.2mg/ml final concentration-Life Technologies Cat # AM2269), proteinase K treatment (Life Technologies cat # AM2548) and then phenol extracted, precipitated with ethanol, then resuspended in 10mM Tris. DNA was quantified using a Qubit fluorimeter (Life Technologies) prior to the library preparation. Sequencing libraries were prepared using the TruSeq ChIP sample preparation kit (Illumina cat#9235121 lot #15027084) following instructions provided by the manufacturer. Libraries were then size selected, purified and quantified prior to sequencing by automated DNA sequencing performed in the University of Vermont Cancer Center Advanced Genome Technologies Core (Messier, et al. Oncotarget 2016) .

Sequencing Platform

instrument_model
Illumina HiSeq 1500

hg38

Number of total reads
46373701
Reads aligned (%)
96.7
Duplicates removed (%)
4.0
Number of peaks
1653 (qval < 1E-05)

hg19

Number of total reads
46373701
Reads aligned (%)
95.7
Duplicates removed (%)
4.7
Number of peaks
1254 (qval < 1E-05)

Base call quality data from DBCLS SRA