Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
MYC

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 cell line
cell type
immortalized breast epithelial cells
plasmid 1
pBABE-hygro-MYC
plasmid 2
pMN-IRES-GFP-PI3KH1047R
plasmid 3
pLKO-tetON-puro-shG9a 1
chip antibody
MYC (N262, homemade)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIP was performed with 10×10^6 cells per reaction. Cells were crosslinked in 1% formaldehyde, quenched in 0.125 M glycine, and lysed in Cell Lysis Buffer (50 mM Tris pH 8.1, 10 mM EDTA, 1% SDS). Lysates were sonicated with Bioruptor Pico (Diagenode) and diluted in Dilution Buffer (20 mM Tris pH 8.1, 150 mM NaCl, 2 mM EDTA, 1% Triton X-100) with pre-incubated mixture of antibody and Dynabeads Protein A and Protein G (Invitrogen). After overnight incubation, samples were washed three times with Washing Buffer (50 mM HEPES pH 7.6, 0.5 M LiCl, 1 mM EDTA, 0.7% sodium deoxycholate, 1% NP-40) then two times with TE Buffer. DNA was eluted overnight in Decrosslinking Buffer (0.1 M NaHCO3, 1% SDS) and purified with QIAquick PCR Purification Kit (Qiagen). Samples were quantified using Qubit fluorometric quantitation (Thermo Fisher). Sample libraries were prepared using ThruPLEX DNA-seq kit as per the manufacturer’s protocol (Rubicon Genomics) and sequenced using Illumina HiSeq2500 with Single Read 50bp protocol multiplexed to achieve an average of 25M reads per sample at the Princess Margaret Genomics Centre (Toronto, Canada).

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg19

Number of total reads
31273863
Reads aligned (%)
27.7
Duplicates removed (%)
71.7
Number of peaks
2176 (qval < 1E-05)

hg38

Number of total reads
31273863
Reads aligned (%)
29.4
Duplicates removed (%)
70.2
Number of peaks
2151 (qval < 1E-05)

Base call quality data from DBCLS SRA