Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
MYC

Cell type

Cell type Class
Breast
Cell type
Mammary epithelial cells
NA
NA

Attributes by original data submitter

Sample

source_name
hTERT-immortalized human mammary epithelial cells
tissue
non-transformed human mammary epithelial cells
gender
female
cell fraction
IMEC WT
chip antibody
anti-MYC sc-764 Santa Cruz Biotechnology

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were crosslinked with 1% formaldehyde for 10 min at room temperature and the reaction was quenched by glycine at a final concentration of 0.125 M, for 5 min at room temperature. Cells were lysed in lysis buffer (50 mM Tris-HCl pH 8, 0.1 % SDS, 10 mM EDTA pH 8, 1 mM PMSF, protease inhibitor cocktail) and chromatin was sonicated to an average size of 0.1-0.5 kb, using a Branson D250 sonifier (4 cycles of 30 seconds, 20% amplitude). Five nanograms of immunoprecipitaded and purified DNA were used to generate ChIP-seq libraries. Briefly, end repair of DNA fragments was achieved by sequential 15 min incubations at 12°C and 25°C with T4 PNK (10U/μl), T4 POL (3U/μl) and 0.1 mM dNTPs. A-base addition was performed by incubating end-repaired DNA fragments with Klenow (3’ → 5’ exo, 5U/μl) and 167 μM dATP for 30 min at 30°C. Adaptor ligation was achieved by using the NEB Quick ligation kit (M2200L) and perfoming an incubation of 15 min at 25°C. Processed DNA fragments were finally amplified with a thermal cycler for 14 cicles, by using the Agilent PfuUltra II Fusion HS DNA Pol kit (600674). All DNA purification steps between the different enzymatic reactions were performed by using Agencourt AMPure XP SPRI beads (Beckman, A63882). The obtained libraries were subjected to quality control on Agilent Bioanalyzer (Agilent Technologies, G2943CA).

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
22553932
Reads aligned (%)
71.3
Duplicates removed (%)
15.9
Number of peaks
640 (qval < 1E-05)

hg38

Number of total reads
22553932
Reads aligned (%)
72.9
Duplicates removed (%)
14.8
Number of peaks
761 (qval < 1E-05)

Base call quality data from DBCLS SRA