Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
MYC

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 cells, Myc ChIP
cell line
MCF7
cell type
human cancer cell line
chip antibody
anti-c-Myc (Cat No. 1472-1, Epitomics)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
For ChIP-seq DNA extracton, 1.2×107 cells were treated with 5 mM dimethyl 3,3'- dithiobispropionimidate (Thermo Scientific) for 30 min at 4°C and incubated with quenching buffer (100 mM Tris-HCl, 150 mM NaCl) for 5 min. Treated cells were cross-linked with 1% (vol/vol) formaldehyde for 10 min at room temperature, quenched with 125 mM glycine for 5 min, lysed in lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris-HCl, pH 8.0), and sonicated by the Bioruptor (Diagenode) to generate DNA fragments ranging from 200 to 600 bp. The sonicated lysates were diluted with ChIP dilution buffer (0.1% TritonX-100, 2 mM EDTA, 20 mM Tris-HCl pH 7.5, 150 mM NaCl, and 1× protease inhibitor), immunoprecipitated with rotation 6-7 hours at 4°C by 3-4 µg of anti-MYC antibodies, pulled down using Protein A/G DYNAL magnetic beads (40 µl of 1:1 mixture), and eluted by the QIAquick PCR Purification Kit (Qiagen). ChIP-seq library preparation and sequencing were performed by a NextSeq500 platform with single-end reads of 75 bases

Sequencing Platform

instrument_model
NextSeq 500

hg19

Number of total reads
41648381
Reads aligned (%)
87.3
Duplicates removed (%)
8.9
Number of peaks
3325 (qval < 1E-05)

hg38

Number of total reads
41648381
Reads aligned (%)
88.8
Duplicates removed (%)
7.9
Number of peaks
3324 (qval < 1E-05)

Base call quality data from DBCLS SRA