Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
TP53

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
Breast mammary gland
treatment
DMSO
antibody
p53
cell line
MCF10A
cell type
Breast epithelial cells

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
For ChIP-Seq: Cells were crosslinked at 80% confluency with 1% formaldehyde for 10 min at room temperature. Crosslinking was quenched with 125mM glycine and the resulting pellet was washed twice with cold PBS and lysed. Samples were subjected to sonication with Diagenode Bioruptor Plus for 40 cycles (30 sec on/off at high setting) for shearing chromatin to 150-500 bp average size. Immunoprecipitation reactions were performed with Diagenode IP-Star Compact Automated System with mentioned antibodies. Immunoprecipitated DNA was reverse-crosslinked at 65°C for 4 hours and then eluted from beads, purified using SPRI beads, and used to construct sequencing libraries. For ChIP-Seq: Libraries were prepared using NEBNext Ultra DNA Library Prep Kit for Illumina (New England Biolabs).

Sequencing Platform

instrument_model
NextSeq 500

hg19

Number of total reads
44618839
Reads aligned (%)
92.1
Duplicates removed (%)
5.4
Number of peaks
1308 (qval < 1E-05)

hg38

Number of total reads
44618839
Reads aligned (%)
94.5
Duplicates removed (%)
3.8
Number of peaks
1600 (qval < 1E-05)

Base call quality data from DBCLS SRA