Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
EN1

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
chip antibody
EN1

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIP-seq: cell monolayers were fixed with 1% formaldehyde for 10 min, at room temperature for H3K27ac and FOXA1 ChIP-seq, or 37C for V5-EN1 and TLE3 ChIP-seq. Cells were fixet with 1.5mM EGS during 30 min and adding 1% paraformaldehyde during the last 10 min for b-catenin ChIP-seq. All cell fixations were wuenched by adding 125mM glycine during 5 min. After 2 ice-cold PBS washes, cells were scrapped off in PBS, pelleted and snap-frozen. RNA-seq: cells were washed 3 times with ice-cold PBS, scrapped off the plates, pelleted and snap frozen into liquid nitrogen. For RNA-extraction, the RNeasy Mini Kit (Qiagen, #74106) was used, with in-column DNA digestion. ChIP-seq: the ThruPLEX DNA-seq Kit (Rubicon Genomics, R400427) was used following manufacturer's instructions. RNA-seq: libraries were prepared using Illumina TruSeq Stranded mRNA sample preparation kits from 500ng of purified total RNA according to the manufacturer's protocol

Sequencing Platform

instrument_model
NextSeq 500

hg19

Number of total reads
52825455
Reads aligned (%)
66.4
Duplicates removed (%)
31.5
Number of peaks
3279 (qval < 1E-05)

hg38

Number of total reads
52825455
Reads aligned (%)
68.8
Duplicates removed (%)
29.6
Number of peaks
2694 (qval < 1E-05)

Base call quality data from DBCLS SRA