Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
TLE3

Cell type

Cell type Class
Breast
Cell type
SUM 149PT
Primary Tissue
Breast
Tissue Diagnosis
Adenocarcinoma Ductal

Attributes by original data submitter

Sample

source_name
SUM149PT
chip antibody
TLE3
treatment
Dox

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
30427527
Reads aligned (%)
77.0
Duplicates removed (%)
19.5
Number of peaks
37925 (qval < 1E-05)

hg38

Number of total reads
30427527
Reads aligned (%)
78.5
Duplicates removed (%)
18.4
Number of peaks
38136 (qval < 1E-05)

Base call quality data from DBCLS SRA