Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
RAD21

Cell type

Cell type Class
Uterus
Cell type
HEC-1-B
Primary Tissue
Uterus
Tissue Diagnosis
Adenocarcinoma Endometrioid

Attributes by original data submitter

Sample

source_name
HEC-1-B cells
cell type
human endometrial adenocarcinoma
antibody
Rad21
genotype
RRFF insertion

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
4 × 10^6 of cells were cross-linked by 1% formaldehyde in 10% FBS/PBS for 10 min at room temperature. Cells were then lysed twice with ice-cold lysis buffer (20 mM Tris-HCl, 2 mM EDTA, 1% Triton X-100, 0.1% SDS, 0.1% sodium deoxycholate and 1× protease inhibitors, pH 7.5) for 10 min with slow rotations. Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3' end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg19

Number of total reads
14614464
Reads aligned (%)
85.4
Duplicates removed (%)
12.7
Number of peaks
3394 (qval < 1E-05)

hg38

Number of total reads
14614464
Reads aligned (%)
86.6
Duplicates removed (%)
11.9
Number of peaks
3333 (qval < 1E-05)

Base call quality data from DBCLS SRA