Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
CBFA2T2

Cell type

Cell type Class
Pluripotent stem cell
Cell type
NCCIT
Primary Tissue
Testis
Tissue Diagnosis
Teratoma

Attributes by original data submitter

Sample

source_name
NCCIT cells
cell line
NCCIT Embryonal Carcinoma cell line
chip antibody
CBFA2T2 (Bethyl, catalog# A303-593A)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were lysed in ChIP buffer (50 mM Tris-HCl pH 7.9, 150 mM NaCl, 1% Triron X-100, 0.5% NP-40, 5 mM EDTA pH 8.0, 1 mM PMSF and protease inhibitor) and chromatin was sonicated to ~200 bp with a Diagenode Bioruptor Libraries were prepared according to manufacturer’s instructions (Illumina). Immunoprecipitated DNA was first end-repaired using End-It Repair Kit (Epicenter), tailed with an A using Klenow exo minus (NEB M0212), and ligated to custom adapters. Fragments of 300±100 bp were size-selected and subjected to ligation-mediated PCR amplification (LM-PCR), using Q5 polymerase (NEB M0530).

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
21489427
Reads aligned (%)
41.6
Duplicates removed (%)
10.1
Number of peaks
985 (qval < 1E-05)

hg38

Number of total reads
21489427
Reads aligned (%)
41.9
Duplicates removed (%)
9.7
Number of peaks
985 (qval < 1E-05)

Base call quality data from DBCLS SRA