Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
TRIM28

Cell type

Cell type Class
Pluripotent stem cell
Cell type
hESC WIBR3
NA
NA

Attributes by original data submitter

Sample

source_name
WIBR3
cell line
WIBR3
medium
hESM
chip antibody
KAP1
antibody manufacturer and catalog number
Abcam ab10483

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Pellets were lysed, resuspended in 1mL of LB1 on ice for 10min (50 mM HEPES-KOH pH 7.4, 140 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 10% Glycerol, 0.5% NP40, 0.25% Tx100, protease inhibitors), then after centrifugation resuspend in LB2 on ice for 10min (10 mM Tris pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA and protease inhibitors). After centrifugation, resuspend in LB3 (10 mM Tris pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% NaDOC, 0.1% SDS and protease inhibitors) and sonicated (Covaris settings: 5% duty, 200 cycle, 140 PIP, 60 min), yielding genomic DNA fragments with a bulk size of 100-300 bp Libraries of immunoprecipitated chromatin and total input control from ChIP were performed with single-end adaptors as previously described (Rowe et al., 2013b). Sequencing was performed on an Illumina HiSeq 2500 (Illumina), with each library sequenced in 100-bp reads run.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg19

Number of total reads
34611103
Reads aligned (%)
66.3
Duplicates removed (%)
6.9
Number of peaks
3836 (qval < 1E-05)

hg38

Number of total reads
34611103
Reads aligned (%)
87.1
Duplicates removed (%)
6.3
Number of peaks
5523 (qval < 1E-05)

Base call quality data from DBCLS SRA