Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
TRIM28

Cell type

Cell type Class
Blood
Cell type
CD34 Hematopoietic stem cells
NA
NA

Attributes by original data submitter

Sample

source_name
TB40-E HCMV strain infected CD34+ cells
cell type
Human hematopoietic stem cells CD34+ freshly purified
disease state
5 days of HCMV infection
sample pool
mixed patients
antibody
against KAP1

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
For Chipseq CD34+ infected cells were crosslinked by 1% formaldehyde and sonicated, and chromatin was immunoprecipitated by using an affinity-purified rabbit polyclonal antibody raised against KAP1 aa 20–418, RBCC (F. R. Santoni de Sio et al.,. Blood 119, 4675 (2012)). Detailed protocols for ChIP are described in D. C. Schultz,. Genes Dev 15, 428 (2001). Reverse cross-linking was performed overnight in the presence of proteinase K and RNase, followed by DNA extraction using the MinElute PCR purification kit (Quiagen) according to manufacturer protocol. The library was generated from 10 ng total DNA using the TruSeq Illumina Preparation Kit.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
163043249
Reads aligned (%)
43.1
Duplicates removed (%)
52.9
Number of peaks
179825 (qval < 1E-05)

hg38

Number of total reads
163043249
Reads aligned (%)
44.1
Duplicates removed (%)
52.0
Number of peaks
180689 (qval < 1E-05)

Base call quality data from DBCLS SRA