Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
PSIP1

Cell type

Cell type Class
Blood
Cell type
CD4+ T cells
NA
NA

Attributes by original data submitter

Sample

source_name
CD4+ T cells
cell type
Primary CD4+ T cells
chip antibody
anti-LEDGF/p75 (Bethyl, A300-848)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
30E7 CD4+ T cells were fixed with 1% formaldehyde (25°C, 10 min) and stopped with 0.125M Glycine. Nuclei were sonicated using a Diagenode Bioruptor (Liege) to produce fragments of ~200 bp. LEDGF/p75-bound chromatin fragments were immunoprecipitated with antibody A300-848. Libraries were generated according to the Illumina TruSeq DNA Sample preparation guide. Briefly, the immunoprecipitated DNA was end-repaired, A-tailed and ligated to TruSeq adapters. After PCR amplification with 15 cycles and gel size selection of ~300bp fragments, libraries were captured and sequenced using the Illumina HiSeq 2000.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
53202962
Reads aligned (%)
50.3
Duplicates removed (%)
43.0
Number of peaks
1950 (qval < 1E-05)

hg38

Number of total reads
53202962
Reads aligned (%)
51.1
Duplicates removed (%)
42.5
Number of peaks
2109 (qval < 1E-05)

Base call quality data from DBCLS SRA