Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
VDR

Cell type

Cell type Class
Blood
Cell type
THP-1
Primary Tissue
Blood
Tissue Diagnosis
Leukemia Acute Myelogenous

Attributes by original data submitter

Sample

source_name
human monocytic cell line THP-1
cell line
monocytic cell line THP-1
treatment
100 nM 1,25(OH)2D3
time
2 h
chip antibody
VDR (Cell Signaling Technologies CST 12550)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
proteins were crosslinked with formaldehyde to DNA, then VDR-bound fragments were pulled down by chromatin immunoprecipitation ChIP-seq library was prepared from 5-10 ng ChIP DNA with the NEBNext Ultra II DNA Library Prep Kit (New England Biolabs) per manufacturer's protocol

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
10347179
Reads aligned (%)
92.7
Duplicates removed (%)
5.4
Number of peaks
1181 (qval < 1E-05)

hg38

Number of total reads
10347179
Reads aligned (%)
94.8
Duplicates removed (%)
4.2
Number of peaks
1085 (qval < 1E-05)

Base call quality data from DBCLS SRA