Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
STAT1

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 THP1
antibodies
Stat1 (D4Y6Z) Cell Signaling Technology Cat# 14995, RRID:AB_2716280
genotype
wildtype

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were washed 2x with ice cold PBS and crosslinked for 10 minutes at room temperature in 1% formaldehyde PBS (thermos fischer #28906). The cross-linked chromatin was sheared by sonication, providing fragments of 200 - 1400 base pairs in length.Protein-DNA complexes were selectively immunoprecipitated using STAT1,STAT2 and IRF9 antibodies. The immunoprecipitated complexes were washed to remove non-specifically bound chromatin, the protein-DNA cross-link was reversed and proteins were removed by proteinase K digest. Four IPs were pooled for each sample, in order to obtain enough DNA precipitated. The DNA associated with the complex was furthermore purified and used for ChIP-seq. For library generation, the NEBNext Ultra II DNA Library Prep Kit for Illumina from NEB was used according to the manufacturer's protocol. The chromatin quality was analyzed on an Agilent 2100 Bioanalyzer and a size selection of 200-1400bp was carried out.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg19

Number of total reads
42194395
Reads aligned (%)
17.7
Duplicates removed (%)
78.1
Number of peaks
439 (qval < 1E-05)

hg38

Number of total reads
42194395
Reads aligned (%)
19.5
Duplicates removed (%)
76.0
Number of peaks
658 (qval < 1E-05)

Base call quality data from DBCLS SRA