Sample information curated by ChIP-Atlas

Antigen

Antigen Class
RNA polymerase
Antigen
RNA polymerase II

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
both Methamphetamine and HIV Tat
cell line
THP1
cell type
Monocytic/Innate Immune
passages
12
chip antibody
RNA Pol II antibody (mAb clone ab5095,Abcam)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
The pellets were sonicated and the chromatin was treated with Rnase, proteinase K and heat (65oC), followed by phenol and chlorophorm extractions, and ethanol precipitation. Pellets were resuspended in 10mM Tris, 1mM EDTA, and quantified in Nanodrop. Libraries were prepared using Illumina Hi-Seq, and mapped to the genome using BWA algorithm using default settings.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg38

Number of total reads
40019315
Reads aligned (%)
94.0
Duplicates removed (%)
12.1
Number of peaks
4427 (qval < 1E-05)

hg19

Number of total reads
40019315
Reads aligned (%)
93.2
Duplicates removed (%)
13.1
Number of peaks
4362 (qval < 1E-05)

Base call quality data from DBCLS SRA