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
THP1 cells
cell type
AML leukemia cell line
cell line
THP1
shRNA
PAF1 shRNA
chip antibody
Pol II(CST, #14958)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
For ChIP-seq, cells were crosslinked with 1% paraformaldehyde for 10 minutes at room temperature with gentle rotation, and then quenched by 0.125 M glycine solution. After washing, nuclei were sonicated using Covaris Sonicator, and the supernatant was used for immunoprecipitation with the indicated antibody. ChIP-sequencing libraries were prepared with Illumina's Tru-seq DNA sample prep kit. Total RNA was extracted from cells using RNeasy mini Kit (Qiagen) followed by ribosomal RNA depletion with the RiboZero kit (Epicenter). Poly(A) depleted and Poly(A)-enriched RNA were separated by 3 rounds of Oligo(dT) magnetic beads (Thermo). For sequencing, 2 μg of resulting RNA was used for ribosomal RNA depletion with the RiboZero kit (Epicenter) and libraries were made with the TruSeq RNA sample Prep Kit (Illumina). ChIP-sequencing libraries were prepared with Illumina's Tru-seq DNA sample prep kit using standard protocols. RNA-seq libraries were prepared with Illumina's TruSeq RNA sample Prep Kit using standard protocols.

Sequencing Platform

instrument_model
NextSeq 500

hg38

Number of total reads
34362886
Reads aligned (%)
90.7
Duplicates removed (%)
8.1
Number of peaks
11984 (qval < 1E-05)

hg19

Number of total reads
34362886
Reads aligned (%)
90.2
Duplicates removed (%)
8.7
Number of peaks
12100 (qval < 1E-05)

Base call quality data from DBCLS SRA