Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
PAF1

Cell type

Cell type Class
Digestive tract
Cell type
HCT 116
Primary Tissue
Colon
Tissue Diagnosis
Carcinoma

Attributes by original data submitter

Sample

source_name
HCT116
cell type
colorectal cancer cell line
cell line
HCT116
shRNA
No shRNA
chip antibody
PAF1 (Abcam, catalog# ab20662, lot# GR243511-1)

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. 4C-seq was performed following the protocol published in (van de Werken et al. 2012). In brief, cross-linked chromatin was digested with DpnII, ligated under diluted conditions. Cross-links were reversed and DNA was further digested by NlaIII and again ligated under diluted conditions. For each viewpoint approximately 3.2 μg of the 4C-seq library was amplified using 16 individual PCR reactions with inverse primers containing Illumina adaptor sequence. Multiplexed samples were sequenced on the Illumina Nextseq500 system using 75 bp single-end reads according to the manufacturer's specifications.

Sequencing Platform

instrument_model
NextSeq 500

hg19

Number of total reads
26317287
Reads aligned (%)
90.5
Duplicates removed (%)
7.6
Number of peaks
3370 (qval < 1E-05)

hg38

Number of total reads
26317287
Reads aligned (%)
93.6
Duplicates removed (%)
5.3
Number of peaks
3417 (qval < 1E-05)

Base call quality data from DBCLS SRA