Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
POLR2C

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 with ORF59 reporter
cell line
HCT116 colorectal line derivative
treatment
nontargeting siRNA, siNT
chip antibody
anti-RPB3 (Rabbit polyclonal, EMD Millipore, Cat#: ABE999, Lot #3764357)

Sequenced DNA Library

library_name
GSM6048109
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were fixed with 0.5% formaldehyde at RT for 10 min then quenched with 150 mM glycine at room temperature, 5 min. Cells were harvested by scraping in cold 1X PBS and pelleted at 1000 x g, 5 min at 4°C. Harvested cells were lysed for 30 min at 4°C in Farnham lysis buffer (5 mM PIPES, 85 mM KCl, 0.5% NP-40, 1 mM PMSF, 1X protease inhibitor cocktail (PIC)). Additional details of Dna shearing, and IP are given in Devlin et al. 2022. For ChIP-seq library preparations, 4 ng of ChIP or input DNA was processed using the KAPA Hyper Prep Kit according to the manufacturer's protocol (Roche KK8504).

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg38

Number of total reads
43663111
Reads aligned (%)
98.1
Duplicates removed (%)
22.8
Number of peaks
19999 (qval < 1E-05)

hg19

Number of total reads
43663111
Reads aligned (%)
97.5
Duplicates removed (%)
23.4
Number of peaks
19918 (qval < 1E-05)

Base call quality data from DBCLS SRA