Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
MED16

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 colorectal cancer cells
cell line
HCT116
factor
MED16
usp22 status
wt
shRNA
shLuc
treatment
T
replicate
2
antibody
Abcam cat# ab130996

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were fixed in 1% formaldehyde for 10 minutes at room temperature, followed by quenching with 0.18 M Glycine for 5 minutes. Cells were harvested and chromatin was extracted 10 ng of DNA from Inputs and IPs were used to prepare libraries using Accel-NGS 2S Plus DNA Library Kit (Swift Biosciences, MI) following manufacturer's protocol with an additional wash at the end using SPRIselect beads (Beckman Coulter, IN) to remove any larger libraries that could interfere with clustering on the instrument

Sequencing Platform

instrument_model
NextSeq 500

hg19

Number of total reads
34796476
Reads aligned (%)
93.6
Duplicates removed (%)
0.3
Number of peaks
709 (qval < 1E-05)

hg38

Number of total reads
34796476
Reads aligned (%)
94.2
Duplicates removed (%)
0.4
Number of peaks
507 (qval < 1E-05)

Base call quality data from DBCLS SRA