Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
CTCF

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
colon-derived
cell line
HCT116
cell type
HCT116 colorectal carcinoma
tissue
colon-derived
chip antibody
CTCF antibody 61311 Active Motif

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Human HCT116 cells were grown to 200,000 cells per well, crosslinked, and sheared using 96-well plate PIXUL sonicator. Fragmented chromatin was used in ChIP assays with the listed antibodies. ChIP and library prep was performed for each factor from a single well using Active Motif's Low Cell ChIP-Seq Kit (Catalog number 53084). Libraries were sequenced on a NextSeq 500 as PE75 or SE75 with dual 8bp indexing, allowing for PCR de-duplication with molecular identifiers at the i5 position (see product manual).

Sequencing Platform

instrument_model
NextSeq 500

hg19

Number of total reads
16315794
Reads aligned (%)
177.3
Duplicates removed (%)
6.1
Number of peaks
2034 (qval < 1E-05)

hg38

Number of total reads
16315794
Reads aligned (%)
178.6
Duplicates removed (%)
6.1
Number of peaks
2069 (qval < 1E-05)

Base call quality data from DBCLS SRA