Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
ZFX

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
Human colon cancer cell line HCT116
tissue
Human colon cancer cell line HCT116
cell line
HCT116
chip antibody
ZFX
sirna
none

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
For RNA-seq, RNA was extracted using Trizol reagent (15596-026) (Life technologies, Carlsbad, CA) following its protocol. For ChIP-seq, cells were crosslinked using 1% formaldehyde andl lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody. For NOMe-seq, after isolating nuclei from the cells, M.CviPI was treated to methylate accessible GpCs. After purifying M.CvPI-treated DNA, sonication was performed. Bisulfite treatment of M.CviPI-methylated DNA resulted to convert all unmethylated Cs to Ts. RNA-seq libraries were made using KAPA Stranded mRNA-Seq Kit with KAPA mRNA Capture Beads (KK8420) (Kapa Biosystems, Woburn, MA). ChIP-seq: Libraries were barcoded (NEXTflex™ DNA Barcodes) (Bio Scientific, Austin, TX). NOMe-seq: Libraries were generated using the Accel-NGS Methyl-Seq DNA Library Kit for Illumina Platforms.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
76138383
Reads aligned (%)
181.7
Duplicates removed (%)
6.2
Number of peaks
7246 (qval < 1E-05)

hg38

Number of total reads
76138383
Reads aligned (%)
184.2
Duplicates removed (%)
6.0
Number of peaks
8661 (qval < 1E-05)

Base call quality data from DBCLS SRA