Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
ZIC5

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 cells
passages
Low passages (6-10)
strain
human
chip antibody
ZIC5CT289 (homemade)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
RNA was extracted using QIAGEN RNeasy kit. DNA after ChIP protocol was isolated using QIAGEN PCR purification kit. ChIP-sequencing libraries were prepared using the KAPA HTP Library Preparation Kit complemented with NEXTflex DNA Barcodes from Bioo Scientific. 10 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 250- 450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit. RNA-sequencing libraries were prepared using the Illumina TruSeq Stranded Total RNA Preparation Kit with Ribo-Depletion. Input RNA quality was validated using the Agilent RNA 6000 Nano Kit. 200ng-1 µg of total RNA was used as starting material. Libraries were validated using the Agilent DNA 1000 Kit

Sequencing Platform

instrument_model
NextSeq 500

hg19

Number of total reads
73620028
Reads aligned (%)
75.0
Duplicates removed (%)
19.1
Number of peaks
6663 (qval < 1E-05)

hg38

Number of total reads
73620028
Reads aligned (%)
76.6
Duplicates removed (%)
18.1
Number of peaks
6625 (qval < 1E-05)

Base call quality data from DBCLS SRA