Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

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
Human colorectal tumor
passages
Low passages (6-10)
cell line
HCT116
chip antibody
N/A

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
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.

Sequencing Platform

instrument_model
NextSeq 500

hg38

Number of total reads
45708303
Reads aligned (%)
98.5
Duplicates removed (%)
4.6
Number of peaks
1255 (qval < 1E-05)

hg19

Number of total reads
45708303
Reads aligned (%)
97.5
Duplicates removed (%)
5.8
Number of peaks
1354 (qval < 1E-05)

Base call quality data from DBCLS SRA