Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
CBX5

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_ChIPseq_HP1alpha
cell line
HCT116
cell type
colon cancer cell line
cell line source gender
male
library strategy
ChIP-seq
chip antibody
anti-HP1alpha (CST:2616)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were grown to ~75% confluency, harvested with trypsin, washed in 1X PBS, and frozen/stored at -80°C. Thawed cells were fixed in 1% formaldehyde and quenched in 0.125M Glycine, then washed twice in 1X PBS. Fixed cells were then resuspended in 500ul lysis buffer (50mM Tris-HCl pH 8.0, 10mM NaCl, 0.2% NP40, 1X PITC) for 30 min on ice with periodic resuspension. Libraries were prepared using NEB UltraII DNA library kit

Sequencing Platform

instrument_model
NextSeq 500

hg19

Number of total reads
40090333
Reads aligned (%)
181.1
Duplicates removed (%)
5.1
Number of peaks
632 (qval < 1E-05)

hg38

Number of total reads
40090333
Reads aligned (%)
186.0
Duplicates removed (%)
4.5
Number of peaks
1281 (qval < 1E-05)

Base call quality data from DBCLS SRA