Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
CBX5

Cell type

Cell type Class
Bone
Cell type
HT-1080
Primary Tissue
Bone
Tissue Diagnosis
Fibrosarcoma

Attributes by original data submitter

Sample

source_name
HT1080_ChIPseq_HP1alpha
cell line
HT1080
cell type
fibrosarcoma
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
60996531
Reads aligned (%)
97.3
Duplicates removed (%)
8.5
Number of peaks
896 (qval < 1E-05)

hg38

Number of total reads
60996531
Reads aligned (%)
98.7
Duplicates removed (%)
7.4
Number of peaks
1133 (qval < 1E-05)

Base call quality data from DBCLS SRA