Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Unclassified
Antigen
Unclassified

Cell type

Cell type Class
Digestive tract
Cell type
SW 480
Primary Tissue
unresolved
Tissue Diagnosis
unresolved

Attributes by original data submitter

Sample

source_name
SW480
cell line
SW480
sirna treatment
siHJURP
antibody
α-ACA Serum (Centromere Ab Pos. Serum, BBI Solutions)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Libraries were constructed using the Illumina TruSeq ChIP Sample Prep Kit (#IP-202-1012-1024). The soluble fraction of CENP-A was obtained by suspending cells in PBS with 0.5% NP-40 for 5 minutes on ice. Nuclei were then pelleted via centrifugation for 1 minute at 1000 RPM. Nuclei were once again resuspended in PBS NP-40 buffer and pelleted via centrifugation as before. Supernatants were pre-cleared via centrifugation at 12000 RPM for 10 minutes and the resulting supernatant was used in the IP. Native ChIP was performed as in (Bui et al., Epigenetics Chromatin 2017) with the exception of a longer MNase digest of 15 minutes. For each of four independent replicates (or duplicates for double knockdowns), libraries were constructed using the Illumina TruSeq ChIP Sample Prep Kit (#IP-202-1012-1024).

Sequencing Platform

instrument_model
NextSeq 500

hg38

Number of total reads
98754744
Reads aligned (%)
95.1
Duplicates removed (%)
13.1
Number of peaks
4659 (qval < 1E-05)

hg19

Number of total reads
98754744
Reads aligned (%)
93.5
Duplicates removed (%)
16.7
Number of peaks
799 (qval < 1E-05)

Base call quality data from DBCLS SRA