Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
SKP2

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
Colon carcinoma
cell line
HCT116
cell type
Cultured cancer cell line
chip antibody
SKP2 antibody (ab68455, Abcam)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
DNA from asynchronous cell cultures was isolated, size fractionated and subject to exunuclease digestion as described in Aladjem et al., Science 281, 1005, 1998. and Wang et al., Molecular and Cellular Biology 24:3373-86, 2004. For ChipSeq, DNA molecules were enriched using each antibodies. Enriched DNA molecules were then amplified randam primer with klenow fragment and sequenced by Illumina Genome Analyzer IIx. Illumina Genomic DNA protocol (Illumina Paired-END DNA Sample Prep Kit). Illumina paired-end sequencing

Sequencing Platform

instrument_model
Illumina Genome Analyzer

hg19

Number of total reads
63452096
Reads aligned (%)
60.4
Duplicates removed (%)
8.3
Number of peaks
66907 (qval < 1E-05)

hg38

Number of total reads
63452096
Reads aligned (%)
61.3
Duplicates removed (%)
7.9
Number of peaks
67036 (qval < 1E-05)

Base call quality data from DBCLS SRA