Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

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
SW 480
cimp status
CIMP (-)
chip antibody
None
cell line
SW 480

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were fixed with 1% formaldehyde for 15 minutes (Brd4 ChIP) or 5 minutes (H3K27ac ChIP). DNA was sonicated to an average length of 200 - 500 bp. IP and Input DNA was reverse crosslinked and purified for library preparation. Illumina sequencing libraries were prepared from the ChIP and Input DNAs by the standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg38

Number of total reads
42994248
Reads aligned (%)
88.7
Duplicates removed (%)
2.8
Number of peaks
1456 (qval < 1E-05)

hg19

Number of total reads
42994248
Reads aligned (%)
87.8
Duplicates removed (%)
4.0
Number of peaks
1425 (qval < 1E-05)

Base call quality data from DBCLS SRA