Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
BRD4

Cell type

Cell type Class
Digestive tract
Cell type
SNU-16
Primary Tissue
Stomach
Site of Extraction
Ascites
Tissue Diagnosis
Carcinoma

Attributes by original data submitter

Sample

source_name
SNU16 cells
cell type
SNU16
chip antibody
BRD4 (Bethyl Laboratories A301-985A100)
treatment
none

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Sonicated chromatin from cross-linked cells was immunoprecipitated using H3K27ac (Abcam ab4729) and BRD4 (Bethyl Laboratories A301-985A100) antibodies. Following crosslink reversal, RNAse and Proteinase K treatment, immunoprecipitated DNA was purified using the ChIP DNA Clean & Concentrator kit (Zymo Research D5205). Libraries were constructed using the NEBNext Ultra II DNA Library Prep Kit for Illumina kit.

Sequencing Platform

instrument_model
Illumina HiSeq 4000

hg38

Number of total reads
28412166
Reads aligned (%)
93.4
Duplicates removed (%)
28.3
Number of peaks
3017 (qval < 1E-05)

hg19

Number of total reads
28412166
Reads aligned (%)
92.1
Duplicates removed (%)
29.2
Number of peaks
1915 (qval < 1E-05)

Base call quality data from DBCLS SRA