Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
TP63

Cell type

Cell type Class
Pancreas
Cell type
BxPC-3
Primary Tissue
Pancreas
Tissue Diagnosis
Adenocarcinoma

Attributes by original data submitter

Sample

source_name
BxPC3
cell type
BxPC3
genotype/variation
wildtype
chip antibodies
39692, CST

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
After cross-link, cells were incubated with cell lysis buffer (10mM Tris pH8.0, 10mM NaCl, 0.2% NP-40) and then resuspended and sonicated in nuclei lysis buffer (50mM Tris pH8.0, 10mM EDTA, 1%SDS) for 15mins, followed by ChIP Library was constructed using Illumina TruSeq ChIP Sample Prep kit following manufacture's protocol. Briefly, ChIP DNA was end repaired, followed by A tailing and size selection (250-500 bp) by gel electrophoresis. 15 PCR cycles were used for final library amplification and the library was analyzed on Bioanalyzer using high sensitivity DNA chip (Agilent) on Bio-analyzer.

Sequencing Platform

instrument_model
NextSeq 500

hg19

Number of total reads
29098686
Reads aligned (%)
82.6
Duplicates removed (%)
15.1
Number of peaks
40730 (qval < 1E-05)

hg38

Number of total reads
29098686
Reads aligned (%)
83.9
Duplicates removed (%)
14.2
Number of peaks
40823 (qval < 1E-05)

Base call quality data from DBCLS SRA