Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Pancreas
Cell type
AsPC-1
Primary Tissue
Pancreas
Tissue Diagnosis
Adenocarcinoma

Attributes by original data submitter

Sample

source_name
AsPC-1
cell line
Pancreatic ductal adenocarcinoma cell line AsPC-1
chip antibody
none

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were fixed 1% formaldehyde, followed by quenching with 125mM of glycine. The cells were washed with ice-cold PBS and were lysed. The crosslinked chromatin was shared with a Bioruptor Sonicator (CosmoBio) and target protein-DNA complexes were isolated with antibody. ChIP-seq libraries were prepared from ~10 ng of ChIP DNA with the use of Ovation Ultralow DR Multiplex System (Nugen). The DNA libraries were clonally amplified on a flow cell and sequenced on HiSeq2500 (HiSeq Control Software v2.2.38, Illumina) with 51-mer paired-end sequence. Image analysis and base calling were performed using Real-Time Analysis Software (v1.18.61, Illumina).

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg38

Number of total reads
97423170
Reads aligned (%)
99.3
Duplicates removed (%)
7.9
Number of peaks
1585 (qval < 1E-05)

hg19

Number of total reads
97423170
Reads aligned (%)
98.8
Duplicates removed (%)
8.2
Number of peaks
778 (qval < 1E-05)

Base call quality data from DBCLS SRA