Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Pancreas
Cell type
SW 1990
Primary Tissue
Pancreas
Tissue Diagnosis
Adenocarcinoma

Attributes by original data submitter

Sample

source_name
SW1990
cell line
Pancreatic ductal adenocarcinoma cell line SW1990
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
98058997
Reads aligned (%)
99.3
Duplicates removed (%)
7.6
Number of peaks
2233 (qval < 1E-05)

hg19

Number of total reads
98058997
Reads aligned (%)
98.7
Duplicates removed (%)
7.9
Number of peaks
1342 (qval < 1E-05)

Base call quality data from DBCLS SRA