Sample information curated by ChIP-Atlas

Antigen

Antigen Class
ATAC-Seq
Antigen
ATAC-Seq

Cell type

Cell type Class
Pancreas
Cell type
PDAC
NA
NA

Attributes by original data submitter

Sample

source_name
flow sorted nuclei_PDAC_PDX
tissue
pancreatic ductal adenocarcinoma (PDAC)
tissue type
patient derived xenografts (PDXs)
treatment
DNA content flow sorted

Sequenced DNA Library

library_strategy
ATAC-seq
library_source
GENOMIC
library_selection
other
library_construction_protocol
Approximately 50,000 flow sorted nuclei were utilized for OMNI ATAC-seq following the protocol by Corces et al. (Corces MR, Trevino AE, Hamilton EG, Greenside PG, Sinnott-Armstrong NA, Vesuna S, et al. An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues. Nature methods 2017;14:959-62). Nuclei were subjected to transposition reaction following cell lysis and washing steps. The transposition reaction was performed at 37 °C for 30 min in a thermomixer with shaking at 1,000 r.p.m. DNA was purified and indexed ATAC-seq libraries amplified by PCR. The enrichment of accessible regions in each library was determined by real-time PCR targeting known highly accessible and closed chromatin sites and expressed as fold difference. Libraries passing this quality control step were sequenced to 51 base pairs from both ends on an Illumina HiSeq 4000 instrument at the Mayo Clinic Center for Individualized Medicine Medical Genomics Facility.

Sequencing Platform

instrument_model
Illumina HiSeq 4000

hg38

Number of total reads
59030398
Reads aligned (%)
90.3
Duplicates removed (%)
34.9
Number of peaks
14660 (qval < 1E-05)

hg19

Number of total reads
59030398
Reads aligned (%)
89.4
Duplicates removed (%)
35.4
Number of peaks
14347 (qval < 1E-05)

Base call quality data from DBCLS SRA