Sample information curated by ChIP-Atlas

Antigen

Antigen Class
ATAC-Seq
Antigen
ATAC-Seq

Cell type

Cell type Class
Blood
Cell type
Plasmacytoid dendritic cells
NA
NA

Attributes by original data submitter

Sample

source_name
Plasmacytoid dendritic cell (pDC)
cell type
Plasmacytoid dendritic cell (pDC)

Sequenced DNA Library

library_strategy
ATAC-seq
library_source
GENOMIC
library_selection
other
library_construction_protocol
Omni-ATAC-seq was performed according to Corces et al., Nature Methods 14, 959-962, 2017 with minor modifications. Prior to transposition dead cells were removed by centrifugation (800 rpm, 4 min, 4°C). The transposition reaction was with 7.5 µl Tagment DNA Enzyme 1 (TDE1) for 60 min at 37°C. Pre-amplification was with NEBNext Ultra II Q5 Master Mix and Nextera PCR Primers (5 cycles). Quantitative PCR amplification was with NEBNext Ultra II Q5 Master Mix, Nextera PCR Primer and SYBR Gold to determine the number of additional cycles. PCR amplification of additional cycles was as for pre-amplification. PCR fragments were purified with Qiagen MinElute PCR Purification Kit and library concentration and quality were determined by Agilent High Sensitive DNA Kit and Bioanalyzer, respectively.

Sequencing Platform

instrument_model
Illumina Genome Analyzer IIx

mm10

Number of total reads
45220783
Reads aligned (%)
95.7
Duplicates removed (%)
5.6
Number of peaks
13057 (qval < 1E-05)

mm9

Number of total reads
45220783
Reads aligned (%)
95.5
Duplicates removed (%)
5.7
Number of peaks
13019 (qval < 1E-05)

Base call quality data from DBCLS SRA