Sample information curated by ChIP-Atlas

Antigen

Antigen Class
ATAC-Seq
Antigen
ATAC-Seq

Cell type

Cell type Class
Blood
Cell type
Monocyte-dendritic cell progenitor
NA
NA

Attributes by original data submitter

Sample

source_name
Bone marrow
cell type
Monocyte/dendric cell progenitor
strain/genotype
C57BL/6 WT

Sequenced DNA Library

library_strategy
ATAC-seq
library_source
GENOMIC
library_selection
other
library_construction_protocol
MDPs, CDPs, and pre-cDC1s were sorted from bone marrow and lysed in ice-cold ATAC-RSB buffer containing 0.1% NP40, 0.1% Tween-20, and 0.01% digitonin. Cells were incubated at 4° C for 3 min, then washed with ATAC-RSB buffer containing only 0.1% Tween-20. Nuclei were spun down by centrifugation and then incubated in 50 µL of transposition buffer (25 µL 2X TD buffer, 22.5 µL dH2O, 2.5 µL Tn5 transposase (Nextera DNA Library Prep Kit, Illumina)) and incubated at 37° C for 30 min. If 10,000 cells could not be obtained for a certain population then the quantity of Tn5 transposase was titrated down proportionately to the number of cells obtained but cells were still incubated in 50 µL total. Transposed DNA was purified with a DNA Clean & Concentrator kit (Zymo Research), eluted in 21 µL of elution buffer, and stored at -20° C until amplification. Nextera DNA Library Prep Kit

Sequencing Platform

instrument_model
NextSeq 500

mm10

Number of total reads
25244462
Reads aligned (%)
82.2
Duplicates removed (%)
12.6
Number of peaks
55789 (qval < 1E-05)

mm9

Number of total reads
25244462
Reads aligned (%)
82.0
Duplicates removed (%)
12.6
Number of peaks
55721 (qval < 1E-05)

Base call quality data from DBCLS SRA