Sample information curated by ChIP-Atlas

Antigen

Antigen Class
ATAC-Seq
Antigen
ATAC-Seq

Cell type

Cell type Class
Blood
Cell type
CD4 CD8 double negative cells
NA
NA

Attributes by original data submitter

Sample

source_name
in-vitro DN2 cells
strain
C57BL/6
genotype
WT
chip antibody
none

Sequenced DNA Library

library_strategy
ATAC-seq
library_source
GENOMIC
library_selection
other
library_construction_protocol
Harvested cells were stained with lineage marker, CD25, CD117, ghost dye red 780. Lineage negative DN2 cells were sorted by FACS AriaII and washed with PBS. 50000 cells were used for library preparation. Washed cells were resuspended in lysis buffer. After washing, cells were treated with transposition mix for 30 min at 37 degrees. Cycle of PCR amplification was determined by q-PCR. 100-800 bps of Libraries were selected from 2% agarose gel.

Sequencing Platform

instrument_model
Illumina HiSeq 4000

mm10

Number of total reads
65875582
Reads aligned (%)
95.2
Duplicates removed (%)
74.0
Number of peaks
57869 (qval < 1E-05)

mm9

Number of total reads
65875582
Reads aligned (%)
95.1
Duplicates removed (%)
74.1
Number of peaks
57819 (qval < 1E-05)

Base call quality data from DBCLS SRA