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
Thymus
strain/background
C57BL/6 (CD45.2)
genotype/variation
Arid1a-KO
cell type
Thymic DN3 T-cell progenitor

Sequenced DNA Library

library_strategy
ATAC-seq
library_source
GENOMIC
library_selection
other
library_construction_protocol
ATAC-seq: ATAC-seq library preparation was done as described in (Buenrostro et al. 2013) using Transposomes from Nextera DNA library preparation kit (Illumina, San Diego, CA) and custom primers. Libraries were run single read on the Illumina NexSeq500. RNA-seq: Total RNA was isolated by use of RNeasy Micro Kit (Qiagen, Hilden, Germany) according to manufacturer's recommendations. RNA-seq libraries were constructed using NuGEN's Ovation Ultralow Library systems (NuGEN Technologies, San Carlos, CA) and were subsequently subjected to 76 cycles of NextSeq500 sequencing (Illumina, San Diego, CA).

Sequencing Platform

instrument_model
NextSeq 500

mm10

Number of total reads
41541742
Reads aligned (%)
97.5
Duplicates removed (%)
48.4
Number of peaks
19673 (qval < 1E-05)

mm9

Number of total reads
41541742
Reads aligned (%)
97.3
Duplicates removed (%)
48.4
Number of peaks
19659 (qval < 1E-05)

Base call quality data from DBCLS SRA