Sample information curated by ChIP-Atlas

Antigen

Antigen Class
ATAC-Seq
Antigen
ATAC-Seq

Cell type

Cell type Class
Blood
Cell type
CD8+ T cells
NA
NA

Attributes by original data submitter

Sample

source_name
Spleen and lymph nodes
strain
C57BL/6J TCRalpha-/- P14
cell type
CD8+ T cells
treatment
anti-CD3 + PMA

Sequenced DNA Library

library_strategy
ATAC-seq
library_source
GENOMIC
library_selection
other
library_construction_protocol
ATAC-seq was performed according to Buenrostro et al. (Nature Methods 2013) with minor modifications: 30,000 to 50,000 sorted CD8+ T cells cells were lysed to extract nuclei. Nuclei were resuspended in 50 ul 1xTD Buffer containing 2.5 μl transposase (Nextera, Illumina). The transposase reaction was conducted for 30 minutes at 37°C, with mild shaking. Library amplification and barcoding were performed with the library amplification kit (KAPA Biosystems) using Index Primers, designed according to Buenrostro et al. (Nature Methods 2013) at a final concentration of 500 nM. PCR reaction was conducted for 10-11 cycles. Library purification was performed with the MinElute PCR Purification Kit (Qiagen) and library size distribution was assessed using the Bioanalyzer High Sensitivity DNA Kit (Agilent). ATAC-seq libraries were quantified prior to pooling and sequencing using the real-time library quantification kit (KAPA Biosystems).

Sequencing Platform

instrument_model
Illumina HiSeq 2500

mm10

Number of total reads
66595065
Reads aligned (%)
97.5
Duplicates removed (%)
48.4
Number of peaks
28857 (qval < 1E-05)

mm9

Number of total reads
66595065
Reads aligned (%)
97.5
Duplicates removed (%)
48.5
Number of peaks
28843 (qval < 1E-05)

Base call quality data from DBCLS SRA