Sample information curated by ChIP-Atlas

Antigen

Antigen Class
ATAC-Seq
Antigen
ATAC-Seq

Cell type

Cell type Class
Blood
Cell type
Thymus
NA
NA

Attributes by original data submitter

Sample

source_name
Thymus
strain
C57BL/6
genotype
Aire+/+
cell type
MECs

Sequenced DNA Library

library_strategy
ATAC-seq
library_source
GENOMIC
library_selection
other
library_construction_protocol
Cells were isolated by tissue digestion and fluorescence activated cell sorting for viable CD45-Ly51loMHCIIhi as MECs and CD45-EpCAM-CD31-Ter-119-Sca-1+ as earskin fibroblasts Cells were suspended in 100ul of cold hypotonic lysis buffer [10mM Tris-HCl (pH 7.5), 10mM NaCl, 3mM MgCl2 and 0.1% NP40], followed by immediate centrifugation at 550g for 30 min. The pellet was re-suspended in 5ul of transposition reaction mix [1ul of Tagment DNA Enzyme and 2.5uL of Tagment DNA Buffer from Nextera DNA Sample Prep Kit (Illumina), 1.5ul H2O], and was incubated for 60 min at 37°C for DNA to be fragmented and tagged. For library preparation, two sequential 7-cycles of PCR were performed in order to enrich small tagmented DNA fragments. After the first PCR, the libraries were selected for small fragments (less than 600bp) using SPRI beads followed by a second round of PCR with the same conditions in order to obtain the final library

Sequencing Platform

instrument_model
NextSeq 500

mm10

Number of total reads
79250710
Reads aligned (%)
82.3
Duplicates removed (%)
44.2
Number of peaks
37581 (qval < 1E-05)

mm9

Number of total reads
79250710
Reads aligned (%)
82.3
Duplicates removed (%)
44.3
Number of peaks
37512 (qval < 1E-05)

Base call quality data from DBCLS SRA