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
d9 1mM_Glucose
strain
C57BL/6
tissue
spleens and peripheral lymph nodes
cell type
CD8 T cells
genotype
OT-I
days of glucose restriction
5

Sequenced DNA Library

library_strategy
ATAC-seq
library_source
GENOMIC
library_selection
other
library_construction_protocol
5x10^4 T cells treated as described were washed in PBS and then lysed in 10 mM Tris-HCl, pH 7.4,10 mM NaCl, 3 mM MgCl2 and 0.1% Igepal CA-630 (all Sigma). Nuclei were then spun down and then resuspend in 25 μl TD (2x reaction buffer), 2.5 μL TDE1 (Nextera Tn5 Transposase) and 22.5 μL nuclease-free water, incubated for 30 min at 37°C. DNA was purified with the Qiagen MinElute PCR Purification Kit (Thermo Fisher Scientific). PCR amplification was performed with the NEBNext High-Fidelity 2x PCR Master Mix (New England Labs) using custom Nextera PCR Primers containing barcodes. Adaptors were removed with AMPure XP beads according to manufacturer's protocol. Libraries were quantified with the Qubit and submitted for sequencing with a HISeq 3000 (Illumina) by the staff at the Deep-sequencing Facility at the Max-Planck-Institute for Immunobiology and Epigenetics.

Sequencing Platform

instrument_model
Illumina HiSeq 3000

mm10

Number of total reads
45650317
Reads aligned (%)
90.1
Duplicates removed (%)
32.3
Number of peaks
19902 (qval < 1E-05)

mm9

Number of total reads
45650317
Reads aligned (%)
90.0
Duplicates removed (%)
32.4
Number of peaks
19868 (qval < 1E-05)

Base call quality data from DBCLS SRA