GSM4555171: Tumor specific T cell, WT3; Mus musculus; ATAC-seq
Sample information curated by ChIP-Atlas
Antigen
Antigen Class
ATAC-Seq
Antigen
ATAC-Seq
Cell type
Cell type Class
Blood
Cell type
T cells
NA
NA
Attributes by original data submitter
Sample
source_name
Tumor specific T cell
strain
C57BL/6
cell type
mouse T cell
genotype
wild type
Sequenced DNA Library
library_strategy
ATAC-seq
library_source
GENOMIC
library_selection
other
library_construction_protocol
A total of 1 × 10e5 B16-F10 cells were injected subcutaneously into 6 to ~10-week-old female C57BL/6J mice (six mice per group). On day 21, mice were euthanized and subcutaneous tumors were digested with 1 mg/ml collagenase D supplemented with 10 U/ml DNase I. OVA-specific CD8+ TILs were sorted using a BD FACS Aria cell sorter, and gene profiling, ATAC-seq library construction and high-throughput sequencing were performed on approximately 50,000 sorted cells. Libraries were prepared according to Vazyme's instructions accompanying the DNA Sample Kit (TD501). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3' end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina Hiseq 4000 instrument following the manufacturer's protocols.