|
| Status |
Public on Feb 17, 2025 |
| Title |
D8-2 CD8T scATAC-seq |
| Sample type |
SRA |
| |
|
| Source name |
Lymphocytes
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Lymphocytes
cell subtype: CD45.1+CD44+CD8+ T cells
strain: C57BL/6
genotype: WT
infection: LCMV-Armstrong
time: D8
|
| Growth protocol |
For effector and memory CD8+ T cell sorting, 5x10^3 P14 CD8+ T cells were transferred into congenically distinct CD45.2+ mice by intravenous (i.v.) injection and then infected with 2x10^5 PFU of LCMV Armstrong intraperitoneally 1 day later. For experiments where P14 cells were collected two days after infection, 1x10^6 P14 CD8+ T cells were transferred and then infected with 2x10^6 PFU of LCMV Arm+ intravenously. Activated P14 T cells (CD8+Vα2+CD45.1+CD44+) were sorted from the spleen.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Briefly, approximately 50,000 FACS-sorted CD8+ T cells were used for the nuclei preparation according to the manufacturer’s instructions. Then, 15,000 nuclei were loaded into a 10x Chromium controller. All library preparation was performed according to the manufacturer’s instructions.
The single-cell ATAC-seq (scATAC-seq) libraries were prepared using 10x Genomics Chromium Cell ATAC Reagent Kit (v1) according to the manufacturer’s protocol.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic single cell |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
10x Genomics
|
| Data processing |
Raw scATAC-seq data was processed using 10x Genomics Cell Ranger ATAC pipeline (v1.2.0), including aligning the demultiplexed FASTQ reads to the mouse reference genome (mm10, v1.2.0, from 10x Genomics)
Counting the unique molecular identifier (UMI) for each cell barcode by using the ‘cellranger-atac count’ function
Downstream scATAC-seq analysis was performed in R (v4.0.0) using Seurat (v4.0.6), Signac (v1.1.1), and ArchR (v1.0.1)
Assembly: mm10
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, peaks.bed.tsv.gz, matrix.mtx.gz
Supplementary files format and content: Binary data with h5 format
|
| |
|
| Submission date |
Feb 24, 2023 |
| Last update date |
Feb 17, 2025 |
| Contact name |
Zhonghui Tang |
| E-mail(s) |
tangzhh99@mail.sysu.edu.cn
|
| Organization name |
Sun Yat-sen University
|
| Street address |
No. 74 Zhongshan Second Road, Guangzhou
|
| City |
Guangzhou |
| State/province |
Guangdong |
| ZIP/Postal code |
510080 |
| Country |
China |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE226067 |
scATAC-seq of antigen-specific CD8+ T cells from different time-course of LCMV-Armstrong infected mice |
| GSE226177 |
Chromatin landscape alteration uncovers multiple transcriptional circuits during memory CD8+ T cell differentiation |
|
| Relations |
| BioSample |
SAMN33437024 |
| SRA |
SRX19497140 |
