|
| Status |
Public on May 31, 2023 |
| Title |
LCMV1: Naive, scATAC |
| Sample type |
SRA |
| |
|
| Source name |
P14 CD8 T cells
|
| Organism |
Mus musculus |
| Characteristics |
background strain: C57BL/6
age: P14
cell type: CD8 T cells
treatment: naïve
|
| Treatment protocol |
PD1 blockade was performed with 5 treatments of 200ug aPD-L1 antibody (10F.9G2, BioXCell) i.p. every 3 days starting 16 days after infection with LCMV Cl13. Analysis was performed one day after final treatment. For control treatments, phosphate-buffered saline (PBS) was administered i.p.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were loaded onto the Chromium Controller (10x Genomics) for a target recovery of 10,000 single cells.
The scRNAseq and scATACseq libraries were generated using 10x Genomics multiome coAssay according to the manufacturer’s protocol.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
P14 naïve CD8 T cells
|
| Data processing |
scRNA-seq and scATAC-seq sample demultiplexing, barcode processing, alignment, filtering, unique molecular identifier (UMI) counting and aggregating sequencing runs were performed using 10x Cell Ranger pipeline (6.0.0) and mm10 genome.
Downstream scRNA-seq amd scATAC-seq analysis was performed in R (version 4.0.2) using Signac and Archr packages
Union peak list was generated using peaks called in ArchR and using macs2 with sample bam files.
Assembly: GRCm38/mm10
Supplementary files format and content: Filtered feature-barcode matrices containing only cellular barcodes corresponding to gene expression and chromatin accessibility
|
| |
|
| Submission date |
Apr 23, 2023 |
| Last update date |
May 31, 2023 |
| Contact name |
E JOHN WHERRY |
| Organization name |
University of Pennsylvania
|
| Department |
Systems Pharmacology and Translational Therapeutics,Institute for Immunology
|
| Street address |
421 Curie Blvd,354 BRB II/III
|
| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19104 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE230363 |
Longitudinal single cell transcriptional and epigenetic mapping of effector, memory, and exhausted CD8 T cells reveals shared biological circuits across distinct cell fates [scRNA-seq and scATAC-seq coAssay] |
|
| Relations |
| BioSample |
SAMN34331746 |
| SRA |
SRX20069178 |
