|
| Status |
Public on Jul 12, 2019 |
| Title |
Ptpn2_CD8_LCMV |
| Sample type |
SRA |
| |
|
| Source name |
Transferred Ptpn2-guide P14+ CD8+ T cells isolated from spleens of mice 30 days after infection with LCMV Clone 13
|
| Organism |
Mus musculus |
| Characteristics |
cell type: CD8+ T-cells
strain: C57BL/6J
genotype/variation: Ptpn2-guide P14+
|
| Treatment protocol |
Mice were treated with 200 microgram CD4 depleting antibody (clone GK1.5) on days -1 and 1
|
| Growth protocol |
C57BL/6 mice were infected with 4 x 10^6 pfu LCMV Clone 13 via IV injection. On day 30 after infection, mice were sacrificed and spleens removed for CD8+ T cell isolation
|
| Extracted molecule |
total RNA |
| Extraction protocol |
CD8+ MACS positive selection was performed on single-cell suspensions of splenocytes from chronically infected mice, followed by FACS. Purifed cells were loaded onto the 10x device (10x Genomics)
Library construction was performed as per standard 10x protocol (Manual CG00052 Rev B)
10X single-cell 3' RNA-seq v2
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
isolation of cd8+ t cells: CD8+ MACS positive selection (Miltenyi) followed by FACS
|
| Data processing |
Sample demultiplexing, barcode processing, alignment, filtering, UMI counting, and aggregation of multiple sequencing runs were performed using the Cell Ranger analysis pipeline (v1.2)
Data normalization, dimension reduction, and differential expression analysis were performed using the Seurat R package (v2.3.4)
Single cell signatures scoring was performed using the FastProject software (v1.1.4)
Genome_build: mm10
Supplementary_files_format_and_content: matrix.mtx file is count matrix in sparse matrix format; barcodes.tsv is list of barcodes for each sample; genes.tsv is list of genes detected in samples
|
| |
|
| Submission date |
Jul 11, 2019 |
| Last update date |
Jul 12, 2019 |
| Contact name |
Brian Christopher Miller |
| E-mail(s) |
[email protected]
|
| Organization name |
Harvard Medical School
|
| Department |
Immunology
|
| Lab |
Sharpe Lab
|
| Street address |
77 Avenue Louis Pasteur
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE134139 |
10X single-cell RNASeq profiling of control or Ptpn2-null P14 CD8+ T-cells from mice chronically infected with LCMV Clone 13 |
| GSE134413 |
PTPN2 regulates the generation of exhausted CD8+ T cell subpopulations and restrains tumor immunity |
|
| Relations |
| BioSample |
SAMN12255044 |
| SRA |
SRX6431051 |
