|
| Status |
Public on Apr 17, 2021 |
| Title |
RosaWT_Control_scRNA-seq |
| Sample type |
SRA |
| |
|
| Source name |
spleen - sorted NK cells
|
| Organism |
Mus musculus |
| Characteristics |
tissue: spleen - sorted NK cells
genotype: Wild type
infection: Control
|
| Treatment protocol |
Murine NK cells were enriched from spleens using negative selection beads. Sorting was accomplished on a FACSAria Fusion sorter (BD) using FACSDiva software (BD)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Illumina 10X genomics 3’ V3
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Raw FASTQ files were aligned to the mm10 reference using CellRanger (v3.1.0) count algorithm
Barcode and UMI count files were aggregated and normalized using CellRanger (v.3.1.0) aggr default options
Quality control and analysis of the matrix file was performed using Seurat V3 software for R. Filtering criteria excluded cells with mt RNA % > 10 and cells with < 200 features
Clustering was done using pca (20 PCS) and Umap on the integrated data
Genome_build: mm10
Supplementary_files_format_and_content: matrix file (h5)containing gene expression information for each feature (gene) and its respective barcode (individual cell). A processed and filtered Seurat R object containing the project metadata, normalization and clustering.
|
| |
|
| Submission date |
Apr 30, 2020 |
| Last update date |
Mar 22, 2023 |
| Contact name |
Megan Cooper |
| E-mail(s) |
cooper_m@wustl.edu, mcimpean@wustl.edu, ktoth@wustl.edu, e.g.schmitt@wustl.edu
|
| Organization name |
Washington University in St Louis
|
| Department |
Pediatrics
|
| Lab |
Dr Megan Cooper
|
| Street address |
MPRB, 6th floor, 4905 Childrens Place
|
| City |
SAINT LOUIS |
| State/province |
MISSOURI |
| ZIP/Postal code |
63110 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE149659 |
Cox10 is Required for Natural Killer Cell Expansion and Memory in Response to Viral Infection |
|
| Relations |
| BioSample |
SAMN14782548 |
| SRA |
SRX8218034 |
