|
| Status |
Public on Oct 07, 2020 |
| Title |
Experiment 1 uninfected (scRNA-seq) |
| Sample type |
SRA |
| |
|
| Source name |
dog breast cancer (TNBC) biopsy 1
|
| Organism |
Canis lupus familiaris |
| Characteristics |
tissue: dog breast cancer (TNBC) biopsy 1
infection: No treatment
dose: 0
|
| Treatment protocol |
Six hours after infection, cells were trypsinized using a standard protocol. Cells were then collected, washed in PBS and the pellet was resuspended in 100 µL. Cells were then counted and the viability of the cells was verified.
|
| Growth protocol |
Around 35 000 cells were seeded in a 6 well plate. Three days later, the medium was removed and 1 mL of virus or vehicle was added. Cells were left in an incubator at 37°C for an hour and 3 mL of fresh medium was added (time 0).
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
10x Genomics single-cell 3' V2 chemistry was used to generate single-cell emulsion.
Single-cell RNA-seq was performed following manufacturer’s protocol (Chromium™ Single Cell 3' Reagent Kit, V2 Chemistry) to obtain single cell 3’ libraries for Illumina sequencing.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
TNBC
|
| Data processing |
The Cell Ranger Single Cell Software Suite 2.0 was used to perform sample demultiplexing, barcode processing, and single cell 3’ gene counting.
Sample demultiplexing and analyses were performed using Seurat toolkit V3.
Genome_build: CanFam3 + vaccinia virus genome (NC_006998)
Supplementary_files_format_and_content: Cellranger v2.0 filtered gene barcodes matrix.
|
| |
|
| Submission date |
Dec 17, 2019 |
| Last update date |
Oct 08, 2020 |
| Contact name |
Kevin Lebrigand |
| Organization name |
IPMC/CNRS
|
| Lab |
Functional Genomics Platform of Nice-Sophia-Antipolis, France.
|
| Street address |
660 route des lucioles
|
| City |
Valbonne - Sophia-Antipolis |
| ZIP/Postal code |
06560 |
| Country |
France |
| |
|
| Platform ID |
GPL21400 |
| Series (2) |
| GSE142184 |
Single-cell RNAseq profiling of dog primary mammary triple-negative breast cancer cells infected or not with a vaccinia virus deleted for the thymidine kinase gene |
| GSE142185 |
Expression profiling of dog primary mammary triple-negative breast cancer cells infected or not with a vaccinia virus deleted for the thymidine kinase gene |
|
| Relations |
| BioSample |
SAMN13614516 |
| SRA |
SRX7397031 |
