|
| Status |
Public on Sep 07, 2023 |
| Title |
Mouse timecourse KPC day30 Tumor scRNAseq pool of 3 mice |
| Sample type |
SRA |
| |
|
| Source name |
Tumor
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Tumor
strain: C57BL/6N
genotype: WT
Sex: F
time: Day 30
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Murine healthy pancreas and tumors were manually minced in small pieces and dissociated with the Tumor Dissociation kit, mouse (Miltenyi Biotec). The obtained single cells suspensions were filtered on 70µm cell strainers, incubated with RBC lysis buffer for 10 minutes on ice and resuspended in the appropriate buffer for cell counting and down-stream application. For the heterotopic and orthotopic inoculation of KC cell line, cells were enriched in the myeloid fraction as CD45+Cd11b+ via FACS sorting. Mouse PB samples were incubated with Red Blood Cell (RBC) lysis buffer (Biolegend) for 10 minutes on ice and washed with Phosphate Buffered Saline (PBS). Cells were centrifuged for 5 minutes at 450 x g and resuspended in the appropriate buffer for down-stream application.
scRNA-Seq libraries were generated using a microfluidics-based approach on Chromium Single-Cell Controller (10X Genomics) using the Chromium Single Cell 3′ Reagent Kit v3.1, according to the manufacturers’ instructions. For the heterotopic and orthotopic inoculation of KC cell line, libraries generated using the Chromium Single Cell 3′ Reagent Kit v2.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
10X Genomics
|
| Data processing |
Fastq files were processed with Cell Ranger (v 4.0.0), using default parameters
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files (gzipped format)
|
| |
|
| Submission date |
Nov 12, 2022 |
| Last update date |
Sep 07, 2023 |
| Contact name |
Renato Ostuni |
| Organization name |
San Raffaele Telethon Institute for Gene Therapy
|
| Street address |
Via Olgettina 58
|
| City |
Milano |
| ZIP/Postal code |
20132 |
| Country |
Italy |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE217846 |
IL-1b+ tumor-associated macrophages fuel pathogenic inflammation in pancreatic cancer - scRNA-seq of murine PDAC samples |
| GSE217847 |
IL-1b+ tumor-associated macrophages fuel pathogenic inflammation in pancreatic cancer |
|
| Relations |
| BioSample |
SAMN31701036 |
| SRA |
SRX18243273 |
