|
| Status |
Public on Sep 07, 2023 |
| Title |
KPC organoid Il1b stimulation 24h single-cell RNA-seq pool |
| Sample type |
SRA |
| |
|
| Source name |
KPC organoid Il1b stimulation 24h
|
| Organism |
Mus musculus |
| Characteristics |
tissue: KPC organoid
strain: --
disease state: PDAC
genotype: Kras+/LSLG12D Trp53fl/f lp48+/Cre
treatment: IL-1b (10 ng/mL)
time: 24h
|
| Treatment protocol |
KPC organoids were stimulated with IL-1b (10 ng/mL) for 24 or 48 hours. Controls were left untreated.
|
| Growth protocol |
KPC organoids were previously established from tumors arising in KPC genetically engineered mouse model (Kras+/LSLG12D Trp53fl/f lp48+/Cre) and were cultured following already published protocols
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Matrigel domes containing murine KPC organoids were dissolved in Cell Recovery Solution (CRS) (Gibco) for 30 min on ice, manually inverting the tubes every 5 min. After addition of ice-cold basal medium, organoid suspensions was centrifuged and supernatant was removed prior to incubation in TrypLE Express (Gibco) for 20 min on an orbital shaker at 37°C. The resulting cell suspension was collected from the supernatant without interfering with the lower fraction containing larger cellular aggregates, centrifuged, and resuspended in ultrapure BSA [400ug/mL] (Invitrogen).
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.
|
| |
|
| 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 |
Jul 20, 2023 |
| 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) |
| GSE217847 |
IL-1b+ tumor-associated macrophages fuel pathogenic inflammation in pancreatic cancer |
| GSE237848 |
IL-1b+ tumor-associated macrophages fuel pathogenic inflammation in pancreatic cancer - Singlecell_mouse_invitro |
|
| Relations |
| BioSample |
SAMN36660399 |
| SRA |
SRX21113542 |
