|
| Status |
Public on Sep 07, 2023 |
| Title |
KPC organoid Il1b stimulation 72h RNA-seq replicate 2 |
| Sample type |
SRA |
| |
|
| Source name |
KPC organoid Il1b stimulation 72h
|
| Organism |
Mus musculus |
| Characteristics |
tissue: --
strain: --
cell line: --
cell type: PDAC tumor organoids
genotype: Kras+/LSLG12D Trp53fl/f lp48+/Cre
treatment: IL-1b (10 ng/mL)
time: 72h
|
| Treatment protocol |
KC and KPC cells were stimulated with IL-1b (10 ng/mL) for 24, 48 or 96 hours. KPC organoids were stimulated with IL-1b (10 ng/mL) for 8, 24, 48 or 72 hours. Controls were left untreated.
|
| Growth protocol |
KC (DT6606) and KPC (K8484) cell lines were previously established from tumors arising in genetically engineered mouse models carrying the G12D oncogenic mutation in the Kras gene (KrasLSL-G12D/+;Pdx1Cre/WT for KC) and the missense point R720H mutation in the Tpr53 gene (KrasLSL-G12D/+;Tpr53LSL-R270H/+;Pdx1Cre/WT for KPC) and were cultured under standard conditions. 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 |
Total RNA was purified using the ReliaPrep RNA Cell Miniprep System.
RNA-Seq libraries were generated using the Smart-seq2 method with minor modification. Briefly, five ng of RNA were retrotranscribed, cDNA was PCR-amplified (15 cycles) and purified with AMPure XP beads. After purification, the concentration was determined using Qubit 3.0 and size distribution was assessed using Agilent 4200 TapeStation system. Then, the tagmentation reaction was performed starting from 0.5 ng of cDNA for 30 minutes at 55°C and the enrichment PCR was carried out using 12 cycles. Libraries were then purified with AMPure XP beads, quantified using Qubit 3.0, assessed for fragment size distribution on an Agilent 4200 TapeStation system.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Smart-seq2
Organoids_KPC_IL1B_72h_Sample2
Organoids_KPC_counts_matrix.csv.gz
|
| Data processing |
Reads were aligned using STAR aligner (v STAR_2.5.3a). Read counts matrices were computed using the featureCounts function from Rsubread package (v 2.0.1).
Assembly: mm10
Supplementary files format and content: Tab-separated counts file (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 |
| GSE237838 |
IL-1b+ tumor-associated macrophages fuel pathogenic inflammation in pancreatic cancer - Bulk_mouse_invitro |
|
| Relations |
| BioSample |
SAMN36660291 |
| SRA |
SRX21112528 |
