Oncogenic KRAS-dependent stromal interleukin-33 directs the pancreatic microenvironment to promote tumor growth [scRNA-seq]
Single-cell RNA-seq · mouse · 11 samples
- What it is
- Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart.
- Organism
- Mus musculus (mouse)
- Samples
- 11 samples: 2 × KC PanIN vs 2 × iKrasG12D;Trp53R172H/+ 14 weeks ON vs 2 × iKrasG12D;Trp53R172H/+ 15 weeks ON + 1 week OFFGroups are read from the sample names, not from the paper. Check the list below.
- Data you can get
- A processed table (series matrix) and supplementary files from NCBI; the raw sequencing reads from ENA. Which of these hold counts depends on the study, so check the file list.
- Paper
- Oncogenic KRAS-Dependent Stromal Interleukin-33 Directs the Pancreatic Microenvironment to Promote Tumor GrowthCancer discovery · 2024
Direct links to NCBI and ENA, no account and no request form. Pick by what you want to do: take the small processed table to look, the supplementary files to re-analyse, or the original raw data to start over.
Processed table
The series matrix: one table of values per sample as the submitters processed it. The smallest download, and it opens in Excel or R. Start here to see what the data look like.
Supplementary files
The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE269888_RAW.tar (it can run to tens of gigabytes).
Raw sequencing reads
The original FASTQ files, straight from the sequencer, held at ENA. Large, and you align them yourself, so only choose this if you need to re-process the study from scratch.
What the files usually look like: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.
Also filed as BioProject PRJNA1124072 and SRA study SRP514012. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 6 samples.
How we read this: 3 replicated groups read from 11 sample titles; they account for 6 of them. These groups are guessed from the sample names, not taken from the paper, so check them against the sample list below before relying on them.
- GSM8329614 KC PanIN 1 KC PanIN
- GSM8329615 KC PanIN 2 KC PanIN
- GSM8329616 iKrasG12D 5 weeks ON
- GSM8329617 iKrasG12D 5 weeks ON + 3 days OFF
- GSM8329618 iKrasG12D;Trp53R172H/+ 14 weeks ON 1 iKrasG12D;Trp53R172H/+ …
- GSM8329619 iKrasG12D;Trp53R172H/+ 14 weeks ON 2 iKrasG12D;Trp53R172H/+ …
- GSM8329620 iKrasG12D;Trp53R172H/+ 15 weeks ON + 1 week OFF 1 iKrasG12D;Trp53R172H/+ …
- GSM8329621 iKrasG12D;Trp53R172H/+ 15 weeks ON + 1 week OFF 2 iKrasG12D;Trp53R172H/+ …
- GSM8329622 iKrasG12D; Trp53R172H/+ OT 2 weeks ON + 3 days OFF
- GSM8329623 Pdgfra-CreERT2/+ OT
- GSM8329624 Pdgfra-CreERT2/+;Il33f/f-eGFP OT
- GSE218178 Adaptation to an acid microenvironment promotes pancreatic cancer organoid growth and drug resistance 183 samples shares microenvironment, pancreatic
- GSE288530 Microenvironmental arginine restriction sensitizes pancreatic cancers to polyunsaturated fatty acids by suppression of lipid synthesis 18 samples shares microenvironment, pancreatic
- GSE269680 CDK8 remodels the tumor microenvironment to resist the therapeutic efficacy of targeted KRASG12D inhibition in pancreatic ductal adenocarcinoma (spatial) 15 samples shares microenvironment, pancreatic
- GSE299487 LY6D Identifies Persistent Tumor-Initiating Cells Driving Pancreatic Tumorigenesis [scRNA-seq] 12 samples shares pancreatic, scrna-seq
- GSE241365 Oncogenic Calreticulin Induces Immune Escape by Stimulating TGF-β Expression and Regulatory T Cell Expansion in the Bone Marrow Microenvironment 12 samples shares microenvironment, oncogenic
- GSE259380 TG6050, an oncolytic vaccinia virus encoding interleukin-12 and anti-CTLA-4 antibody induces tumor regression through profound tumor microenvironment remodeling and strong antitumor adaptive immune response [RNA-seq] 149 samples shares microenvironment
- GSE305266 The cortical microenvironment drives early immune organization and controls early osteoclastogenesis in bone healing 90 samples shares microenvironment
- GSE311286 Analysis of murine normal pancreatic organoids, pancreatitis-derived organoids, and PDAC organoids in complete media and of pancreatitis-derived organoids, and PDAC organoids cultured alone or cocultured with pancreatic stellate cells in reduced media 75 samples shares pancreatic
Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.