Targeting heterogeneous tumor microenvironments in pancreatic cancer mouse models of metastasis by TGFB depletion
Single-nucleus RNA-seq · mouse · 12 samples
- What it is
- Single-nucleus RNA-seqGene activity measured in individual nuclei (used when whole cells are hard to isolate, for example from frozen tissue). Read from the summary: GEO's own type field only says 'expression profiling by sequencing', so confirm it in the paper.
- Organism
- Mus musculus (mouse)
- Samples
- 12 samples: 12 samples, each with a distinct title — no replicated groupsGroups 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.
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 GSE275596_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 PRJNA1151736 and SRA study SRP528362. Searching any of these in the dataset finder brings you back here.
Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.
How we read this: Read from 12 sample titles: 12 distinct titles with little repetition. 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.
- GSM8480617 KPC-4545 Control
- GSM8480618 KPC-4545 TGFB-TRAP
- GSM8480619 KPC-4545 anti-IL-1B
- GSM8480620 KPC-4545 anti-PD-1
- GSM8480621 KPC-4545 anti-PD-1 + TGFB-TRAP
- GSM8480622 KPC-4545 anti-PD-1 + anti-IL-1B
- GSM8480623 KPC-3403 Control
- GSM8480624 KPC-3403 TGFB-TRAP
- GSM8480625 KPC-3403 anti-IL-1B
- GSM8480626 KPC-3403 anti-PD-1
- GSM8480627 KPC-3403 anti-PD-1 + TGFB-TRAP
- GSM8480628 KPC-3403 anti-PD-1 + anti-IL-1B
- GSE324743 Hepatocytes promote liver metastasis of pancreatic cancer by providing exogenous serine 24 samples shares pancreatic, metastasis
- GSE251864 Optimization of a Mouse Model of Pancreatic Cancer to More Closely Simulate the Human Phenotypes of Metastasis and Cachexia 22 samples shares pancreatic, metastasis
- GSE287625 Mitochondrial Ca2+ controls pancreatic cancer growth and metastasis by regulating epithelial cell plasticity 18 samples shares pancreatic, metastasis
- GSE275780 Dual Targeting of STING and PI3Kγ Eliminates Regulatory B Cells to Overcome STING Resistance for Pancreatic Cancer Immunotherapy [RNA-seq] 17 samples shares pancreatic, targeting
- GSE324997 Hepatocytes promote liver metastasis of pancreatic cancer by providing exogenous serine, 2. 16 samples shares pancreatic, metastasis
- GSE262721 Targeting plasticity in the pyrimidine synthesis pathway potentiates macrophage-mediated phagocytosis in pancreatic cancer models 10 samples shares pancreatic, targeting
- GSE328371 KMT2D depletion promote KRAS-induced pancreatic carcinogenesis independent of TP53 24 samples shares pancreatic, depletion
- GSE270744 Single Cell Analysis Reveals The Essential Role of TGFbeta Pathway in Shaping Immune-suppressive Microenvironment and Promoting CRPC Development 48 samples shares tgfb
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.