Gene expression profile at single cell level of murine colon organoids harbouring colorectal cancer-associated driver mutations [scRNA-seq]
Single-cell RNA-seq · mouse · 9 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
- 9 samples: 9 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 GSE218339_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 PRJNA903177 and SRA study SRP408634. 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 9 sample titles: 9 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.
- GSM6742618 Wild Type, biological replicate 1, scRNAseq
- GSM6742619 Wild Type, biological replicate 2, scRNAseq
- GSM6742620 APCmin/+ mCherry, biological replicate 1, scRNAseq
- GSM6742621 APCmin/+ mCherry, biological replicate 2, scRNAseq
- GSM6742622 KRAS G12D/+ EYFP, scRNA-seq
- GSM6742623 KRAS LSL-G12D/+ EYFP p53 Null, scRNA-seq
- GSM6742624 p53 Null mBanana, scRNA-seq
- GSM6742625 p53 R172H: Hom mBanana, biological replicate 1, scRNAseq
- GSM6742626 p53 R172H: Hom mBanana, biological replicate 2, scRNAseq
- GSE306627 TGFβ signaling in cancer-associated fibroblasts drives a hepatic gp130-dependent pro-metastatic inflammatory program in colorectal cancer 42 samples shares cancer-associated, colorectal
- GSE239632 Cancer-associated Histone H3 N-terminal arginine mutations disrupt PRC2 activity and impair differentiation [RNA-Seq] 15 samples shares cancer-associated, mutations
- GSE308848 Targeting AEBP1 to mitigate pro-tumor activity of cancer-associated fibroblasts and increase therapeutic efficacy to anti-PD-1 [scRNA-Seq] 12 samples shares cancer-associated, scrna-seq
- GSE285873 Ceramides drive colorectal cancer metastasis through a revival stemness program [scRNA-seq] 10 samples shares colorectal, scrna-seq
- GSE223323 Enterocyte like differentiation defines metabolic gene signatures of CMS3 colorectal cancers and provides therapeutic vulnerability 148 samples shares colorectal
- GSE276018 Integrated Multi-Omics Analysis Reveals Epigenetic and Sex-Specific Alterations in Colorectal Cancer Cachexia 88 samples shares colorectal
- 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 organoids
- GSE253034 RNA sequencing analysis of control, photon- and proton- irradiated salivary gland organoids at 2 and 6 days post irradiation 48 samples shares organoids
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.