GEO series

Single cell profiling of SW480 subtype-specific subcutaneous and orthotopic xenografts (SW480-CBC and SW480-RSC) as presented in "Colorectal Cancer Stem Cell Subtypes Orchestrate Distinct Tumor Microenvironments" [scRNA-seq]

GSE254890 Mus musculus (mouse) Single-cell RNA-seq 14 samples Submitted 2024/04/25 Platform GPL25526

At a glance

Single-cell RNA-seq · mouse · 14 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)
Topic: Colorectal cancerThis series is part of our curated briefing on it.
Samples: 14 samples: 14 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.

Summary (written by the submitters)

Tumor heterogeneity derives from diverse populations of cancer cells that contribute unique properties to the microenvironment and tumor progression. While multiple classification systems have been developed to define tumor subtypes in colorectal cancer (CRC), the lack of single cell resolution has prohibited a better understanding of how these distinct cancer cell subtypes influence the overall tumor phenotype.

Read the full summary ↓

Here were report that two cancer stem cell subtypes that are oncogenic versions of the intestinal Crypt Base Columnar (CBC) and Regenerative Stem Cell (RSC) populations, are commonly co-present in human CRC. We develop subtype-specific xenograft models utilizing a heterogeneous patient cell line (SW480) that contains CBCs and RSCs, and we define their tumor microenvironments at high resolution via single cell RNA sequencing. RSCs create differentiated, inflammatory, slow growing tumors. CBCs create proliferative, immune-suppressive, invasive tumors. With this enhanced resolution, we unify current CRC patient classification schema with TME phenotypes and organization.

This dataset

Open GSE254890 in finder → Find more RNA-seq datasets → Colorectal cancer landscape →

Download · which file do I need?

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.

1 · Just have a look

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.

Series matrix ↓

2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE254890_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓

3 · Start from the raw reads

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.

Raw reads on ENA ↗

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 PRJNA1072238 and SRA study SRP487691. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

14 samples, each with a distinct title — no replicated groups

Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.

How we read this: Read from 14 sample titles: 14 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.

Samples in this study

GSM8059841 SW480 subcutaneous tumor, replicate 1, scRNAseq
GSM8059842 SW480 subcutaneous tumor, replicate 2, scRNAseq
GSM8059843 SW480-CBC subcutaneous tumor, replicate 1, scRNAseq
GSM8059844 SW480-CBC subcutaneous tumor, replicate 2, scRNAseq
GSM8059845 SW480-RSC subcutaneous tumor, replicate 1, scRNAseq
GSM8059846 SW480-RSC subcutaneous tumor, replicate 2, scRNAseq
GSM8059847 SW480-CBC orthotopic tumor, replicate 1, scRNAseq
GSM8059848 SW480-CBC orthotopic tumor, replicate 2, scRNAseq
GSM8059849 SW480-CBC orthotopic tumor, replicate 3, scRNAseq
GSM8059850 SW480-CBC orthotopic tumor, replicate 4, scRNAseq
GSM8059851 SW480-RSC orthotopic tumor, replicate 1, scRNAseq
GSM8059852 SW480-RSC orthotopic tumor, replicate 2, scRNAseq
GSM8059853 SW480-RSC orthotopic tumor, replicate 3, scRNAseq
GSM8059854 SW480-RSC orthotopic tumor, replicate 4, scRNAseq

More Colorectal cancer datasets

GSE250000 Bulk RNA-sequencing of transduced colorectal cancer cell line HCT-116 and breast cancer cell line MCF-7 overexpressing full-lenght p53β or p53β-stop-lost. 4 samples same disease briefing
GSE12032 Inherent gene signature of stage II and III colorectal cancer leads in individual recurrence 198 samples same disease briefing
GSE109308 Single-cell transcriptomic survey of adenomatous polyposis patients with germline APC mutations 97 samples same disease briefing
GSE110009 Single cell transcriptome landscape of primary and metastatic tumor in colon cancer 76 samples same disease briefing
GSE124480 Gene expression of human colon cancer HCT116 cells 5 samples same disease briefing

Search all RNA-seq datasets in GEO →

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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.