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Enrichment of ornithine decarboxylase degron transduced colorectal cancer cells for extended application of cancer stem cell models [colorectal cancer]

GSE282048 Homo sapiens (human) RNA-seq (gene expression) 32 samples Submitted 2025/07/09 Platform GPL16791Platform GPL24676
At a glance

RNA-seq (gene expression) · human · 32 samples

What it is
RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
Organism
Homo sapiens (human)
Topic
Colorectal cancerThis series is part of our curated briefing on it.
Samples
32 samples: 16 conditions, mostly in duplicateGroups 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
Enrichment of ornithine decarboxylase degron transduced colorectal cancer cells for extended application of cancer stem cell modelsScientific reports · 2025
Summary (written by the submitters)
Cancer stem cells (CSCs) are present in small quantities in tumor populations. To permit various analyses of CSCs, we attempted to enrich and expand ornithine decarboxylase (ODC) degron-transduced colorectal cancer (CRC) cells, which retain low proteasome activity. ZsGreen fluorescence-positive (ZsGreen+) cells were collected by sorting the ODC degron-transduced HCT116, DLD1, and SW480 cells, which were defined as enriched ZsGreen+ cells.
Read the full summary ↓
ZsGreen+ cells still maintained CSC properties. These cells had higher stem cell marker expression and increased resistance to chemotherapy with 5-fluorouracil and oxaliplatin. ZsGreen+ HCT116 and DLD1 cells had greater sphere-forming ability and enhanced tumorigenicity compared to ZsGreen- control cells. Time-lapse microscopy showed that a single enriched ZsGreen+ HCT116 cell had asymmetric cell division. Thus, model CSCs were acquired in sufficient quantity. Using these cells, we performed a comprehensive microRNA analysis; miR- 491-3p was a candidate to suppress cancer stemness. Finally, we found that up- regulated genes in the enriched HCT116 ZsGreen+ cells correlated with those up- regulated in human clinical spheroid samples established from patient-derived xenografts derived from CRC tissue samples, further supporting the acquisition of enriched model CSCs. These cells would be useful in identifying novel CSC markers and developing medicine for anti-CSC therapy.
Published in
Enrichment of ornithine decarboxylase degron transduced colorectal cancer cells for extended application of cancer stem cell models
Ikeshima R, Takahashi H, Yamamoto H et al. · Scientific reports 2025 · PMID 40595888 · doi:10.1038/s41598-025-04277-w
This dataset
Open GSE282048 in finder → Find more human 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 GSE282048_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: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.

Also filed as BioProject PRJNA1186715 and SRA study SRP545525. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40595888) ↗
Study design
16 conditions, mostly in duplicate
Pt28_sphere ×2 Pt30_sphere ×2 Pt36_sphere ×2 Pt40_sphere ×2 Pt41_sphere ×2 Pt42_sphere ×2 Pt45_sphere ×2 Pt48_sphere ×2 +8 more

Supports a between-group comparison across 32 samples.

How we read this: 16 replicated groups read from 32 sample titles; they account for 32 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.

Samples in this study
More Colorectal cancer datasets

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