GEO series
Integrated transcriptomic and bioelectrical profiling of stem-like cellular states in a colorectal cancer using SdFFF and UHF-DEP
GSE342462
Homo sapiens
Expression profiling by high throughput sequencing
12 samples
Submitted 2026/08/08
Platform GPL28038
Summary
Cancer stem-like cells (CSCs) enrichment and characterization remain an analytical challenge, as conventional marker-based approaches are often time-consuming and can alter cellular properties. Here, we develop a complete label-free protocol for the enrichment and characterization of cellular states associated to stemness properties in colorectal cancer model, based on the coupling adjustment of sedimentation field-flow fractionation (SdFFF) and ultra-high-frequency dielectrophoresis (UHF-DEP). To this end, the operating conditions of SdFFF were adapted to a low conductivity dielectrophoresis buffer while maintaining the hyperlayer elution regime. Fractionated cellular subpopulation exhibits phenotypic differences in proliferative status, clonogenic potential, stem-cell related protein levels and UHF-DEP highlights significantly different high-frequency crossover distributions. Transcriptome sequencing revealed dysregulation of pathways associated with stemness, cell adhesion, membrane organization, calcium signaling and ion-channel activity, that can be linked to dielectric signatures. Overall, UHF-DEP coupling to SdFFF permit to enrich, characterize and quantify stem cell-like subpopulation within heterogeneous population of cancer cells.
This dataset
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Direct links to NCBI, no account and no request form: the whole study as GSE342462_RAW.tar, processed values as the series matrix, the supplementary file directory, and per-sample supplementary files for any of the 12 samples. Raw sequencing reads are also available from ENA.
Also filed as BioProject PRJNA1507902 and SRA study SRP724360. Searching any of these in the dataset finder brings you back here.
Study design
4 × F1 subpopulation derived from SdFFF sorting of SW480 cells, vs 4 × F3 subpopulation derived from SdFFF sorting of SW480 cells, vs 4 × PT subpopulation derived from SdFFF sorting of SW480 cells,
Supports a between-group comparison across 12 samples.
3 replicated groups read from 12 sample titles; they account for 12 of them. Check it against the sample list below before relying on it.
Samples in this study
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- GSM9931050 F1 subpopulation derived from SdFFF sorting of SW480 cells, biological replicate 1
- GSM9931051 F1 subpopulation derived from SdFFF sorting of SW480 cells, biological replicate 2
- GSM9931052 F1 subpopulation derived from SdFFF sorting of SW480 cells, biological replicate 3
- GSM9931053 F1 subpopulation derived from SdFFF sorting of SW480 cells, biological replicate 4
- GSM9931054 F3 subpopulation derived from SdFFF sorting of SW480 cells, biological replicate 1
- GSM9931055 F3 subpopulation derived from SdFFF sorting of SW480 cells, biological replicate 2
- GSM9931056 F3 subpopulation derived from SdFFF sorting of SW480 cells, biological replicate 3
- GSM9931057 F3 subpopulation derived from SdFFF sorting of SW480 cells, biological replicate 4
- GSM9931058 PT subpopulation derived from SdFFF sorting of SW480 cells, biological replicate 1
- GSM9931059 PT subpopulation derived from SdFFF sorting of SW480 cells, biological replicate 2
- GSM9931060 PT subpopulation derived from SdFFF sorting of SW480 cells, biological replicate 3
- GSM9931061 PT subpopulation derived from SdFFF sorting of SW480 cells, biological replicate 4
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