SOX9 suppresses colon cancer via inhibiting epithelial-mesenchymal transition and SOX2 induction
RNA-seq (gene expression) · mouse · 39 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
- Mus musculus (mouse)
- Samples
- 39 samples: 7 conditions, mostly with about 6 replicates eachGroups 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
- SOX9 suppresses colon cancer via inhibiting epithelial-mesenchymal transition and SOX2 inductionThe Journal of clinical investigation · 2025
Read the full summary ↓
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 GSE239716_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: 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 PRJNA1000611 and SRA study SRP452412. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 39 samples.
How we read this: 7 replicated groups read from 39 sample titles; they account for 39 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.
- GSM7670320 Apcfl_fl_1 Apcfl_fl
- GSM7670321 Apcfl_fl_2 Apcfl_fl
- GSM7670322 Apcfl_fl_3 Apcfl_fl
- GSM7670323 Apcfl_fl_4 Apcfl_fl
- GSM7670324 Apcfl_flSox9fl_fl_1 Apcfl_flSox9fl_fl
- GSM7670325 Apcfl_flSox9fl_fl_2 Apcfl_flSox9fl_fl
- GSM7670326 Apcfl_flSox9fl_fl_3 Apcfl_flSox9fl_fl
- GSM7670327 Apcfl_flSox9fl_fl_4 Apcfl_flSox9fl_fl
- GSM7670328 Aff_1 Aff
- GSM7670329 Aff_2 Aff
- GSM7670330 Aff_3 Aff
- GSM7670331 Aff_4 Aff
- GSM7670332 Aff_5 Aff
- GSM7670333 Aff_6 Aff
- GSM7670334 Aff.Sff_1 Aff.Sff
- GSM7670335 Aff.Sff_2 Aff.Sff
- GSM7670336 Aff.Sff_3 Aff.Sff
- GSM7670337 Aff.Sff_4 Aff.Sff
- GSM7670338 Aff.Sff_5 Aff.Sff
- GSM7670339 Aff.Sff_6 Aff.Sff
- GSM7670340 Control_1 Control
- GSM7670341 Control_2 Control
- GSM7670342 Control_3 Control
- GSM7670343 Control_4 Control
- GSM7670344 Control_5 Control
- GSM7670345 Control_6 Control
- GSM7670346 Sff_1 Sff
- GSM7670347 Sff_2 Sff
- GSM7670348 Sff_3 Sff
- GSM7670349 Sff_4 Sff
- GSM7670350 Sff_5 Sff
- GSM7670351 Sff_6 Sff
- GSM8446972 colon, AShet, rep1 colon, AShet,
- GSM8446973 colon, AShet, rep2 colon, AShet,
- GSM8446974 colon, AShet, rep3 colon, AShet,
- GSM8446975 colon, AShet, rep4 colon, AShet,
- GSM8446976 colon, AShet, rep5 colon, AShet,
- GSM8446977 colon, AShet, rep6 colon, AShet,
- GSM8446978 colon, AShet, rep7 colon, AShet,
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- GSE261712 Disulfiram treatment suppresses antibody-producing reactions by inhibiting macrophage activation and B cell pyrimidine metabolism 27 samples shares suppresses, inhibiting
- GSE265871 Methylation of SRSF2P95H by SETD2 suppresses myeloid-derived suppressor cell function by inhibiting inflammatory signaling in myelodysplastic syndrome 13 samples shares suppresses, inhibiting
- GSE246928 Endothelial RNF20 Suppresses Endothelial-to-Mesenchymal Transition and Safeguards Physiological Angiocrine Signaling to Prevent Congenital Heart Disease 12 samples shares suppresses, transition
- GSE293222 High-Fat Diet-Induced Liver-Gut Crosstalk Suppresses Autophagy and Exacerbates Colitis [colon] 12 samples shares suppresses, colon
- GSE303505 Epithelial-mesenchymal transition is associated with altered immune composition and cytotoxic function in triple-negative breast cancer 12 samples shares epithelial-mesenchymal, transition
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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.