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Effect of KO-2806 and cabozantinib treatment on gene expression in KI-12-0073 clear cell renal cell carcinoma (ccRCC) xenografts

GSE294454 Homo sapiens (human) RNA-seq (gene expression) 20 samples Submitted 2026/04/30 Platform GPL24676
At a glance

RNA-seq (gene expression) · human · 20 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
Kidney cancerThis series is part of our curated briefing on it.
Samples
20 samples: 5 × KI-12-0073 xenograft, Vehicle, vs 5 × KI-12-0073 xenograft, KO-2806, vs 5 × KI-12-0073 xenograft, Cabozantinib, vs 5 × KI-12-0073 xenograft, KO-2806 plus Cabozantinib,Groups 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)
Anti-angiogenic tyrosine kinase inhibitors (TKIs) targeting vascular endothelial growth factor receptor (VEGFR) remain the backbone of therapy in advanced renal cell carcinoma (RCC). However, durability of responses is limited, and resistance typically arises. There is therefore a need for therapeutic agents that enhance responses to TKIs, including in patients who progress on prior TKI therapies.
Read the full summary ↓
Here we show that the farnesyl transferase inhibitor (FTI) KO-2806 inhibits mTORC1 signaling in endothelial cells to enhance the antiangiogenic properties of TKIs. This activity correlates with tumor regressions and robust inhibition of tumor vasculature in preclinical models of clear cell RCC (ccRCC) exposed to the combination of anti-VEGFR TKIs and KO-2806. Additionally, the KO-2806 plus anti-VEGFR TKI combinations retain activity in tumors previously exposed to TKIs, suggesting potential benefit of KO-2806 as a combination partner across the treatment continuum in RCC.
This dataset
Open GSE294454 in finder → Find more human RNA-seq datasets → Kidney 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 GSE294454_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 PRJNA1249482 and SRA study SRP577748. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
5 × KI-12-0073 xenograft, Vehicle, vs 5 × KI-12-0073 xenograft, KO-2806, vs 5 × KI-12-0073 xenograft, Cabozantinib, vs 5 × KI-12-0073 xenograft, KO-2806 plus Cabozantinib,

Supports a between-group comparison across 20 samples.

How we read this: 4 replicated groups read from 20 sample titles; they account for 20 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 Kidney cancer datasets

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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.