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RIPK4 driven by TP53 mutations promotes resistance to PANoptosis and metastasis of CRC by phosphorylation of MTHFD1 [Anokis_seq]

GSE252262 Homo sapiens (human) RNA-seq (gene expression) 12 samples Submitted 2025/02/01 Platform GPL24676
At a glance

RNA-seq (gene expression) · human · 12 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)
Samples
12 samples: 3 × 620 att vs 3 × 620 det vs 3 × LoVo att vs 3 × LoVo detGroups 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)
In this study, we found that RIPK4 protein driven by TP53 mutation is highly expressed in CRC, which can promote the phosphorylation level of MTHFD1 (Methylenetetrahydrofolate Dehydrogenase, Cyclohydrolase And Formyltetrahydrofolate Synthetase 1), a key enzyme of carbon metabolism, promote the generation of NADPH in CRC cells, and reduce the level of ROS, thus promoting PANoptosis resistance and distant metastasis of CRC cells.
Read the full summary ↓
We explain the novel mechanism of metastasis induced by the TP53 mutation in terms of post-translational modification and clarify the biological role of the RIPK4 protein in CRC, which can be used as a new target for the treatment of metastatic CRC.
This dataset
Open GSE252262 in finder → Find more human RNA-seq datasets →
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 GSE252262_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 PRJNA1059030 and SRA study SRP480659. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
3 × 620 att vs 3 × 620 det vs 3 × LoVo att vs 3 × LoVo det

Supports a between-group comparison across 12 samples.

How we read this: 4 replicated groups read from 12 sample titles; they account for 12 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
Datasets on a similar topic

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