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PIK3CA and KRAS codon-specific mutations differentially toggle pathway activity and alter sensitivity to inavolisib (GDC-0077)

GSE248412 Homo sapiens (human) Single-cell RNA-seq 26 samples Submitted 2025/06/15 Platform GPL20301Platform GPL24676Platform GPL18573
At a glance

Single-cell RNA-seq · human · 26 samples

What it is
Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart. Read from the summary: GEO's own type field only says 'expression profiling by sequencing', so confirm it in the paper.
Organism
Homo sapiens (human)
Samples
26 samples: 20 distinct titles, 6 of them repeatedGroups 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
KRAS Codon-Specific Mutations Differentially Toggle PI3K Pathway Signaling and Alter Sensitivity to Inavolisib (GDC-0077)Molecular cancer therapeutics · 2025
Summary (written by the submitters)
To explore the single and combinatorial effect of MEK and PI3KCA inhibitors in CRC lines with PIK3CA/KRAS mutations, we used the MULTI-seq CMOs to perform a highly multiplexed single-cell RNA-seq.
Published in
KRAS Codon-Specific Mutations Differentially Toggle PI3K Pathway Signaling and Alter Sensitivity to Inavolisib (GDC-0077)
Song KW, Ong CC, Lin E et al. · Molecular cancer therapeutics 2025 · PMID 40625102 · doi:10.1158/1535-7163.MCT-24-0995
This dataset
Open GSE248412 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 GSE248412_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: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.

Also filed as BioProject PRJNA1043704 and SRA study SRP473409. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40625102) ↗
Study design
20 distinct titles, 6 of them repeated
LIB5455515_SAM24414655_S4_L ×2 LIB5455516_SAM24414655_S5_L ×2 LIB5455517_SAM24414655_S6_L ×2 LIB5455512_SAM24414654_S1_L ×2 LIB5455513_SAM24414654_S2_L ×2 LIB5455514_SAM24414654_S3_L ×2

How we read this: Read from 26 sample titles: 20 distinct titles with little repetition. 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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