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Effect of knockout of Samsn1 on gene expression during E.coli infection in Raw264.7 cells

GSE262688 Mus musculus (mouse) RNA-seq (gene expression) 12 samples Submitted 2025/06/01 Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 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
Mus musculus (mouse)
Samples
12 samples: 3 × Raw264.7 cells, wild type, untreated vs 3 × Raw264.7 cells, wild type, E.coli treated vs 3 × Raw264.7 cells, Samsn1 konckout, untreated vs 3 × Raw264.7 cells, Samsn1 konckout, E.coli treatedGroups 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 sepsis, infection and immunosuppression occur simultaneously. We currently found that Samsn1 expression is increased on myeloid cells in sepsis. And, Samsn1 is currently recognized as a negative regulator of immune response. So we constructed Samsn1 knockout Raw264.7 cells to study the effect of Samsn1 on macrophage function and the gene expression of macrophages with infection.
This dataset
Open GSE262688 in finder → Find more mouse 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 GSE262688_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 PRJNA1092993 and SRA study SRP498458. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
3 × Raw264.7 cells, wild type, untreated vs 3 × Raw264.7 cells, wild type, E.coli treated vs 3 × Raw264.7 cells, Samsn1 konckout, untreated vs 3 × Raw264.7 cells, Samsn1 konckout, E.coli treated

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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