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RNA-Seq analysis of SUN1 knockout and control CT26 cells and tumors

GSE250602 Mus musculus (mouse) RNA-seq (gene expression) 24 samples Submitted 2024/03/29 Platform GPL21103
At a glance

RNA-seq (gene expression) · mouse · 24 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
24 samples: 5 conditions, mostly in duplicateGroups 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
A computational pipeline for identifying gene targets and signalling pathways in cancer cells to improve lymphocyte infiltration and immune checkpoint therapy efficacyEBioMedicine · 2024
Summary (written by the submitters)
T cell infiltration is essential for immune checkpoint inhibitors to be effective in treating solid cancers. Through a bioinformatic pipeline, we identified a target gene SUN1 that might relate to modulating immune cell infiltration and immune response. Thus, we generated one Sun1_knockout CT26 cell line (Sun1_KO) and two control CT26 cell lines (Sun1_Control) using CRISPR-Cas9.
Read the full summary ↓
By performing RNA-seq on cultured cells, tumors grown in syngeneic model, and purified tumor cells from tumors grown in syngeneic model, we set out to understand how mouse Sun1 can affect immune-related pathways and immune cell infiltration and anti-PD1 efficacy in BALB/c mice.
Published in
A computational pipeline for identifying gene targets and signalling pathways in cancer cells to improve lymphocyte infiltration and immune checkpoint therapy efficacy
Nasr S, Li L, Asad M et al. · EBioMedicine 2024 · PMID 38805852 · doi:10.1016/j.ebiom.2024.105167
This dataset
Open GSE250602 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 GSE250602_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 PRJNA1054607 and SRA study SRP479059. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38805852) ↗
Study design
5 conditions, mostly in duplicate
Sun1_Control1_CT26_tumors ×8 Sun1_KO_CT26_tumors ×7 Sun1_KO_CT26_purified_tumor_cells ×2 Sun1_Control1_CT26_purified_tumor_cells ×2 Sun1_Control2_CT26_purified_tumor_cells ×2 Sun1_KO_CT26_cultured_cells ×1 Sun1_Control1_CT26_cultured_cells ×1 Sun1_Control2_CT26_cultured_cells ×1

Supports a case/control comparison: 9 samples read as cases, 2 as controls.

How we read this: 5 replicated groups read from 24 sample titles; they account for 21 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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