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NF-κB transcription factors RelA and c-Rel selectively control CD4+ T-cell function in multiple sclerosis and cancer

GSE239704 Homo sapiens (human) RNA-seq (gene expression) 34 samples Submitted 2024/03/28 Platform GPL24676Platform GPL24247
At a glance

RNA-seq (gene expression) · human · 34 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
34 samples: 6 conditions, mostly with about 4 replicates eachGroups 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
NF-κB subunits RelA and c-Rel selectively control CD4+ T cell function in multiple sclerosis and cancerThe Journal of experimental medicine · 2024
SuperSeries — this record groups several sub-series.
Summary (written by the submitters)
This SuperSeries is composed of the SubSeries listed below.
Published in
NF-κB subunits RelA and c-Rel selectively control CD4+ T cell function in multiple sclerosis and cancer
Lalle G, Lautraite R, Bouherrou K et al. · The Journal of experimental medicine 2024 · PMID 38563819 · doi:10.1084/jem.20231348
This dataset
Open GSE239704 in finder → Find more 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 GSE239704_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 PRJNA1000587 and SRA study SRP452373. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38563819) ↗
Study design
6 conditions, mostly with about 4 replicates each
Control human Tconv, dono ×4 RELA-KO human Tconv, dono ×4 REL-KO human Tconv, dono ×4 Rela-KO mouse Tconv cells, ×4 Rel-KO mouse Tconv cells, ×4 Ctrl mouse Tconv cells, ×4 DLN-Tconv from B16OVA-bearing Rel-icKO mice ×1 DLN-Tconv from B16OVA-bearing Ctrl mice ×1 +8 more

Supports a case/control comparison: 4 samples read as cases, 10 as controls.

How we read this: 6 replicated groups read from 34 sample titles; they account for 24 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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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.