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A mutant Bcl11b protein interferes with Bcl11a function during T lymphocyte and neuronal development [RNA-seq]

GSE221764 Mus musculus (mouse) RNA-seq (gene expression) 11 samples Submitted 2024/09/27 Platform GPL21273Platform GPL17021
At a glance

RNA-seq (gene expression) · mouse · 11 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
11 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 mutant BCL11B-N440K protein interferes with BCL11A function during T lymphocyte and neuronal developmentNature immunology · 2024
Summary (written by the submitters)
CD24-TCRb- thymocytes emerged the thymus of mice carrying Bcl11b N440K variant and Tcf7 deficient mice. To investigate the feature of these cells, we performed RNA-seq.
Published in
A mutant BCL11B-N440K protein interferes with BCL11A function during T lymphocyte and neuronal development
Okuyama K, Yamashita M, Koumoundourou A et al. · Nature immunology 2024 · PMID 39487351 · doi:10.1038/s41590-024-01997-5
This dataset
Open GSE221764 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 GSE221764_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 PRJNA915977 and SRA study SRP414847. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39487351) ↗
Study design
5 conditions, mostly in duplicate
Vav1-Cre, ×3 thymocytes, CD24-TCRb-, Bcl11b +/+, ×2 thymocytes, CD24-TCRb-, Bcl11b +/N440K, ×2 thymocytes, CD24-TCRb-, Bcl11b D/N440K, ×2 thymocytes, CD24-TCRb-, Tcf7 +/+, ×2

Supports a between-group comparison across 11 samples.

How we read this: 5 replicated groups read from 11 sample titles; they account for 11 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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