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A mutant Bcl11b protein interferes with Bcl11a function during T lymphocyte and neuronal development

GSE221765 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 19 samples Submitted 2024/09/27 Platform GPL17021Platform GPL21273
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 19 samples

What it is
ChIP-seq / ATAC-seq (genome binding and open chromatin)Where proteins bind the genome, or which regions are open and active.
Organism
Mus musculus (mouse)
Samples
19 samples: 8 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
SuperSeries — this record groups several sub-series.
Summary (written by the submitters)
This SuperSeries is composed of the SubSeries listed below.
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 GSE221765 in finder → Find more mouse ChIP / ATAC / CUT&Tag 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 GSE221765_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: Look for peak files (.bed, .narrowPeak) and signal tracks (.bigWig) among the supplementary files; the raw reads are on ENA.

Also filed as BioProject PRJNA915975 and SRA study SRP414847. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39487351) ↗
Study design
8 conditions, mostly in duplicate
thymocytes, Bcl11b-ChIP, Bcl11b +/+, ×3 thymocytes, Bcl11b-ChIP, Bcl11b +/N440K, ×3 Vav1-Cre, ×3 thymocytes, total input, Bcl11b +/+, ×2 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 19 samples.

How we read this: 8 replicated groups read from 19 sample titles; they account for 19 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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