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Transcriptional function of E2A, Ebf1, Pax5, Ikaros and Aiolos analyzed by in vivo acute protein degradation in early B cell development [CUT&RUN]

GSE259358 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 22 samples Submitted 2024/06/21 Platform GPL30172
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 22 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
22 samples: 9 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
Transcriptional function of E2A, Ebf1, Pax5, Ikaros and Aiolos analyzed by in vivo acute protein degradation in early B cell developmentNature immunology · 2024
Summary (written by the submitters)
Early B-lymphopoiesis depends on E2A, Ebf1, Pax5 and Ikaros family members. Here, we used acute protein degradation in vivo to identify direct target genes of these transcription factors in pro-B, small pre-B and immature B-cells. E2A, Ebf1 and Pax5 predominantly function as transcriptional activators by inducing open chromatin at their target genes, have largely unique functions and maintain cell viability in vivo by activating Bcl2l1.
Read the full summary ↓
Ikaros and Aiolos cooperatively control early B-cell development and act as dedicated repressors to suppress open chromatin at their target genes. The surrogate light-chain genes Igll1 and Vpreb1 are directly activated by Ebf1 and Pax5 in pro-B cells and directly repressed by Ikaros and Aiolos in small pre-B cells. Pax5 and E2A contribute to V(D)J recombination by activating Rag1, Rag2, Dntt, Irf4 and Irf8. Like Pax5, Ebf1 also represses the cohesin-release factor gene Wapl to mediate prolonged loop extrusion across the Igh locus. In summary, in vivo protein degradation has provided unprecedented insight into the control of early B-lymphopoiesis by five transcription factors.
Published in
Transcriptional function of E2A, Ebf1, Pax5, Ikaros and Aiolos analyzed by in vivo acute protein degradation in early B cell development
Fedl AS, Tagoh H, Gruenbacher S et al. · Nature immunology 2024 · PMID 39179932 · doi:10.1038/s41590-024-01933-7
This dataset
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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 GSE259358_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 PRJNA1081364 and SRA study SRP492017. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39179932) ↗
Study design
9 conditions, mostly in duplicate
Cut&Run bone marrow Pro-B cells Ikzf1(AID/AID) ×2 Cut&Run bone marrow Pro-B cells Ikzf3(AID/AID) ×2 Cut&Run bone marrow Pro-B cells Pax5(AID/AID)… ×2 Cut&Run bone marrow Pro-B cells E2A(AID/AID) … ×2 Cut&Run bone marrow Pre-B cells Ikzf1(AID/AID) ×2 Cut&Run bone marrow Pre-B cells Ikzf3(AID/AID) ×2 Cut&Run bone marrow Pre-B cells Pax5(AID/AID)… ×2 Cut&Run bone marrow Pre-B cells E2A(AID/AID) … ×2 +5 more

Supports a between-group comparison across 18 samples.

How we read this: 9 replicated groups read from 22 sample titles; they account for 18 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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