GEO series

Ki67-mediated chromatin accessibility impedes B-cell antigen-receptor gene rearrangement

GSE246986 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 24 samples Submitted 2024/05/31 Platform GPL24247

At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 24 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: 24 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: Ki67 deficiency impedes chromatin accessibility and BCR gene rearrangementThe Journal of experimental medicine · 2024

Summary (written by the submitters)

B and T cells can recognise and respond to a vast array of foreign pathogens by virtue of the diverse antigen-receptor repertoire generated by gene rearrangement during development. Here, we show that deficiency in Ki67, a nuclear protein ubiquitously expressed throughout the cell cycle, impairs B-cell development at specific, early stages.

Read the full summary ↓

We identified that Ki67 maintains global chromatin accessibility in lymphocyte progenitors at stages where antigen-receptor gene rearrangements occur and that gene rearrangement is less efficient in the absence of Ki67. That the defects in B cell development are caused by disrupted antigen-receptor gene rearrangement is shown by pre-rearranged antigen-receptor genes fully compensating for loss of Ki67. Collectively, these results identify a unique contribution from Ki67 to somatic antigen-receptor gene rearrangement.

Published in

Ki67 deficiency impedes chromatin accessibility and BCR gene rearrangement

Ding Z, Hagan M, Yan F et al. · The Journal of experimental medicine 2024 · PMID 38842525 · doi:10.1084/jem.20232160

This dataset

Open GSE246986 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 GSE246986_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 PRJNA1035491 and SRA study SRP470112. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38842525) ↗

Study design

6 conditions, mostly with about 4 replicates each

WT Pre-pro-B ×4 Mki67-/- Pre-pro-B ×4 WT Pro-B ×4 Mki67-/- Pro-B ×4 WT Small pre-B ×4 Mki67-/- Small pre-B ×4

Supports a between-group comparison across 24 samples.

How we read this: 6 replicated groups read from 24 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

GSM7881784 WT Pre-pro-B 1 WT Pre-pro-B
GSM7881785 WT Pre-pro-B 2 WT Pre-pro-B
GSM7881786 WT Pre-pro-B 3 WT Pre-pro-B
GSM7881787 WT Pre-pro-B 4 WT Pre-pro-B
GSM7881788 Mki67-/- Pre-pro-B 1 Mki67-/- Pre-pro-B
GSM7881789 Mki67-/- Pre-pro-B 2 Mki67-/- Pre-pro-B
GSM7881790 Mki67-/- Pre-pro-B 3 Mki67-/- Pre-pro-B
GSM7881791 Mki67-/- Pre-pro-B 4 Mki67-/- Pre-pro-B
GSM7881792 WT Pro-B 1 WT Pro-B
GSM7881793 WT Pro-B 2 WT Pro-B
GSM7881794 WT Pro-B 3 WT Pro-B
GSM7881795 WT Pro-B 4 WT Pro-B
GSM7881796 Mki67-/- Pro-B 1 Mki67-/- Pro-B
GSM7881797 Mki67-/- Pro-B 2 Mki67-/- Pro-B
GSM7881798 Mki67-/- Pro-B 3 Mki67-/- Pro-B
GSM7881799 Mki67-/- Pro-B 4 Mki67-/- Pro-B
GSM7881800 WT Small pre-B 1 WT Small pre-B
GSM7881801 WT Small pre-B 2 WT Small pre-B
GSM7881802 WT Small pre-B 3 WT Small pre-B
GSM7881803 WT Small pre-B 4 WT Small pre-B
GSM7881804 Mki67-/- Small pre-B 1 Mki67-/- Small pre-B
GSM7881805 Mki67-/- Small pre-B 2 Mki67-/- Small pre-B
GSM7881806 Mki67-/- Small pre-B 3 Mki67-/- Small pre-B
GSM7881807 Mki67-/- Small pre-B 4 Mki67-/- Small pre-B

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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.