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Image-based identification and isolation of micronucleated cells to dissect cellular consequences

GSE291811 Homo sapiens (human) RNA-seq (gene expression) 29 samples Submitted 2025/04/15 Platform GPL30173
At a glance

RNA-seq (gene expression) · human · 29 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
29 samples: 11 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
Image-based identification and isolation of micronucleated cells to dissect cellular consequenceseLife · 2025
Summary (written by the submitters)
Recent advances in isolating cells based on visual phenotypes have transformed our ability to identify the mechanisms and consequences of complex traits. Micronucleus (MN) formation is a frequent outcome of genome instability, triggers extensive disease-associated changes in genome structure and signaling coincident with MN rupture, and is almost exclusively defined by visual analysis.
Read the full summary ↓
Automated MN detection in microscopy images has proved extremely challenging, limiting unbiased discovery of the mechanisms and consequences of MN formation and rupture. In this study we describe two new MN segmentation modules: a rapid model for classifying micronucleated cells and their rupture status (VCS MN), and a robust model for accurate MN segmentation (MNFinder) from a broad range of fluorescence microscopy images. As a proof-of- concept, we define the transcriptome of non-transformed human cells with intact or ruptured MN after inducing chromosome missegregation by combining VCS MN with photoactivation-based cell isolation and RNASeq. Surprisingly, we find that neither MN formation nor rupture triggers a strong unique transcriptional response. Instead, transcriptional changes appear correlated with small increases in aneuploidy in these cell classes. Our MN segmentation modules overcome a significant challenge with reproducible MN quantification, and, joined with visual cell sorting, enable the application of powerful functional genomics assays, including pooled CRISPR screens and time-resolved analyses of cellular and genetic consequences, to a wide-range of questions in MN biology.
Published in
Image-based identification and isolation of micronucleated cells to dissect cellular consequences
DiPeso L, Pendyala S, Huang HZ et al. · eLife 2025 · PMID 40455079 · doi:10.7554/eLife.101579
This dataset
Open GSE291811 in finder → Find more human 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 GSE291811_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 PRJNA1235274 and SRA study SRP569948. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40455079) ↗
Study design
11 conditions, mostly in duplicate
2022.03.18-MN1 ×2 2022.03.18-MN0 ×2 2022.04.14-MN0-800 ×2 2022.04.14-MN1-200 ×2 2022.04.14-MN1-800 ×2 2022.05.18-BAY ×2 2022.07.01-BAY-200_2 ×2 2022.07.01-BAY-800_2 ×2 +10 more

Supports a between-group comparison across 22 samples.

How we read this: 11 replicated groups read from 29 sample titles; they account for 22 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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