GEO series

HAND2 invades nucleolar condensates to pioneer lineage-specific cardiac pacemaker gene programs [RNA-Seq]

GSE278736 Mus musculus (mouse) RNA-seq (gene expression) 12 samples Submitted 2025/08/05 Platform GPL30172

At a glance

RNA-seq (gene expression) · mouse · 12 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: 12 samples
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: HAND2 invades nucleolar condensates to pioneer lineage-specific cardiac pacemaker gene programsNature communications · 2025

Summary (written by the submitters)

Sub-nuclear localization of heterochromatin enables stable lineage-specific gene repression. The mechanisms by which pioneer transcription factors (TFs) access these loci to selectively activate lineage-specific genes remain poorly understood. Here, using a model of TF-induced cardiac reprogramming, we show that Hand2’s ability to reprogram cells requires its selective compartmentalization within perinucleolar heterochromatin wherein many key target genes reside.

Read the full summary ↓

We identify the nucleolar targeting region of Hand2, which is mechanistically separable from DNA-binding. Using a series of separation of function mutants, we find that compartmentalization creates high local concentrations of Hand2 homodimers required for binding of suboptimal DNA motifs within lineage-specific gene enhancers. Altogether, our results establish a causal relationship between TF sub-nuclear localization and selective activation of lineage-specific gene programs. Thus, our data support the notion that lineage-specific programs are functionally compartmentalized within the nucleus, and we provide a mechanistic model by which TF sub-nuclear localization orchestrates selective activation of lineage specific genes.

Published in

HAND2 invades nucleolar condensates to pioneer lineage-specific cardiac pacemaker gene programs

Kulkarni K, Quinn G, Dela Rosa J et al. · Nature communications 2025 · PMID 41073403 · doi:10.1038/s41467-025-64076-9

This dataset

Open GSE278736 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 GSE278736_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 PRJNA1168539 and SRA study SRP536429. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41073403) ↗

Samples in this study

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+ 12 more — browse all 12 samples with per-sample file links →

Datasets on a similar topic

GSE299217 HAND2 invades nucleolar condensates to pioneer lineage-specific cardiac pacemaker gene programs [ATAC, Cut & Tag] 5 samples shares hand2, lineage-specific, condensates, nucleolar, pacemaker, programs, invades, pioneer
GSE297660 WDR5 Remodels NANOG Condensates to Drive Transcriptional Programs and Sustain Stem Cell Identity 18 samples shares condensates, programs
GSE297961 WDR5 Remodels NANOG Condensates to Drive Transcriptional Programs and Sustain Stem Cell Identity [Nanog_WT_R153A_RNAseq] 6 samples shares condensates, programs
GSE299636 WDR5 Remodels NANOG Condensates to Drive Transcriptional Programs and Sustain Stem Cell Identity [ChIP-seq] 28 samples shares condensates, programs
GSE223771 Hand1 KO HAND2 replacement RNA-Seq data 11 samples shares hand2
GSE299253 Hand1 gene replacement with Hand2 reveals overlap in function with unique occurrence of omphalocele and heart defects [scRNA-seq] 9 samples shares hand2
GSE311982 Endocardial HAND2 orchestrates hypoxic and TGFbeta signaling to modulate coronary artery formation [RNA-Seq] 8 samples shares hand2
GSE311983 Endocardial HAND2 orchestrates hypoxic and TGFbeta signaling to modulate coronary artery formation [scRNA-seq] 2 samples shares hand2

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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.