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LncRNA CISTR-ACT regulates cell size in human and mouse by guiding FOSL2 [RNA-Seq]

GSE273476 Homo sapiens (human) RNA-seq (gene expression) 181 samples Submitted 2025/11/18 Platform GPL24676Platform GPL24247Platform GPL30173
At a glance

RNA-seq (gene expression) · human · 181 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
181 samples: 81 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
LncRNA CISTR-ACT regulates cell size in human and mouse by guiding FOSL2Nature communications · 2025
Summary (written by the submitters)
Organisms regulate cell size and shape to function efficiently. Aberrant cell morphogenesis is commonly associated with disease, yet gene-regulatory mechanisms remain unknown. CISTR-ACT was the first lncRNA involved in inter-chromosomal contacts and Mendelian disease, and is associated with mean corpuscular volume (red blood cell size).
Read the full summary ↓
Here, functional dissection of CISTR-ACT’s DNA- and RNA-encoded mechanisms by in vitro and in vivo perturbations reveal that CISTR-ACT regulates cell size across cell types and species. CISTR-ACT’s locus is embedded in a stable inter-chromosomal environment which contains cell size genes that are regulated by CISTR-ACT in trans. CISTR-ACT’s RNA also has function and directly interacts with transcription factor FOSL2 to guide its regulation of cell morphogenesis and cell-cell adhesion genes. In the absence of CISTR-ACT, the FOSL2-chromatin binding is perturbed. Our study exemplifies how a functionally conserved lncRNA regulates cell size with multiple modes of action and ultimately contributes to clinically relevant phenotypes.
Published in
LncRNA CISTR-ACT regulates cell size in human and mouse by guiding FOSL2
Kiriakopulos K, Soleimanpour K, McMurray BJ et al. · Nature communications 2025 · PMID 41397992 · doi:10.1038/s41467-025-67591-x
This dataset
Open GSE273476 in finder → Find more 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 GSE273476_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 PRJNA1141988 and SRA study SRP523187. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41397992) ↗
Study design
81 conditions, mostly in duplicate
WT female mouse blood animal ×6 WT male mouse bone marrow animal ×4 NPC WT ×3 NPC CISTR KO ×3 Cistr KO male mouse cerebellum animal2 ×3 Cistr KO male mouse cerebellum animal3 ×3 Cistr KO male mouse cerebral cortex animal2 ×3 Cistr KO male mouse cerebral cortex animal3 ×3 +76 more

Supports a case/control comparison: 2 samples read as cases, 66 as controls.

How we read this: 81 replicated groups read from 181 sample titles; they account for 178 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

+ 141 more — browse all 181 samples with per-sample file links →

Datasets on a similar topic

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