GEO series

Transient proliferation by reversible YAP- and mitogen-control of the cyclin D1/p27 ratio

GSE313416 Homo sapiens (human) RNA-seq (gene expression) 63 samples Submitted 2026/03/11 Platform GPL24676

At a glance

RNA-seq (gene expression) · human · 63 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: 63 samples: 63 samples, each with a distinct title — no replicated groupsGroups 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: Transient proliferation by reversible YAP and mitogen control of the cyclin D1/p27 ratioCommunications biology · 2026

Summary (written by the submitters)

Hippo-YAP signaling orchestrates epithelial tissue repair and is therefore an attractive target in regenerative medicine. A challenge has been to understand how YAP activity is integrated with mitogen signaling and contact inhibition to control a transient proliferative response. Here we show that reduced contact inhibition, increased mitogen signaling, and YAP-TEAD activation converge on increasing the nuclear cyclin D1/p27 protein ratio during early G1 phase, towards a threshold ratio that dictates whether individual cells enter or exit the cell cycle.

Read the full summary ↓

YAP increases this ratio in concert with inducing mitogen signaling, by increasing EGFR and other receptors that signal primarily through ERK. After a delay, contact inhibition suppresses YAP activity, which gradually downregulates mitogen signaling and the cyclin D1/p27 ratio. Increasing YAP activity by ablating the suppressor Merlin/NF2 reveals a balancing mechanism whereby YAP suppression and contact inhibition of proliferation can be recovered but only at higher local cell density. Thus, critical for regeneration, robust proliferation responses result from the YAP-induced and receptor-mediated prolonged increase in the cyclin D1/p27 ratio, which is reversed by delayed suppression of receptor signaling after contact inhibition of YAP.

Published in

Transient proliferation by reversible YAP and mitogen control of the cyclin D1/p27 ratio

Ferrick KR, Upadhya SW, Fan Y et al. · Communications biology 2026 · PMID 41611993 · doi:10.1038/s42003-026-09590-2

This dataset

Open GSE313416 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 GSE313416_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 PRJNA1379470 and SRA study SRP654381. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41611993) ↗

Study design

63 samples, each with a distinct title — no replicated groups

Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.

How we read this: Read from 63 sample titles: 63 distinct titles with little repetition. 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

GSM9367708 WT RPE1 starved replicate 1 DMSO
GSM9367709 WT RPE1 starved replicate 1 LATSi 3h
GSM9367710 WT RPE1 starved replicate 1 LATSi 6h
GSM9367711 WT RPE1 serum replicate 1 DMSO
GSM9367712 WT RPE1 serum replicate 1 LATSi 1h
GSM9367713 WT RPE1 serum replicate 1 LATSi 3h
GSM9367714 WT RPE1 serum replicate 1 LATSi 6h
GSM9367715 WT RPE1 starved replicate 2 DMSO
GSM9367716 WT RPE1 starved replicate 2 LATSi 3h
GSM9367717 WT RPE1 starved replicate 2 LATSi 6h
GSM9367718 WT RPE1 serum replicate 2 DMSO
GSM9367719 WT RPE1 serum replicate 2 LATSi 1h
GSM9367720 WT RPE1 serum replicate 2 LATSi 3h
GSM9367721 WT RPE1 serum replicate 2 LATSi 6h
GSM9367722 WT RPE1 starved replicate 3 DMSO
GSM9367723 WT RPE1 starved replicate 3 LATSi 3h
GSM9367724 WT RPE1 starved replicate 3 LATSi 6h
GSM9367725 WT RPE1 serum replicate 3 DMSO
GSM9367726 WT RPE1 serum replicate 3 LATSi 1h
GSM9367727 WT RPE1 serum replicate 3 LATSi 3h
GSM9367728 WT RPE1 serum replicate 3 LATSi 6h
GSM9367729 CA-YAP RPE1 starved replicate 1 DMSO
GSM9367730 CA-YAP RPE1 starved replicate 1 DOX 6h
GSM9367731 CA-YAP RPE1 starved replicate 1 DOX 12h
GSM9367732 CA-YAP RPE1 starved replicate 1 DMSO 24h
GSM9367733 CA-YAP RPE1 starved replicate 1 DOX 24h
GSM9367734 CA-YAP RPE1 starved replicate 1 DOX 36h
GSM9367735 CA-YAP RPE1 serum replicate 1 DMSO
GSM9367736 CA-YAP RPE1 serum replicate 1 DOX 6h
GSM9367737 CA-YAP RPE1 serum replicate 1 DOX 12h
GSM9367738 CA-YAP RPE1 serum replicate 1 DMSO 24h
GSM9367739 CA-YAP RPE1 serum replicate 1 DOX 24h
GSM9367740 CA-YAP RPE1 serum replicate 1 DOX 36h
GSM9367741 CA-YAP RPE1 starved replicate 2 DMSO
GSM9367742 CA-YAP RPE1 starved replicate 2 DOX 6h
GSM9367743 CA-YAP RPE1 starved replicate 2 DOX 12h
GSM9367744 CA-YAP RPE1 starved replicate 2 DMSO 24h
GSM9367745 CA-YAP RPE1 starved replicate 2 DOX 24h
GSM9367746 CA-YAP RPE1 starved replicate 2 DOX 36h
GSM9367747 CA-YAP RPE1 serum replicate 2 DMSO

+ 23 more — browse all 63 samples with per-sample file links →

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Search all human RNA-seq datasets in GEO →

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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.