GEO series

Creb5 controls its own expression and directly induces the joint-interzone regulatory program [RNAseq_Prx1]

GSE281190 Mus musculus (mouse) RNA-seq (gene expression) 12 samples Submitted 2025/06/05 Platform GPL24247

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: 11 distinct titles, 1 of them repeatedGroups 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: Creb5 controls its own expression and directly induces the joint interzone regulatory programProceedings of the National Academy of Sciences of the United States of America · 2025

Summary (written by the submitters)

Our prior work indicated that the transcription factor Creb5 plays a crucial role in the genesis of synovial joints. Here, we perform an integrative analysis of the transcriptome, chromatin accessibility, and Creb5-chromatin occupancy in Creb5-expressing synovial joint progenitor cells. This analysis revealed that Creb5 directly binds to both its own two promoters and to the regulatory regions of the early joint markers, Gdf5 and Sfrp2; each of whose expression in the joint-interzone is Creb5-dependent.

Read the full summary ↓

Functional enhancer analysis indicated that Creb5 binding sites in its own two promoters are necessary for these sequences to drive transgene expression in a pattern that mimics endogenous Creb5 expression. While Creb5 directly regulates both Gdf5 and Sfrp2 expression in the inner joint-interzone by binding to either CREs or TREs in their regulatory elements, Creb5 activates Barx1 expression specifically in the outer joint-interzone; and thus initiates both the formation of the joint-interzone and regionalization of cell fates within this tissue.

Published in

Creb5 controls its own expression and directly induces the joint interzone regulatory program

Zhang CH, Shahini A, Cook LE et al. · Proceedings of the National Academy of Sciences of the United States of America 2025 · PMID 40472036 · doi:10.1073/pnas.2501830122

This dataset

Open GSE281190 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 GSE281190_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 PRJNA1182704 and SRA study SRP543494. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40472036) ↗

Study design

11 distinct titles, 1 of them repeated

E14_5_Prx1Cre_iCreb ×2

How we read this: Read from 12 sample titles: 11 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

GSM8612413 E14_5_Prx1Cre_iTdtomato3a
GSM8612414 E14_5_Prx1Cre__iCreb53a
GSM8612415 E14_5_Prx1Cre_iTdtomato3b
GSM8612416 E14_5_Prx1Cre_iCreb53b
GSM8612417 E14_5_Prx1Cre_iTdtomato3c
GSM8612418 E14_5_Prx1Cre_iCreb53c
GSM8612419 E14_5_Prx1Cre_iTdtomato4a
GSM8612420 E14_5_Prx1Cre_iCreb54a
GSM8612421 E14_5_Prx1Cre_iTdtomato5b
GSM8612422 E14_5_Prx1Cre_iCreb55
GSM8612423 E14_5_Prx1Cre_iTdtomato6d
GSM8612424 E14_5_Prx1Cre_iCreb56

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