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EVOLUTIONARY CO-OPTION OF AN ANCESTRAL CLOACAL REGULATORY LANDSCAPE WITH THE EMERGENCE OF DIGITS AND GENITALS [RNA-seq]

GSE250266 Mus musculus (mouse) RNA-seq (gene expression) 12 samples Submitted 2024/04/17 Platform GPL13112

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: 3 × RNA-seq in E18.5 mutant female urogenital sinus vs 3 × RNA-seq in E18.5 mutant male urogenital sinus vs 3 × RNA-seq in E18.5 wild type female urogenital sinus vs 3 × RNA-seq in E18.5 wild type male urogenital sinusGroups 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: EVOLUTIONARY CO-OPTION OF AN ANCESTRAL CLOACAL REGULATORY LANDSCAPE DURING THE EMERGENCE OF DIGITS AND GENITALSbioRxiv : the preprint server for biology · 2024

Summary (written by the submitters)

The existence of homologies between fins and tetrapod limb skeletal parts as well as of the nature of those mechanisms underlying the transition of the former towards the latter, have been a rich source of discussion for more than a century. While the recent use of gene expression patterns to try and infer evolutionary scenarios has been a popular and successful approach, in particular the distribution of Hox transcript domains, it has failed to provide clearcut evidence as to whether fishes do have bony elements related by ancestry to tetrapod hands and feet.

Read the full summary ↓

In tetrapods, posterior Hoxd genes transcription in digits is controlled by a well-characterized series of enhancers forming a large regulatory landscape, which has its syntenic counterpart in zebrafish. We show here that the deletion of the orthologous landscape in fishes does not affect the transcription of these genes in fin buds. Instead, it abrogates hoxd expression in the cloaca, an essential structure related to the mammalian uro-genital sinus. We also report that Hoxd gene function in the mammalian uro-genital sinus depends on enhancers located in the same regulatory landscape and thus conclude that an ancestral Hox ‘cloacal’ regulation was co-opted, in tetrapod, as a playground to subsequently accompany the evolution of both external genitals and digits regulatory landscapes, along with the emergence of these developmentally and phylogenetically related structures.

Published in

EVOLUTIONARY CO-OPTION OF AN ANCESTRAL CLOACAL REGULATORY LANDSCAPE DURING THE EMERGENCE OF DIGITS AND GENITALS

Hintermann A, Bolt CC, Hawkins MB et al. · bioRxiv : the preprint server for biology 2024 · PMID 38585989 · doi:10.1101/2024.03.24.586442

This dataset

Open GSE250266 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 GSE250266_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 PRJNA1053268 and SRA study SRP478205. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38585989) ↗

Study design

3 × RNA-seq in E18.5 mutant female urogenital sinus vs 3 × RNA-seq in E18.5 mutant male urogenital sinus vs 3 × RNA-seq in E18.5 wild type female urogenital sinus vs 3 × RNA-seq in E18.5 wild type male urogenital sinus

Supports a case/control comparison: 6 samples read as cases, 6 as controls.

How we read this: 4 replicated groups read from 12 sample titles; they account for 12 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

GSM7976440 RNA-seq in E18.5 mutant female urogenital sinus replicate 1 RNA-seq in E18.5 mutant…
GSM7976441 RNA-seq in E18.5 mutant female urogenital sinus replicate 2 RNA-seq in E18.5 mutant…
GSM7976442 RNA-seq in E18.5 mutant female urogenital sinus replicate 3 RNA-seq in E18.5 mutant…
GSM7976443 RNA-seq in E18.5 mutant male urogenital sinus replicate 1 RNA-seq in E18.5 mutant…
GSM7976444 RNA-seq in E18.5 mutant male urogenital sinus replicate 2 RNA-seq in E18.5 mutant…
GSM7976445 RNA-seq in E18.5 mutant male urogenital sinus replicate 3 RNA-seq in E18.5 mutant…
GSM7976446 RNA-seq in E18.5 wild type female urogenital sinus replicate 1 RNA-seq in E18.5 wild t…
GSM7976447 RNA-seq in E18.5 wild type female urogenital sinus replicate 2 RNA-seq in E18.5 wild t…
GSM7976448 RNA-seq in E18.5 wild type female urogenital sinus replicate 3 RNA-seq in E18.5 wild t…
GSM7976449 RNA-seq in E18.5 wild type male urogenital sinus replicate 1 RNA-seq in E18.5 wild t…
GSM7976450 RNA-seq in E18.5 wild type male urogenital sinus replicate 2 RNA-seq in E18.5 wild t…
GSM7976451 RNA-seq in E18.5 wild type male urogenital sinus replicate 3 RNA-seq in E18.5 wild t…

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