{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Rodrigo Senovilla-Ganzo"],"organism":["Mus musculus"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-16735"],"description":["As the body plan, the embryonic brain bauplan reflects the shared features of vertebrate brains. Yet, disagreements among sparse histogenetic frameworks have undermined the bauplan’s power to trace homologies. Here, we generate and integrate five vertebrate single-cell multi-omic atlases of early embryonic brains, revealing a conserved cellular blueprint that defines equivalent progenitor domains across species. Our cellular neuromeric model provides an unified and unbiased framework for the vertebrate brain bauplan and revises the regionalisation of the prosencephalon, refining its molecular boundaries and developmental relationships. Furthermore, cross-species gene-network analyses expose regulatory complexity beyond classical neuromeric patterning, resolving networks into modules aligned with regional cell types or cell class (progenitor/neuron). Evolutionarily, two main developmental constraints emerge: brain bauplan genes, early essential for regional identity, and pleiotropic stemness gene modules, indispensable across all proliferating cells. In turn, later development displays tissue-specific and less essential modules, explaining its rapid divergence into species-specific features. Together, these findings reveal a dual evolutionary constraint—neuromeric identity and pleiotropic stemness—that underlies the conservation of early vertebrate brains. This duality explains how deeply conserved regulatory architectures coexist with evolutionary flexibility to develop into the immense diversity of vertebrate nervous systems."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sequencing - The obtained libraries were sequenced on a Novaseq 6000 (Illumina) for an approximated 50.000 reads per cell (500 million reads).","Growth Protocol - Chick: Fertilized chick eggs (Gallus gallus) were purchased from Granja Santa Isabel and incubated at 37.5 °C in humidified atmosphere until required developmental stage. The day when eggs were incubated was considered embryonic day (E)0.  Mouse: Adult C57BL/6 mice (Mus musculus) were obtained from a mice breeding colony at Achucarro Basque Center for Neuroscience (Spain). They were housed in a 12/12-hour light/dark cycle (8 AM, lights on) and provided with ad libitum food and water. T The day when the vaginal plug was detected was referred to as embryonic day 0.5 (E0.5) -to accommodate to La Manno et al (2021) dating. Gecko: Fertilized ground Madagascar gecko eggs (Paroedura picta) were obtained from a breeding colony at Achucarro Basque Center for Neuroscience. They were housed in a 12/12-hour light/dark cycle (8 AM, lights on, 27ºC/ 8 PM light off, 22ºC) and provided with ad libitum food (live crickets) and water. Gecko eggs were incubated at 28 °C in a low humidified atmosphere until required developmental stage. The day when eggs were incubated was considered E0.","Sample Collection - Embryos were collected in RNAase free conditions and dissected to extract the brain (neural tube).","Nucleic Acid Extraction - In both, snATAC-seq and scRNA-seq, barcoded fragments were generated for each bead-cell (Gel Beads-in-emulsion (GEMs)). For this step, oligonucleotides containing (i) an Illumina P5 sequence, (ii) a 16 nt 10x Barcode and (iii) a Read 1 (Read 1N) sequence were released in each GEM and mixed with DNA fragments and Master Mix. After incubation and amplification, the GEMs were broken and pooled. Next, P7 and a sample index were added during library construction via PCR.","Sample Treatment - No treatment was applied as all samples were obtained on wild type conditions. No treatment was applied as all samples were obtained on wild type conditions. No treatment was applied as all samples were obtained on wild type conditions.","Library Construction - In both, snATAC-seq and scRNA-seq, barcoded fragments were generated for each bead-cell (Gel Beads-in-emulsion (GEMs)). For this step, oligonucleotides containing (i) an Illumina P5 sequence, (ii) a 16 nt 10x Barcode and (iii) a Read 1 (Read 1N) sequence were released in each GEM and mixed with DNA fragments and Master Mix. After incubation and amplification, the GEMs were broken and pooled. Next, P7 and a sample index were added during library construction via PCR."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Sequence Alignment - For both species, 10X CellRanger v7.1.0 was employed for alignment and demultiplexing of FASTQ files to obtain feature-barcode matrices. The genomes used as reference for each species alignment were: mm10-2020-A for mouse, galGal6 (Ensembl 99) and also bGalGal1 (Ensembl 112) for ATAC/SCENIC+ pipeline, and our custom annotation for the gecko genome. The quality control statistics related to this alignment steps and others are summarized in Supplementary Table S3.  Afterwards, data matrices were imported to R (v4.1.0), where Seurat (v4.1.0)117 was employed to further analysis, as describe in their vignettes (https://satijalab.org/seurat/).","Data Transformation - The output matrix of both in-house samples and published datasets were independently input to Seurat and processed following a common pipeline (Figure 35).(Figure 35). The cell-cycle phase was determined by CellCycleScore() function, using \\\"RRM2\\\", \\\"PCNA\\\", \\\"SLBP\\\", \\\"WDR76\\\", \\\"MCM5\\\" as S-phase genes and \\\"CENPF\\\", \\\"TPX2\\\", \\\"HMGB2\\\", \\\"UBE2C\\\", \\\"BUB1B\\\", \\\"TOP2A\\\", \\\"CENPE\\\", \\\"TACC3\\\", \\\"BUB1\\\", \\\"AURKA\\\", \\\"CDC20\\\" as G2M genes 118, and the mitochondrial percentage of each cell was calculated with PercentageFeatureSet(pattern= “T-”). As an initial filter, poor-quality cells and doublets were first filtered considering the number of detected genes (e.g. < 8000 and > 1500) and mitochondrial percentage (> 5%). However, manual identification of poor-quality clusters was performed by adapting these threesholds. Samples of equal temporal stages (and different in the case of zebrafish) were merged into one Seurat object, were subject to normalize and scale, and regress-out cell-cycle, mitochondrial percentage with the SCTransform() v1 method. Additionally, replicates were integrated to remove the potential batch effect associated with the merge of independent experiments with FindIntegrationAnchors(reduction= “rpca”) and IntegrateData() function. This procedure was also applied to zebrafish timepoints in order to obtain a more homogeneous integration of their cell types irrespective of maturation trajectories. From here, the “integrated” dataset is employed for downstream processing and visualization, gene expression levels were displayed from the “SCT” normalized assay, and SCENIC and SAMap comparative analysis employed raw counts (assay “RNA”)."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq 6000"],"pubmed_abstract":["As the body plan, the embryonic brain bauplan reflects the shared features of vertebrate brains. Yet, disagreements among sparse histogenetic frameworks have undermined the bauplan’s power to trace homologies. Here, we generate and integrate five vertebrate single-cell multi-omic atlases of early embryonic brains, revealing a conserved cellular blueprint that defines equivalent progenitor domains across species. Our cellular neuromeric model provides an unified and unbiased framework for the vertebrate brain bauplan and revises the regionalisation of the prosencephalon, refining its molecular boundaries and developmental relationships. Furthermore, cross-species gene-network analyses expose regulatory complexity beyond classical neuromeric patterning, resolving networks into modules aligned with regional cell types or cell class (progenitor/neuron). Evolutionarily, two main developmental constraints emerge: brain bauplan genes, early essential for regional identity, and pleiotropic stemness gene modules, indispensable across all proliferating cells. In turn, later development displays tissue-specific and less essential modules, explaining its rapid divergence into species-specific features. Together, these findings reveal a dual evolutionary constraint—neuromeric identity and pleiotropic stemness—that underlies the conservation of early vertebrate brains. This duality explains how deeply conserved regulatory architectures coexist with evolutionary flexibility to develop into the immense diversity of vertebrate nervous systems. <h4>Graphical abstract</h4>"],"study_type":["RNA-seq of coding RNA from single cells"],"species":["Mus musculus"],"pubmed_title":["A dual genetic constraint underlies the conservation of early brains in vertebrates"],"pubmed_authors":["Rodrigo Senovilla-Ganzo, Christina Bekiari, Eneritz Rueda-Alaña, Tetsuya Yamada, Bastienne Zaremba, Ana María Aransay,  Laura Escobar,  Mats Nilsson, Marco Grillo,  Henrik Kaessmann,  Fernando García-Moreno","Rodrigo Senovilla-Ganzo"],"additional_accession":[]},"is_claimable":false,"name":"A dual genetic constraint underlies the conservation of early brains in vertebrates","description":"As the body plan, the embryonic brain bauplan reflects the shared features of vertebrate brains. Yet, disagreements among sparse histogenetic frameworks have undermined the bauplan’s power to trace homologies. Here, we generate and integrate five vertebrate single-cell multi-omic atlases of early embryonic brains, revealing a conserved cellular blueprint that defines equivalent progenitor domains across species. Our cellular neuromeric model provides an unified and unbiased framework for the vertebrate brain bauplan and revises the regionalisation of the prosencephalon, refining its molecular boundaries and developmental relationships. Furthermore, cross-species gene-network analyses expose regulatory complexity beyond classical neuromeric patterning, resolving networks into modules aligned with regional cell types or cell class (progenitor/neuron). Evolutionarily, two main developmental constraints emerge: brain bauplan genes, early essential for regional identity, and pleiotropic stemness gene modules, indispensable across all proliferating cells. In turn, later development displays tissue-specific and less essential modules, explaining its rapid divergence into species-specific features. Together, these findings reveal a dual evolutionary constraint—neuromeric identity and pleiotropic stemness—that underlies the conservation of early vertebrate brains. This duality explains how deeply conserved regulatory architectures coexist with evolutionary flexibility to develop into the immense diversity of vertebrate nervous systems.","dates":{"release":"2026-03-15T00:00:00Z","modification":"2026-03-15T02:04:35.606Z","creation":"2026-03-05T11:05:58.022Z"},"accession":"E-MTAB-16735","cross_references":{"ENA":["ERP189932"],"EFO":["EFO_0002944","EFO_0004170","EFO_0003789","EFO_0005684","EFO_0004917","EFO_0005518","EFO_0003816","EFO_0004184","EFO_0003969"],"doi":["10.1101/2025.10.29.684766"]}}