{"id":["DOI:10.1101/2025.10.24.684328"],"title":["Hierarchical lineage architecture of human and avian spinal cord revealed by single-cell genomic barcoding"],"publication_date":["2025-10-24"],"authors":{"ORCID:0000-0002-7776-7985":{"id":["ORCID:0000-0002-7776-7985"],"family_name":["Boezio"],"personal_name":["Giulia"],"affiliations":{"ROR:04tnbqb63":{"organization_name":["The Francis Crick Institute"]}},"HDBItheme":["Neural"]},"ORCID:0000-0002-6950-7438":{"id":["ORCID:0000-0002-6950-7438"],"family_name":["Depotter"],"personal_name":["Jasper R. L"],"affiliations":{"ROR:04tnbqb63":{"organization_name":["The Francis Crick Institute"]}},"HDBItheme":["Neural"]},"ORCID:0000-0002-6078-5466":{"id":["ORCID:0000-0002-6078-5466"],"family_name":["Frith"],"personal_name":["Thomas J. R."],"affiliations":{"ROR:04tnbqb63":{"organization_name":["The Francis Crick Institute"]}}},"ORCID:0000-0003-0047-257X":{"id":["ORCID:0000-0003-0047-257X"],"family_name":["Radley"],"personal_name":["Arthur"],"affiliations":{"ROR:04tnbqb63":{"organization_name":["The Francis Crick Institute"]}}},"ORCID:0000-0002-9781-6879":{"id":["ORCID:0000-0002-9781-6879"],"family_name":["Strohbuecker"],"personal_name":["Stephanie"],"affiliations":{"ROR:04tnbqb63":{"organization_name":["The Francis Crick Institute"]}}},"AUTHTEMP:00076":{"id":["AUTHTEMP:00076"],"family_name":["Cunha"],"personal_name":["Ana C."],"affiliations":{"ROR:04tnbqb63":{"organization_name":["The Francis Crick Institute"]}}},"ORCID:0000-0003-0912-0079":{"id":["ORCID:0000-0003-0912-0079"],"family_name":["Howell"],"personal_name":["Michael"],"affiliations":{"ROR:04tnbqb63":{"organization_name":["The Francis Crick Institute"]}}},"ORCID:0000-0002-1020-5240":{"id":["ORCID:0000-0002-1020-5240"],"family_name":["Briscoe"],"personal_name":["James"],"affiliations":{"ROR:04tnbqb63":{"organization_name":["The Francis Crick Institute"]}},"HDBItheme":["Neural"]}},"abstract":["The formation of neural circuits depends on the precise spatial and temporal organisation of neuronal populations during development. In the vertebrate spinal cord, progenitors are patterned into molecularly defined domains, but how lineage relationships shape neuronal diversity and function has remained unclear. Here, we combine genomic barcoding with singlecell RNA sequencing in chick and human embryos to generate cell-type-resolved clonal maps. We find that spinal neurogenesis follows a hierarchical organisation in which the neural tube first partitions into five broad subdivisions that resolve into the eleven progenitor domains generating the cardinal neuronal classes. This bifurcating architecture implies a patterning mechanism of sequential binary decisions. The most prominent lineage restriction occurs at the embryonic alar-basal boundary, separating sensory-processing from motor-control circuits. Individual progenitors generate neurons across multiple temporal waves while remaining constrained within their lineage subdivision, demonstrating persistence of spatial identity despite temporal competence changes. Among sensory populations, we identify two developmental routes, via unifated or bifated progenitors, to pain- and itch-processing interneurons. These principles are conserved between chick and human, with clonal analysis in human embryos revealing that most fate choices are resolved by six weeks post-conception. Together, these findings provide a framework for spinal cord development and reveal lineage compartmentalisation as a fundamental principle in neural circuit assembly and evolution."],"HDBItheme":["Neural"],"datasets":{"GEO:GSE312424":{"id":["GEO:GSE312424"],"title":["Hierarchical lineage architecture of human and avian spinal cord revealed by single-cell genomic barcoding"],"description":["Expression profiling by high throughput sequencing\nThe formation of neural circuits depends on the precise spatial and temporal organisation of neuronal populations during development. In the vertebrate spinal cord, progenitors are patterned into molecularly defined domains, but how lineage relationships shape neuronal diversity and function has remained unclear. Here, we combine genomic barcoding with single- cell RNA sequencing in chick and human embryos to generate cell-type-resolved clonal maps. We find that spinal neurogenesis follows a hierarchical organisation in which the neural tube first partitions into five broad subdivisions that resolve into the eleven progenitor domains generating the cardinal neuronal classes. This bifurcating architecture implies a patterning mechanism of sequential binary decisions. The most prominent lineage restriction occurs at the embryonic alar-basal boundary, separating sensory-processing from motor-control circuits. Individual progenitors generate neurons across multiple temporal waves while remaining constrained within their lineage subdivision, demonstrating persistence of spatial identity despite temporal competence changes. Among sensory populations, we identify two developmental routes, via unifated or bifated progenitors, to pain- and itch-processing interneurons. These principles are conserved between chick and human, with clonal analysis in human embryos revealing that most fate choices are resolved by six weeks post-conception. Together, these findings provide a framework for spinal cord development and reveal lineage compartmentalisation as a fundamental principle in neural circuit assembly and evolution.\nscRNA-seq of chicken spinal cord at three developmental stages (HH28, HH31, HH35) & human embryonic slice cultures from CS16-17 human embryo spinal cords kept in culture for a 7days; viral barcode-based LARRY lineage tracing of spinal cord progenitors in both species"],"authors":{"ORCID:0000-0002-7776-7985":{"id":["ORCID:0000-0002-7776-7985"],"family_name":["Boezio"],"personal_name":["Giulia"],"affiliations":{"ROR:04tnbqb63":{"organization_name":["The Francis Crick Institute"]}},"HDBItheme":["Neural"]},"ORCID:0000-0002-6950-7438":{"id":["ORCID:0000-0002-6950-7438"],"family_name":["Depotter"],"personal_name":["Jasper R. L"],"affiliations":{"ROR:04tnbqb63":{"organization_name":["The Francis Crick Institute"]}},"HDBItheme":["Neural"]},"ORCID:0000-0002-6078-5466":{"id":["ORCID:0000-0002-6078-5466"],"family_name":["Frith"],"personal_name":["Thomas J. R."],"affiliations":{"ROR:04tnbqb63":{"organization_name":["The Francis Crick Institute"]}}},"ORCID:0000-0003-0047-257X":{"id":["ORCID:0000-0003-0047-257X"],"family_name":["Radley"],"personal_name":["Arthur"],"affiliations":{"ROR:04tnbqb63":{"organization_name":["The Francis Crick Institute"]}}},"ORCID:0000-0002-9781-6879":{"id":["ORCID:0000-0002-9781-6879"],"family_name":["Strohbuecker"],"personal_name":["Stephanie"],"affiliations":{"ROR:04tnbqb63":{"organization_name":["The Francis Crick Institute"]}}},"AUTHTEMP:00076":{"id":["AUTHTEMP:00076"],"family_name":["Cunha"],"personal_name":["Ana C."],"affiliations":{"ROR:04tnbqb63":{"organization_name":["The Francis Crick Institute"]}}},"ORCID:0000-0003-0912-0079":{"id":["ORCID:0000-0003-0912-0079"],"family_name":["Howell"],"personal_name":["Michael"],"affiliations":{"ROR:04tnbqb63":{"organization_name":["The Francis Crick Institute"]}}},"ORCID:0000-0002-1020-5240":{"id":["ORCID:0000-0002-1020-5240"],"family_name":["Briscoe"],"personal_name":["James"],"affiliations":{"ROR:04tnbqb63":{"organization_name":["The Francis Crick Institute"]}},"HDBItheme":["Neural"]},"ORCID:0000-0003-1614-4511":{"id":["ORCID:0000-0003-1614-4511"],"family_name":["Volteras"],"personal_name":["Dimitris"],"affiliations":{"ROR:04tnbqb63":{"organization_name":["The Francis Crick Institute"]}}},"ORCID:0000-0002-8139-8844":{"id":["ORCID:0000-0002-8139-8844"],"family_name":["Libby"],"personal_name":["Ashley RG"],"affiliations":{"ROR:04tnbqb63":{"organization_name":["The Francis Crick Institute"]}}}},"tags":["sequencing"]}},"code":{"SWHID:swh:1:dir:1ef35bbbe8c72eb4326d099d6745793dd140bb0b":{"id":["SWHID:swh:1:dir:1ef35bbbe8c72eb4326d099d6745793dd140bb0b"],"title":["Hierarchical lineage architecture of human and avian spinal cord revealed by single-cell genomic barcoding"],"description":["This repository contains the code, data references, and notebooks used in the analyses for the paper: Hierarchical lineage architecture of human and avian spinal cord revealed by single-cell genomic barcoding\n \nThe repository includes: - Python notebooks, Python scripts, and R Markdown files for data processing and figure generation - Links to data hosted on GEO (GSE312424) - A reproducible environment for Python code\nThe repository does not include: - Raw FASTQ files and preprocessed Seurat/h5ad objects (available to download from GSE312424) - LARRY clone output (generated by the nf-LARRY pipeline: https://github.com/FrancisCrickInstitute/LARRY; available to download from GSE312424)"],"authors":{"ORCID:0000-0002-7776-7985":{"id":["ORCID:0000-0002-7776-7985"],"family_name":["Boezio"],"personal_name":["Giulia"],"affiliations":{"ROR:04tnbqb63":{"organization_name":["The Francis Crick Institute"]}},"HDBItheme":["Neural"]},"ORCID:0000-0002-6950-7438":{"id":["ORCID:0000-0002-6950-7438"],"family_name":["Depotter"],"personal_name":["Jasper R. L"],"affiliations":{"ROR:04tnbqb63":{"organization_name":["The Francis Crick Institute"]}},"HDBItheme":["Neural"]},"ORCID:0000-0002-1020-5240":{"id":["ORCID:0000-0002-1020-5240"],"family_name":["Briscoe"],"personal_name":["James"],"affiliations":{"ROR:04tnbqb63":{"organization_name":["The Francis Crick Institute"]}},"HDBItheme":["Neural"]}}},"SWHID:swh:1:dir:b7bd64d8476924cc1e385d7968e2e55a232657e1":{"id":["SWHID:swh:1:dir:b7bd64d8476924cc1e385d7968e2e55a232657e1"],"title":["LARRY clonal composition pipeline"],"description":["A bioinformatics pipeline that determines the clonal composition of cells. Cells have been labeled with (a) LARRY barcode(s). Clones are cells that originate from the same LARRY labelled cel (belong to the same lineage). The pipeline requires 10x Chromium Single Cell data (GEX) and paired-end Illumina sequences of PCR-enriched LARRY labels (LARRY). It takes a samplesheet and FASTQ files as input "],"authors":{"ORCID:0000-0002-6950-7438":{"id":["ORCID:0000-0002-6950-7438"],"family_name":["Depotter"],"personal_name":["Jasper R. L"],"affiliations":{"ROR:04tnbqb63":{"organization_name":["The Francis Crick Institute"]}},"HDBItheme":["Neural"]}}}}}