{"doi":"10.1016/j.devcel.2022.01.008","title":"A single-cell Arabidopsis root atlas reveals developmental trajectories in wild-type and cell identity mutants","abstract":"In all multicellular organisms, transcriptional networks orchestrate organ development. The Arabidopsis root, with its simple structure and indeterminate growth, is an ideal model for investigating the spatiotemporal transcriptional signatures underlying developmental trajectories. To map gene expression dynamics across root cell types and developmental time, we built a comprehensive, organ-scale atlas at single-cell resolution. In addition to estimating developmental progressions in pseudotime, we employed the mathematical concept of optimal transport to infer developmental trajectories and identify their underlying regulators. To demonstrate the utility of the atlas to interpret new datasets, we profiled mutants for two key transcriptional regulators at single-cell resolution, shortroot and scarecrow. We report transcriptomic and in vivo evidence for tissue trans-differentiation underlying a mixed cell identity phenotype in scarecrow. Our results support the atlas as a rich community resource for unraveling the transcriptional programs that specify and maintain cell identity to regulate spatiotemporal organ development.","journal":"Developmental Cell","year":2022,"id":231872,"datarank":4.422031632847052,"base_score":5.8971538676367405,"endowment":5.8971538676367405,"self_citation_contribution":0.8845730801455112,"citation_network_contribution":3.537458552701541,"self_endowment_contribution":0.8845730801455112,"citer_contribution":3.537458552701541,"corpus_percentile":95.01817900518294,"corpus_rank":645,"citation_count":363,"citer_count":100,"citers_with_citation_signal":100,"citers_with_endowment":100,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.9029,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2022-01-01","fair_score":68.75,"fair_percentile":91.13420972179762,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":552764,"name":"Che‐Wei Hsu","orcid":"0000-0003-3709-9748","position":1,"is_corresponding":false},{"id":552765,"name":"Trevor M. Nolan","orcid":"0000-0003-1362-2557","position":2,"is_corresponding":false},{"id":548302,"name":"Benjamin Cole","orcid":"0000-0001-9652-624X","position":3,"is_corresponding":false},{"id":552766,"name":"Isaiah Taylor","orcid":"0000-0002-6535-8658","position":4,"is_corresponding":false},{"id":48108,"name":"Laura Greenstreet","orcid":"0000-0003-0635-3870","position":5,"is_corresponding":false},{"id":48124,"name":"Stephen X. Zhang","orcid":"0000-0001-6123-1193","position":6,"is_corresponding":false},{"id":48107,"name":"Anton Afanassiev","orcid":"0000-0003-2387-8783","position":7,"is_corresponding":false},{"id":552767,"name":"Anna Hendrika Cornelia Vlot","orcid":"0000-0001-9538-987X","position":8,"is_corresponding":false},{"id":48123,"name":"Geoffrey Schiebinger","orcid":"0000-0002-8290-7997","position":9,"is_corresponding":false},{"id":273950,"name":"Philip N. Benfey","orcid":"0000-0001-5302-758X","position":10,"is_corresponding":false},{"id":28491,"name":"Uwe Ohler","orcid":"0000-0002-0881-3116","position":11,"is_corresponding":false},{"id":525220,"name":"Rachel Shahan","orcid":"0000-0001-7702-9432","position":0,"is_corresponding":true}],"reference_count":109,"raw_metadata":null,"created_at":"2026-07-19T00:20:51.245255Z","pmid":"35134336","pmcid":"PMC9014886","fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":83.3333,"fair_a":81.25,"fair_i":20.0,"fair_r":45.8333,"fair_zscore":1.3577,"fair_rationale":{"fair_score":68.75,"has_llm":true,"taxonomy_version":"fair_taxonomy_v5","dimensions":{"F":{"name":"Findable","score":83.33,"criteria":[{"key":"f_dataset_pid","label":"Persistent identifier for the data","kind":"llm","weight":2.0,"fraction":1.0,"verdict":"yes","evidence":"GSE152766","grounded":true,"rationale":"The paper provides a GEO accession (GSE152766), which is a persistent identifier scheme.","anchors":["RDA-F1-01D — FAIR Data Maturity Model: 'Data is identified by a persistent identifier' (priorit","RDA-F1-02D — FAIR Data Maturity Model: 'Data is identified by a globally unique identifier'","FsF-F1-02D — F-UJI/FAIRsFAIR: 'Data is assigned a persistent identifier'"],"scored":true,"signal":null},{"key":"f_repository_named","label":"Named repository","kind":"llm","weight":2.0,"fraction":1.0,"verdict":"yes","evidence":"GEO","grounded":true,"rationale":"GEO is a named data repository (curated archive that issues accessions and commits to retention).","anchors":["RDA-F4-01M — FAIR Data Maturity Model: metadata is offered so it can be harvested and indexed (","NIH DMS Policy Element 4 (NOT-OD-21-014) — name the repository where data will be archived","NSTC Desirable Characteristics of Data Repositories (2022) — 'Long-Term Sustainability', 'Reten"],"scored":true,"signal":null},{"key":"f_data_availability_statement","label":"Data-availability statement","kind":"llm","weight":2.0,"fraction":1.0,"verdict":"yes","evidence":"Single-cell RNA-seq data have been deposited at GEO with the accession number GSE152766 and are publicly available as of the date of publication.","grounded":true,"rationale":"The statement points to a repository record (GEO) with an accession, corresponding to Colavizza category 3.","anchors":["Colavizza, Hrynaszkiewicz, Staden, Whitaker & McGillivray (2020), 'The citation advantage of li","Springer Nature research data policy — Data Availability Statements: standard statement templat","RDA-F3-01M — metadata clearly and explicitly includes the identifier of the data it describes"],"scored":false,"signal":null},{"key":"f_discovery_metadata","label":"Description of the dataset as an object","kind":"llm","weight":2.0,"fraction":0.5,"verdict":"partial","evidence":"we integrated 110,427 cells into an organ-scale atlas","grounded":true,"rationale":"The dataset's extent (number of cells) is stated in running prose, but there is no itemised inventory of files or variables.","anchors":["RDA-F2-01M — 'Rich metadata is provided to allow discovery' (priority Essential)","FsF-F2-01M — F-UJI: 'Metadata includes descriptive core elements to support data findability'","FsF-R1-01MD — F-UJI: 'Metadata specifies the content of the data'"],"scored":false,"signal":null},{"key":"f_dataset_cited","label":"Dataset formally cited","kind":"llm","weight":1.0,"fraction":0.5,"verdict":"partial","evidence":"Single-cell RNA-seq data have been deposited at GEO with the accession number GSE152766","grounded":true,"rationale":"The dataset identifier GSE152766 appears only in the body text, not as a reference-list entry.","anchors":["FORCE11 Joint Declaration of Data Citation Principles (2014) — data should be cited as a first-","RDA-F3-01M — metadata clearly and explicitly includes the identifier of the data it describes","FsF-F3-01M — F-UJI: 'Metadata includes the identifier of the data it describes'"],"scored":true,"signal":null}]},"A":{"name":"Accessible","score":81.25,"criteria":[{"key":"a_data_openly_accessible","label":"Access route free of preconditions","kind":"llm","weight":2.0,"fraction":1.0,"verdict":"yes","evidence":"Single-cell RNA-seq data have been deposited at GEO with the accession number GSE152766 and are publicly available as of the date of publication.","grounded":true,"rationale":"The text gives a route to the data with no precondition stated; 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[majority verdict 'no' (4/5 passes agreed)]","anchors":["FsF-R1.3-02D — F-UJI: 'Data is available in a file format recommended by the target research co","RDA-R1.3-02D — data is expressed in a machine-understandable community standard","RDA-I1-01D — data uses a knowledge representation expressed in a standardised format"],"scored":true,"signal":null},{"key":"i_community_standard_vocabulary","label":"Community standard / vocabulary","kind":"llm","weight":1.0,"fraction":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"No community data or metadata standard (e.g., MIAME, MINSEQE) is named for the data; only generic methods are described.","anchors":["RDA-R1.3-01M — 'Metadata complies with a community standard' (priority Essential)","RDA-R1.3-01D — 'Data complies with a community standard'","RDA-I2-01M — '(Meta)data use vocabularies that follow FAIR principles'"],"scored":false,"signal":null},{"key":"i_qualified_references","label":"Identifiers for the resources the data depend on","kind":"llm","weight":0.5,"fraction":1.0,"verdict":"yes","evidence":"10.6084/m9.figshare.4688752.v1","grounded":true,"rationale":"The reference list includes a figshare DOI for an external resource (Bouché 2017), which is an identifier for a resource other than the paper's own dataset. [majority verdict 'yes' (3/5 passes agreed)]","anchors":["RDA-I3-01M — '(meta)data include references to other (meta)data'","RDA-I3-03M — 'metadata includes qualified references to other metadata'","FsF-I3-01M — F-UJI: 'Metadata includes links between the data and its related entities'"],"scored":false,"signal":null}]},"R":{"name":"Reusable","score":45.83,"criteria":[{"key":"r_reuse_license","label":"Reuse licence","kind":"llm","weight":2.0,"fraction":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"The CC BY 4.0 license on the article does not explicitly apply to the data; no license for the data is stated.","anchors":["RDA-R1.1-01M — 'Metadata includes information about the licence under which the data can be reu","RDA-R1.1-02M — 'Metadata refers to a standard reuse licence'","RDA-R1.1-03M — 'Metadata refers to a machine-understandable reuse licence'"],"scored":true,"signal":null},{"key":"r_provenance_methods","label":"Provenance of the data","kind":"llm","weight":1.0,"fraction":1.0,"verdict":"yes","evidence":"Sequencing was performed with a NovaSeq 6000 instrument (Illumina) to produce 100bp paired end reads.","grounded":true,"rationale":"The paper names the specific sequencing instrument (NovaSeq 6000) and platform (10X Genomics) used to produce the data. 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Cite the genomics / sequencing repository accession (e.g. from GEO (GSE accession), SRA (SRP/SRR) or ENA/BioProject (PRJEB/PRJNA)) in the reference list.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"Single-cell RNA-seq data have been deposited at GEO with the accession number GSE152766","why":"The dataset identifier GSE152766 appears only in the body text, not as a reference-list entry.","gain":4.17,"priority":"important","scored":true},{"key":"r_versioning","dimension":"R","label":"Snapshot identified","action":"Version the deposit and cite the exact version analysed (a version-specific DOI, or an accession with its version suffix). A reader reproducing your work against 'the current release' is reproducing it against a different dataset.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"as of the date of publication","why":"No version token is given, but a date (publication date) pins the snapshot. 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A dataset that needs a €2,000 licence to open is not reusable. Prefer open genomics / sequencing formats such as FASTQ, BAM or VCF.","Cite the dataset in the reference list like a publication — creator, year, title, repository, DOI/accession — and cite it in-text where it is used. Only a reference- list entry is machine-readable to Crossref/DataCite, and only a citation lets the data earn credit. Cite the genomics / sequencing repository accession (e.g. from GEO (GSE accession), SRA (SRP/SRR) or ENA/BioProject (PRJEB/PRJNA)) in the reference list.","Version the deposit and cite the exact version analysed (a version-specific DOI, or an accession with its version suffix). A reader reproducing your work against 'the current release' is reproducing it against a different dataset.","Add a 'Data Records' section: itemise every file in the deposit and every variable or sample it holds, with counts and units. Describe the dataset as an object in its own right, not as a by-product of the findings — this is what makes it discoverable to someone who is not looking for your paper."],"model":"deepseek/deepseek-v4-flash","agent_version":"fair_agent_v8","fulltext_source":"unpaywall_pdf"},"fair_model":"deepseek/deepseek-v4-flash","fair_agent_version":"fair_agent_v8","fair_fulltext_source":"unpaywall_pdf","fair_has_llm":true,"fair_computed_at":"2026-07-20T10:50:32.241129Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}