{"$schema":"https://prc-trypcell-atlas.com/schema/dataset-registry.schema.json","schemaVersion":"1.1.0","registryVersion":"2026.07.27.2","releasedAt":"2026-07-27","scope":"Public parasite single-cell transcriptomics records curated for TrypCell Atlas","alignedWith":[{"name":"Schema.org Dataset","url":"https://schema.org/Dataset","status":"basic JSON-LD mapping implemented; stable identifiers and file-level distributions remain incomplete"},{"name":"Bioschemas Dataset 1.0-RELEASE","url":"https://bioschemas.org/profiles/Dataset/1.0-RELEASE","status":"mapping in progress; the current registry is not claimed to be profile-conformant"},{"name":"FAIR Guiding Principles","url":"https://www.go-fair.org/fair-principles/","status":"FAIR-informed implementation target; no blanket FAIR-conformance claim"}],"totals":{"studies":6,"catalogueCellEntries":57674},"portalDerivedAnalysis":{"status":"implemented-and-separately-labelled","availableFor":["brg-2021-bsf","how-2022-tsetse"],"analysisRecordFormatVersion":"1.0","methods":["Grouped detection rates, raw-count means and quartiles","Kruskal–Wallis H with pooled ranks and tie correction","Benjamini–Hochberg adjustment across the currently compared genes","Ordinal epsilon-squared and descriptive Cliff’s delta","Raw-count aggregation by author Sample ID"],"inputBoundary":"Calculations use unchanged author-deposited raw-count columns and current user-selected cells or filters.","limitation":"Individual cells are not independent biological replicates. 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Zenodo 5163554 records CC BY 4.0 for its deposited archive; file-level evidence has not yet established that the same grant covers coordinates and metadata decoded from the separately hosted author H5AD service.","counts":{"displayed":10894,"displayedBasis":"8,599 author-filtered WT cells plus 2,295 author-filtered ZC3H20-KO cells","finalSinglets":10894},"fieldStatus":{"identity":"verified","biology":"verified-with-boundary","counts":"verified","reference":"verified","expression":"verified","coordinates":"verified","rights":"verified-with-boundary"},"primaryEvidence":[{"label":"Version-of-record paper","url":"https://www.nature.com/articles/s41467-021-25607-2","role":"Study design, strain, chemistry, reference and author cell-count boundary","checkedAt":"2026-07-27"},{"label":"Zenodo 5163554","url":"https://zenodo.org/records/5163554","role":"Processed matrices, analysis archive, checksum and CC BY 4.0 licence","checkedAt":"2026-07-27"},{"label":"ENA PRJEB41744","url":"https://www.ebi.ac.uk/ena/browser/view/PRJEB41744","role":"Raw sequencing accession and submitted-file manifest","checkedAt":"2026-07-27"}]},{"id":"how-2022-tsetse","recordVersion":"2026.07.27.2","portalRecord":"/datasets/erp132258/","title":"Tsetse midgut, proventriculus and salivary-gland single-cell atlas","citation":"Howick VM et al. 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Optional cell-level statistics are separately labelled as portal-derived exploratory outputs.","recordStatus":"verified-with-boundary","articleLicence":"Article: CC BY 4.0","dataLicence":"Zenodo metadata uses “other-open”; the associated article licence is not applied to the data files","codeAvailability":"Analysis code and rendered outputs are included in the Zenodo v1.0 archive","codeLicence":"Zenodo record uses the non-standard identifier “other-open”; inspect the source record before reuse","portalMetadataLicence":"Not yet assigned; no reuse licence is implied for portal-curated metadata","lastVerified":"2026-07-27","knownBoundary":"DP is a FACS sorting group, not a strain. C5 is predominantly J10 and C6 predominantly 1738, so stage and strain effects may be confounded. Poor 1738/J10 VSG matching to the 927 reference can underestimate VSG abundance. 387 of 388 processed cells match current ENA aliases; 29784_4#45 remains unresolved.","counts":{"displayed":388,"displayedBasis":"78 midgut + 34 proventriculus + 276 salivary-gland cells passing author QC; excludes 46 in-vitro validation cells","finalSinglets":388},"fieldStatus":{"identity":"verified","biology":"verified-with-boundary","counts":"verified","reference":"verified","expression":"verified","coordinates":"verified","rights":"verified-with-boundary"},"primaryEvidence":[{"label":"Version-of-record paper","url":"https://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1010346","role":"Strains, cell counts, Smart-seq2 workflow, mapping pipeline and interpretation limits","checkedAt":"2026-07-27"},{"label":"Zenodo 6047732","url":"https://zenodo.org/records/6047732","role":"Author matrices, metadata, embeddings, code and repository licence identifier","checkedAt":"2026-07-27"},{"label":"ENA ERP132258","url":"https://www.ebi.ac.uk/ena/browser/view/ERP132258","role":"Raw sequencing accession and run aliases","checkedAt":"2026-07-27"}]},{"id":"brg-2023-replicative","recordVersion":"2026.07.27.2","portalRecord":"/datasets/prjeb58781/","title":"Bloodstream-form and procyclic-form cell-cycle single-cell atlas","citation":"Briggs EM et al. eLife 12:e86325 (2023).","doi":"https://doi.org/10.7554/eLife.86325","organism":"Trypanosoma brucei brucei","organismIdentifier":"NCBI Taxonomy:5702","organismIdentifierUrl":"https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=5702","strain":"T. brucei Lister 427-derived bloodstream- and procyclic-form lines; subclone not specified in this portal passport","accessions":["ENA PRJEB58781","Zenodo 7508131"],"measurementTechnique":"Chromium Single Cell 3′ v3.1","cellCount":12006,"cellCountBasis":"4,366 bloodstream-form plus 7,640 procyclic-form rows in author phase tables","sampleContext":"Fresh and frozen replicative bloodstream and procyclic forms","reference":"Author mapping: T. brucei WT427 2018 with 3′ UTRs extended by 2,500 bp; L. major Friedlin co-reference used to remove L. major cells and mixed-species multiplets; Cell Ranger 7","expressionLayer":"Author-normalized non-negative fractional expression","embeddingLayer":"Separate author UMAP and MNN spaces for BSF and PCF","portalProcessing":"FlatBuffer-to-static-array conversion only; no alignment, normalization, phase reassignment or recomputation","recordStatus":"verified","articleLicence":"Article: CC BY 4.0","dataLicence":"Zenodo record: CC BY 4.0","codeAvailability":"R Markdown, rendered analyses and processed objects are included in Zenodo","codeLicence":"Zenodo 7508131: CC BY 4.0","portalMetadataLicence":"Not yet assigned; no reuse licence is implied for portal-curated metadata","lastVerified":"2026-07-27","knownBoundary":"BSF and PCF coordinates were calculated separately and must not be treated as one shared space. The displayed expression layer contains author-normalized fractional values, not raw UMI counts.","counts":{"displayed":12006,"displayedBasis":"4,366 BSF (2,767 fresh + 1,599 frozen) plus 7,640 PCF (3,305 fresh + 4,335 frozen)","finalSinglets":12006},"fieldStatus":{"identity":"verified","biology":"verified-with-boundary","counts":"verified","reference":"verified","expression":"verified-with-boundary","coordinates":"verified-with-boundary","rights":"verified"},"primaryEvidence":[{"label":"Version-of-record paper","url":"https://elifesciences.org/articles/86325","role":"Study design, strain lineage, chemistry, mapping reference and counts","checkedAt":"2026-07-27"},{"label":"Zenodo 7508131","url":"https://zenodo.org/records/7508131","role":"Author processed files, analysis code and CC BY 4.0 licence","checkedAt":"2026-07-27"},{"label":"ENA PRJEB58781","url":"https://www.ebi.ac.uk/ena/browser/view/PRJEB58781","role":"Raw sequencing accession","checkedAt":"2026-07-27"}]},{"id":"reu-2023-skin","recordVersion":"2026.07.27.2","portalRecord":"/datasets/gse174198/","title":"Early infection and tissue adaptation in an artificial human skin model","citation":"Reuter C et al. 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Reusable author PCA coordinates were not deposited; the portal sample index is explicitly non-analytical. Methods specify the SMART-Seq v4 kit, while the Figure 4 caption calls the workflow Smart-seq2/Nextera.","counts":{"displayed":170,"displayedBasis":"139 MCF/skin cells after three paper-specified exclusions plus 31 BSF cells","finalSinglets":170},"fieldStatus":{"identity":"verified","biology":"verified-with-boundary","counts":"verified","reference":"verified","expression":"verified-with-boundary","coordinates":"not-deposited","rights":"verified-with-boundary"},"primaryEvidence":[{"label":"Version-of-record paper","url":"https://www.nature.com/articles/s41467-023-43437-2","role":"Article number, strains, workflow, cell counts, reference and PCA boundary","checkedAt":"2026-07-27"},{"label":"GEO GSE174198","url":"https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE174198","role":"Deposited expression tables, sample metadata and raw-data links","checkedAt":"2026-07-27"}]},{"id":"lai-2026-cruzi","recordVersion":"2026.07.27.2","portalRecord":"/datasets/e-mtab-14406/","title":"In-vitro Trypanosoma cruzi Silvio X10/7 A1 lifecycle single-cell atlas","citation":"Laidlaw RF et al. 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The author CELL×GENE active matrix contains signed scaled values, not raw counts. Silvio X10/7 A1 is the biological strain; Dm28c 2018 is the mapping reference.","counts":{"displayed":31065,"displayedBasis":"Valid cells retained after author quality control"},"fieldStatus":{"identity":"verified","biology":"verified-with-boundary","counts":"verified","reference":"verified-with-boundary","expression":"verified-with-boundary","coordinates":"verified","rights":"verified-with-boundary"},"primaryEvidence":[{"label":"Version-of-record paper","url":"https://www.nature.com/articles/s41467-026-73098-w","role":"Biological strain, study design, cell count, mapping workflow and data availability","checkedAt":"2026-07-27"},{"label":"BioStudies E-MTAB-14406","url":"https://www.ebi.ac.uk/biostudies/arrayexpress/studies/E-MTAB-14406","role":"Single-cell sample metadata and raw-read accessions","checkedAt":"2026-07-27"},{"label":"Zenodo 14229160","url":"https://zenodo.org/records/14229160","role":"Release-68 Dm28c UTR annotation asset, checksum and CC BY 4.0 licence","checkedAt":"2026-07-27"},{"label":"Author analysis repository","url":"https://github.com/No2Ross/TcruziAtlas","role":"Public analysis code named by the authors","checkedAt":"2026-07-27"}]},{"id":"inc-2026-cruzi","recordVersion":"2026.07.27.2","portalRecord":"/datasets/prjna1200704/","title":"Mammalian-stage Trypanosoma cruzi Dm28c single-cell transcriptomics","citation":"Inchausti L et al. eLife 14, RP105822; Version of Record published 7 April 2026.","doi":"https://doi.org/10.7554/eLife.105822","organism":"Trypanosoma cruzi","organismIdentifier":"NCBI Taxonomy:5693","organismIdentifierUrl":"https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=5693","strain":"DM28c","accessions":["BioProject PRJNA1200704","SRA SRR31781067","Zenodo 18760090"],"measurementTechnique":"Chromium Next GEM Single Cell 3′ v3.1 after methanol fixation","cellCount":3151,"cellCountBasis":"Final retained singlets after removing 41 doublets from 3,192 post-QC cells","sampleContext":"Amastigotes and cell-derived trypomastigotes obtained from infected rat H9c2 myoblasts (ATCC CRL-1446), plus transitional cells","reference":"Dm28c 2018 genome, TriTrypDB release 62, combined with Dm28c maxicircle kDNA; 11,362 3′ UTRs annotated with peaks2UTR; kallisto bustools 0.51.1","expressionLayer":"Two author-deposited real-valued kallisto bustools technical matrices","embeddingLayer":"Final author UMAP coordinates and post-doublet cell metadata are not deposited","portalProcessing":"Source and workflow indexing only; no reconstructed atlas or inferred final labels","recordStatus":"verified-with-boundary","articleLicence":"eLife article: CC BY","dataLicence":"Zenodo record: CC BY 4.0","codeAvailability":"Public GitHub workflow audited at revision 0396b4d7b3e3089b302997166e76dc69b0423d1e","codeLicence":"A code-specific licence has not yet been independently verified","portalMetadataLicence":"Not yet assigned; no reuse licence is implied for portal-curated metadata","lastVerified":"2026-07-27","knownBoundary":"Final post-doublet metadata, cluster counts, UMAP and Seurat/H5AD object are not deposited. The version-of-record Methods and current public R script use different nUMI and nGene thresholds. SRA “isolation source: Axenic culture” is a repository field and does not replace the infected-H9c2 experimental source.","counts":{"displayed":3151,"displayedBasis":"Final singlets retained for downstream analysis; no cell-level atlas is reconstructed because final metadata are not deposited","preDoublet":3192,"doubletsRemoved":41,"finalSinglets":3151},"fieldStatus":{"identity":"verified-with-boundary","biology":"verified-with-boundary","counts":"verified-with-boundary","reference":"verified","expression":"verified-with-boundary","coordinates":"not-deposited","rights":"verified-with-boundary"},"primaryEvidence":[{"label":"eLife Version of Record","url":"https://elifesciences.org/articles/105822","role":"Study design, publication status, cell-count boundary and analysis workflow","checkedAt":"2026-07-27"},{"label":"Zenodo 18760090","url":"https://zenodo.org/records/18760090","role":"Deposited technical matrices, supporting files and CC BY 4.0 licence","checkedAt":"2026-07-27"},{"label":"BioProject PRJNA1200704","url":"https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1200704","role":"Raw sequencing and BioSample provenance","checkedAt":"2026-07-27"},{"label":"Public analysis workflow","url":"https://github.com/bioinfo-iibce/scRNAseq_Tcruzi","role":"Code revision and paper-versus-script threshold audit","checkedAt":"2026-07-27"}]}],"interpretation":{"cellCount":"Cell totals are catalogue entries with study-specific counting boundaries, not a harmonised pooled cohort.","licence":"Article, data and code licences are separate. An article licence is never assumed to license deposited data files.","processing":"Author results, portal format conversion and portal reanalysis are separate provenance classes.","portalAnalysis":"The portal does not recompute atlas embeddings or clusters. It does provide separately labelled exploratory cell-level statistics for two raw-count atlases.","reuse":"Users must cite the primary paper and repository and inspect the source record for current reuse terms."}}