{"schemaVersion":"1.0.0","auditedAt":"2026-07-27","study":{"title":"Vector-borne Trypanosoma brucei parasites develop in artificial human skin and persist as skin tissue forms","citation":"Reuter C et al. Nature Communications 14, 7660 (2023).","doi":"https://doi.org/10.1038/s41467-023-43437-2","pmc":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10667367/","species":"Trypanosoma brucei","primaryStrain":"Pleomorphic EATRO 1125 AnTat 1.1, used for the main single-parasite RNA-seq study","secondaryComparator":"Monomorphic Lister 427 MITat 1.2 13-90, used for syringe-injection comparison","technology":"SMART-Seq v4 Ultra Low Input RNA Kit, Nextera XT libraries and paired-end 2 × 75-cycle sequencing on a NextSeq 500.","technologyBoundary":"The Methods name the SMART-Seq v4 kit; the Figure 4 caption describes the workflow as Smart-seq2 and Nextera. TrypCell preserves both source wordings."},"paperCounts":{"cellsPassingQc":170,"groups":{"metacyclic0h":44,"skin4h":24,"skin12h":26,"skin24h":23,"skin7d":22,"bloodstream":31},"mcfAndSkinTotal":139,"bsfTotal":31,"exclusions":["0h_1_B5_1","0h_1_G2","0h_1_C5_1"],"exclusionReason":"The Methods section identifies these three 0 h libraries as excluded because BARP expression indicated that they were not metacyclic forms.","qc":"MCF/skin libraries retained >200 and <1,000 detected genes with library sizes from 2 × 10^5 to 2 × 10^6; the BSF upper gene threshold was <2,100."},"geo":{"accession":"GSE174198","bioproject":"PRJNA728721","sraStudy":"SRP319235","url":"https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE174198","samples":186,"publicSince":"2021-05-30","lastUpdated":"2023-12-08","files":[{"name":"GSE174198_single_trypanosomes_normalized_reads.txt.gz","role":"Normalized MCF and skin time-course expression table","bytes":1070241,"featureRows":8318,"depositedCellColumns":142,"portalRetainedCells":139,"unit":"Non-negative author-deposited normalized expression","sha256":"2d44e5c55705412c6e6a963a9d9ef9630d6e1d9733ab33f871f7177da989ba47"},{"name":"GSE174198_count_table_bsf_processed.csv.gz","role":"Processed BSF integer gene-count table","bytes":204173,"featureRows":11707,"depositedCellColumns":31,"portalRetainedCells":31,"unit":"Non-negative author-deposited integer gene count","sha256":"ba92fe8f2358785d99f0acc060ef83c5e2e8b41a52027ff9d086d0165b77d924"},{"name":"GSE174198_count_table_bsf_unprocessed.csv.gz","role":"Unprocessed BSF table, including bsf_8","bytes":210437,"featureRows":11707,"depositedCellColumns":32,"portalRetainedCells":0,"unit":"Non-negative integer gene count","sha256":"7354c2b396f70c1133edfb341022e4f01784f07e2bf69df7b3b33aada2aff8d4"}],"expressionBoundary":"The MCF/skin file contains normalized fractional values, whereas the processed BSF file contains integer gene counts. TrypCell keeps the two matrices, units, summaries and colour scales separate."},"sra":{"manifestRetrieved":"2026-07-26","manifestSha256":"73141c82184e1acd93d521717587ff444c5bd37519bbeb0d7e0db2f0e9553689","runs":186,"samples":186,"experiments":186,"biosamples":186,"spots":1421823967,"bases":164722681451,"sizeMb":54847,"parasite":{"organism":"Trypanosoma brucei","runs":185,"spots":606037276,"bases":92117665952,"sizeMb":37892,"model":"NextSeq 500"},"human":{"organism":"Homo sapiens","run":"SRR14690811","sample":"GSM5348322","runs":1,"spots":815786691,"bases":72605015499,"sizeMb":16955,"model":"Illumina NovaSeq 6000"},"boundary":"GSE174198 is a mixed series. The single human-skin 10x run is recorded as host-tissue evidence and is not represented as a parasite cell in TrypCell."},"authorAnalysis":{"aligner":"RNASTAR 2.6.1b","reference":"TREU927 release 48 plus ERCC sequences","quantification":"featureCounts 2.0.1","detectedGeneRule":"At least 5 aligned reads","pca":"The paper reports an unbiased PCA using the 1,000 highest-variance genes across 170 QC-passing parasite transcriptomes.","sourceDataWorkbook":{"name":"41467_2023_43437_MOESM15_ESM.xlsx","bytes":110825,"sha256":"5bd04b9659ce427db33b214bbbce8690d095e08cf2ae952bf7001a98fb542028","sheets":19,"figure4SheetPresent":false},"code":"The paper states that code is available on GitHub, but neither the PMC article XML nor the Nature article page exposes a repository URL. TrypCell therefore does not claim an auditable author code archive.","embeddingBoundary":"The official Source Data workbook contains no Figure 4 sheet or PCA coordinate table. TrypCell does not trace points from the paper image and does not label recomputed coordinates as author PCA."},"portalExplorer":{"skinCells":139,"bsfCells":31,"skinFeatures":8318,"bsfFeatures":11707,"overlappingFeatureIds":8318,"layout":"Real cells are arranged by collection time and deposited sample order. The layout is an index for selection and hover, not an analytical embedding.","download":"The audit JSON, selected-gene data and cell metadata can be downloaded without changing the deposited values."}}