{"schemaVersion":"1.0.0","auditedAt":"2026-07-27","study":{"title":"Single-cell transcriptomics reveals expression profiles of Trypanosoma brucei sexual stages","citation":"Howick VM et al. PLOS Pathogens 18, e1010346 (2022).","doi":"https://doi.org/10.1371/journal.ppat.1010346","pmc":"https://pmc.ncbi.nlm.nih.gov/articles/PMC8939820/","species":"Trypanosoma brucei brucei","strains":{"1738":"MOVS/KE/70/EATRO 1738","J10":"MCRO/ZM/73/J10"},"sortingBoundary":"DP is an author FACS sorting group for double-positive cells, not a parasite strain.","technology":"Modified Smart-seq2 with Nextera XT library preparation","mapping":"Reads were mapped to the T. b. brucei 927 genome with HISAT2 2.1.0 and counted with HTSeq 0.7.1."},"paperCounts":{"tsetseParasitesSequenced":515,"tsetseCellsPassingQc":388,"tissues":{"midgut":78,"proventriculus":34,"salivaryGland":276},"validationTranscriptomes":48,"validationSingleCells":46,"validationControls":"One no-cell control and one ten-cell control accompany the 46 in-vitro procyclic single-cell transcriptomes.","qcRule":"The paper removed cells with fewer than 40 or more than 3,000 detected genes, or fewer than 1,000 total reads."},"ena":{"submittedAccession":"ERP132258","canonicalStudyAccession":"PRJEB47937","url":"https://www.ebi.ac.uk/ena/browser/view/ERP132258","manifestRetrieved":"2026-07-26","manifestSha256":"cd6e707610e5dc01b9ac195742d336c0e508b70422205fcda8097c9e6812a4f0","metadataSha256":"7367f805904b9493cfa2134c0bcdc0ea7ce3bfe1af4daa1083892bcf8eae53d7","samples":468,"experiments":468,"runs":468,"layout":"PAIRED","strategy":"RNA-Seq","source":"TRANSCRIPTOMIC SINGLE CELL","selection":"PolyA","fastqFiles":936,"fastqBytes":29773667312,"submittedFiles":553,"submittedCramFiles":468,"submittedCraiFiles":85,"submittedBytes":23358202792,"sraFiles":0,"runGroups":[{"runPrefix":"28745_8","runs":45,"instrument":"Illumina HiSeq 4000","processedAtlasMatches":0,"interpretation":"This run group does not occur in the 388-cell fly-stage metadata. Its size is close to the 46 validation single cells, but the ENA sample titles do not support assigning individual runs to the validation set with certainty."},{"runPrefix":"28959_8","runs":201,"instrument":"Illumina HiSeq 2500","processedAtlasMatches":165,"interpretation":"165 author-processed fly-stage cells resolve exactly to this ENA run alias; 36 ENA runs are outside the final 388-cell matrix."},{"runPrefix":"29784_4","runs":222,"instrument":"Illumina HiSeq 2500","processedAtlasMatches":222,"interpretation":"All 222 ENA aliases resolve to author-processed fly-stage cells. One additional processed cell, 29784_4#45, is absent from the current ENA report."}],"processedMetadataMatch":{"processedCells":388,"exactRunAliasMatches":387,"unmatchedProcessedCell":"29784_4#45","rawRunsInFlyAssociatedGroups":423,"rawRunsOutsideProcessedAtlas":36},"boundary":"The current ENA report is not numerically identical to either the 515 tsetse parasites sequenced or the 388-cell author matrix. TrypCell preserves all three counts and does not infer missing run-to-cell relationships."},"zenodo":{"record":"6047732","doi":"https://doi.org/10.5281/zenodo.6047732","url":"https://zenodo.org/records/6047732","publicationDate":"2022-02-11","archive":{"name":"vhowick/tryps_single_cell-v1.0.zip","bytes":35789818,"md5":"61deb6e0af0189b5b29130e700f1ad8a","files":43,"directories":10},"processedObjects":[{"name":"counts_howick_tryps_sce.csv","role":"Raw count matrix","rows":9225,"columns":388,"bytes":7644381,"sha256":"b7a30be73b2c8bad31814fcfb5fe926ba59c9a81a7da3e76213eaa67a2634f86"},{"name":"coldata_howick_tryps_sce.csv","role":"Cell metadata","rows":388,"columns":48,"bytes":152402,"sha256":"0330c662d10617933ea0ce0fc0b83c5017020b00a8cca4553fccbf433d2cff8f"},{"name":"rowdata_howick_tryps_sce.csv","role":"Gene metadata","rows":9225,"columns":21,"bytes":1355316,"sha256":"bb63d9709815e454a5b209768ddcb113bf73d506f6a2e51480102caafbb88862"},{"name":"howick_tryps_sce.rds","role":"Author SC3 object","rows":388,"columns":9225,"bytes":8586156,"sha256":"4d37bb2ddeb134e6fa15b039f136f090f5142971da822c6a8b267ac3320fdcf2"}],"analysisCode":"The archive contains R Markdown, rendered analysis outputs and supporting CSV/RDS files for the main figures and supplementary analyses."},"authorAtlas":{"cells":388,"genes":9225,"tissueCounts":{"MG":78,"PV":34,"SG":276},"clusterCounts":{"C1":63,"C2":44,"C3":83,"C4":55,"C5":60,"C6":83},"umap":"The deposited cell metadata contains author fig1_UMAP_1 and fig1_UMAP_2 coordinates for every one of the 388 cells.","expression":"The deposited CSV is the author raw-count matrix. Smart-seq2 counts are not UMI counts and should not be merged directly with 10x UMI matrices.","interpretationBoundary":"Cluster C5 is predominantly J10 and C6 predominantly 1738, so their separation may reflect strain as well as stage. Poor matching of 1738/J10 VSG transcripts to the 927 reference can underestimate VSG abundance.","portalBoundary":"The TrypCell view uses the deposited coordinates, cluster names and counts directly. TrypCell does not reconstruct coordinates by tracing points from the paper figure."}}