{"schemaVersion":"1.0.0","retrieved":"2026-07-26","title":"Single-cell RNA-seq reveals trans-sialidase-like superfamily gene expression heterogeneity in Trypanosoma cruzi populations","sources":{"paper":"https://pmc.ncbi.nlm.nih.gov/articles/PMC13056360/","doi":"https://doi.org/10.7554/eLife.105822","bioProject":"https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1200704","enaRun":"https://www.ebi.ac.uk/ena/browser/view/SRR31781067","bioSample":"https://www.ebi.ac.uk/ena/browser/view/SAMN45910119","zenodo":"https://zenodo.org/records/18760090","code":"https://github.com/bioinfo-iibce/scRNAseq_Tcruzi"},"paper":{"published":"2026-04-07","pmcid":"PMC13056360","cellsAfterQualityFilteringBeforeDoubletRemoval":3192,"cellsRetainedAfterDoubletRemoval":3151,"detectedGenes":14321,"annotatedProteinCodingGenes":15319,"meanGenesPerCell":1088,"meanUmisPerCell":2461,"doubletsRemoved":41,"reportedClusters":[{"id":0,"labelEn":"Cell-derived trypomastigotes","labelZh":"细胞来源锥鞭毛体","cellsBeforeDoubletRemoval":2201,"marker":"C4B63-16g183"},{"id":1,"labelEn":"Amastigotes","labelZh":"无鞭毛体","cellsBeforeDoubletRemoval":824,"marker":"C4B63-16g155"},{"id":2,"labelEn":"Putative amastigote–trypomastigote transition","labelZh":"推定无鞭毛体—锥鞭毛体过渡细胞","cellsBeforeDoubletRemoval":167,"marker":null}]},"experimentalSource":{"parasiteStages":"Amastigotes and cell-derived trypomastigotes from infected host-cell culture","hostSpecies":"Rattus norvegicus","hostCellLine":"H9c2 rat myoblasts","hostCellLineAccession":"ATCC CRL-1446","boundary":"The paper's infected-H9c2 experimental source and the SRA repository field “isolation source: Axenic culture” are different metadata layers. The repository wording is preserved but is not used as the biological sample origin."},"rawSequencing":{"bioProject":"PRJNA1200704","bioSample":"SAMN45910119","secondarySample":"SRS23597921","experiment":"SRX27142470","run":"SRR31781067","sampleAlias":"T. cruzi amastigotes and trypomastigotes","organism":"Trypanosoma cruzi","strain":"DM28c","isolationSource":"Axenic culture","isolationSourceBoundary":"Repository-supplied SRA field; insufficient on its own to describe the infected-H9c2 experimental source","instrumentPlatform":"ILLUMINA","instrumentModel":"Illumina HiSeq 2500","libraryLayout":"PAIRED","libraryStrategy":"RNA-Seq","librarySource":"TRANSCRIPTOMIC SINGLE CELL","librarySelection":"PolyA","readCount":882316647,"baseCount":104995680993,"firstPublic":"2026-02-22","fastq":[{"name":"SRR31781067_1.fastq.gz","bytes":19989510573,"md5":"879d363cbc29f7b2f9dc7300daedae3b","url":"https://ftp.sra.ebi.ac.uk/vol1/fastq/SRR317/067/SRR31781067/SRR31781067_1.fastq.gz"},{"name":"SRR31781067_2.fastq.gz","bytes":41306757344,"md5":"743876f2279637e09f568f465e466454","url":"https://ftp.sra.ebi.ac.uk/vol1/fastq/SRR317/067/SRR31781067/SRR31781067_2.fastq.gz"}]},"quantification":{"reference":"T. cruzi Dm28c 2018 genome, TriTrypDB release 62, combined with Dm28c maxicircle kDNA","referenceZh":"T. cruzi Dm28c 2018基因组（TriTrypDB release 62）与Dm28c大环kDNA组合参考","utrAnnotation":"11,362 coding-sequence 3′ UTR regions annotated with peaks2UTR","utrAnnotationZh":"使用peaks2UTR为11,362个编码序列标注3′ UTR","method":"kallisto bustools pseudoalignment","options":["--filter","--em"],"note":"The --em option can produce fractional expected counts; the deposited Matrix Market files declare real-valued entries.","noteZh":"--em选项可产生小数形式的期望计数；作者提交的Matrix Market文件声明为实数型条目。","matrices":[{"name":"cells_x_genes.mtx","barcodeFile":"cells_x_genes.barcodes.txt","geneFile":"cells_x_genes.genes.txt","barcodeRows":82818,"geneColumns":19132,"nonZeroEntries":16359799},{"name":"cells_x_genes_2.mtx","barcodeFile":"cells_x_genes.barcodes_2.txt","geneFile":"cells_x_genes.genes_2.txt","barcodeRows":82813,"geneColumns":19132,"nonZeroEntries":16337978}],"commonBarcodesMergedByPublicCode":82751,"geneListsIdentical":true},"methodAudit":{"paperThresholds":{"nUMI":"> 1,200","nGene":"> 100","log10GenesPerUMI":"> 0.8","mitoRatio":"< 0.1"},"publicCodeThresholds":{"nUMI":"> 3,000","nGene":"> 130","log10GenesPerUMI":"> 0.8","mitoRatio":"< 0.1"},"status":"The nUMI and nGene thresholds differ between the version-of-record Methods and the current public R script. TrypCell Atlas does not choose between them; author confirmation is required before a reproducible rerun is labelled as the paper workflow.","statusZh":"正式论文方法与当前公开R脚本的nUMI和nGene阈值不同。TrypCell Atlas不替作者选择；在把重算结果标记为“论文流程”之前，需要作者确认。","clusterCountBoundary":"The paper reports 3,192 post-QC transcriptomes and cluster counts summing to 3,192, then states that 41 doublets—all in cluster 2—were removed and 3,151 singlets retained for downstream analysis. No final post-removal cluster-count table or reusable Seurat/H5AD object is deposited in Zenodo record 18760090.","clusterCountBoundaryZh":"论文报告3,192个质量过滤后转录组，三个cluster的计数总和也是3,192；随后又说明移除了41个双细胞（全部来自cluster 2），下游保留3,151个singlet。Zenodo 18760090没有提交移除后的最终cluster计数表，也没有可复用的Seurat/H5AD对象。","portalStatus":"Source provenance and deposited matrices are indexed. A reconstructed UMAP is not published in TrypCell Atlas because author UMAP coordinates and final cell metadata are not deposited."},"codeAudit":{"repositoryRevision":"0396b4d7b3e3089b302997166e76dc69b0423d1e","script":"final_code_scRNAseq_Tcruzi.R","scriptSha256":"d1f6d4bf875119b00b4b57d28e806ac422c927d0152f8e2134751f893cf0d591","readmeSha256":"bc5e549404b4ea8700c4f0bd6828d709be457e18ae1862f61b1a916dab9d4d81"},"zenodo":{"record":18760090,"title":"scRNA-seq Analysis of Trypanosoma cruzi Populations","license":"CC BY 4.0","published":"2026-02-24","fileCount":17,"totalBytes":461333115,"files":[{"name":"cells_x_genes.genes.txt","category":"quantification","bytes":241515,"md5":"01def374155e736b8baaf262ebd398d3","descriptionEn":"Feature list for technical matrix 1","descriptionZh":"技术矩阵1的基因列表","downloadUrl":"https://zenodo.org/api/records/18760090/files/cells_x_genes.genes.txt/content"},{"name":"cells_x_genes.barcodes.txt","category":"quantification","bytes":1407906,"md5":"98b29e5a8732c7eefc5a242b1b442a49","descriptionEn":"82,818 barcodes for technical matrix 1","descriptionZh":"技术矩阵1的82,818个条形码","downloadUrl":"https://zenodo.org/api/records/18760090/files/cells_x_genes.barcodes.txt/content"},{"name":"cells_x_genes.genes_2.txt","category":"quantification","bytes":241515,"md5":"01def374155e736b8baaf262ebd398d3","descriptionEn":"Feature list for technical matrix 2","descriptionZh":"技术矩阵2的基因列表","downloadUrl":"https://zenodo.org/api/records/18760090/files/cells_x_genes.genes_2.txt/content"},{"name":"anotacion_dm28c_con_mt.gff","category":"annotation","bytes":14498432,"md5":"c020676e448481890ee9908fbfbd900c","descriptionEn":"Dm28c annotation including mitochondrial features","descriptionZh":"包含线粒体特征的Dm28c注释","downloadUrl":"https://zenodo.org/api/records/18760090/files/anotacion_dm28c_con_mt.gff/content"},{"name":"cells_x_genes.barcodes_2.txt","category":"quantification","bytes":1407821,"md5":"3cd4554c077ccd0b29b401d3f2ebc7fd","descriptionEn":"82,813 barcodes for technical matrix 2","descriptionZh":"技术矩阵2的82,813个条形码","downloadUrl":"https://zenodo.org/api/records/18760090/files/cells_x_genes.barcodes_2.txt/content"},{"name":"cells_x_genes.mtx","category":"quantification","bytes":221226276,"md5":"0320356e1f31f25fba12ef6315033b89","descriptionEn":"82,818 × 19,132 real-valued sparse matrix","descriptionZh":"82,818 × 19,132实数型稀疏矩阵","downloadUrl":"https://zenodo.org/api/records/18760090/files/cells_x_genes.mtx/content"},{"name":"cells_x_genes_2.mtx","category":"quantification","bytes":221482578,"md5":"e464a00e3e2aa1771425fdeab4fc68d3","descriptionEn":"82,813 × 19,132 real-valued sparse matrix","descriptionZh":"82,813 × 19,132实数型稀疏矩阵","downloadUrl":"https://zenodo.org/api/records/18760090/files/cells_x_genes_2.mtx/content"},{"name":"Dm28c_disruptive_compartment_positions.bed","category":"annotation","bytes":742,"md5":"7330f2520f42b87c43d700791b0927cd","descriptionEn":"Disruptive genomic-compartment intervals","descriptionZh":"扰动基因组区室范围","downloadUrl":"https://zenodo.org/api/records/18760090/files/Dm28c_disruptive_compartment_positions.bed/content"},{"name":"phosphatases_dm28c.csv","category":"gene-set","bytes":7913,"md5":"2f10d1253e3757b815a5d261bd5113ac","descriptionEn":"Dm28c phosphatase gene set","descriptionZh":"Dm28c磷酸酶基因集","downloadUrl":"https://zenodo.org/api/records/18760090/files/phosphatases_dm28c.csv/content"},{"name":"polymerase_dm28c.csv","category":"gene-set","bytes":5397,"md5":"d94b73e1ad05ec0e226e72dd6ec192c4","descriptionEn":"Dm28c polymerase gene set","descriptionZh":"Dm28c聚合酶基因集","downloadUrl":"https://zenodo.org/api/records/18760090/files/polymerase_dm28c.csv/content"},{"name":"tcs_high.txt","category":"gene-set","bytes":297,"md5":"3c973e078680fd2a8f9a7a5921b53d97","descriptionEn":"Frequently detected TcS subset","descriptionZh":"高频检出的TcS子集","downloadUrl":"https://zenodo.org/api/records/18760090/files/tcs_high.txt/content"},{"name":"tcs_low_all.txt","category":"gene-set","bytes":8216,"md5":"2edf94f9c9c37f8e2370242f29cf98f9","descriptionEn":"Full low-detection TcS set","descriptionZh":"完整低检出TcS基因集","downloadUrl":"https://zenodo.org/api/records/18760090/files/tcs_low_all.txt/content"},{"name":"tcs_low.txt","category":"gene-set","bytes":136,"md5":"a455ee11ee0aca1db0bc815a5d5a87a3","descriptionEn":"Sampled low-detection TcS subset","descriptionZh":"抽样低检出TcS子集","downloadUrl":"https://zenodo.org/api/records/18760090/files/tcs_low.txt/content"},{"name":"transporters_dm28c.csv","category":"gene-set","bytes":29121,"md5":"2914a939391254f939b018b4a49447da","descriptionEn":"Dm28c transporter gene set","descriptionZh":"Dm28c转运蛋白基因集","downloadUrl":"https://zenodo.org/api/records/18760090/files/transporters_dm28c.csv/content"},{"name":"Ribsoomal_RNA.csv","category":"gene-set","bytes":2445,"md5":"d993afccee1ae581ab0e423cc65b0ae2","descriptionEn":"rRNA exclusion list (deposited filename retained)","descriptionZh":"rRNA排除列表（保留作者文件名）","downloadUrl":"https://zenodo.org/api/records/18760090/files/Ribsoomal_RNA.csv/content"},{"name":"abundance_tripos_1.txt","category":"supporting","bytes":771401,"md5":"b6bcef4112974c54289048938e085835","descriptionEn":"Supporting trypomastigote abundance data","descriptionZh":"锥鞭毛体丰度支持数据","downloadUrl":"https://zenodo.org/api/records/18760090/files/abundance_tripos_1.txt/content"},{"name":"Dm28c_core_compartment_positions.bed","category":"annotation","bytes":1404,"md5":"2b2f3a20c0b456ffd3648e7bd8b6ea77","descriptionEn":"Core genomic-compartment intervals","descriptionZh":"核心基因组区室范围","downloadUrl":"https://zenodo.org/api/records/18760090/files/Dm28c_core_compartment_positions.bed/content"}]}}