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Trypanosoma brucei brucei

NCBI Taxonomy:5702

EATRO 1125 AnTa1.1 90:13 (paper spelling)

Chromium Single Cell 3′ GEM, Library & Gel Bead Kit v3

10,894 · 8,599 WT plus 2,295 ZC3H20-KO cells in author-filtered matrices

In-vitro bloodstream-form differentiation time course and ZC3H20 knockout

TREU927 nuclear genome, TriTrypDB release 50; Lister 427 maxi-circle M94286.1

Author-hosted raw transcript counts

Author UMAP and PCA

Atlas decoding and coordinate rounding do not alter author results. Optional cell-level Kruskal–Wallis/BH, Cliff’s delta and sample aggregations are portal-derived exploratory outputs and are exported in a separate analysis record.

Article: CC BY 4.0

Zenodo 5163554 archive: CC BY 4.0

Analysis code is included in the Zenodo 5163554 archive

Zenodo 5163554 applies CC BY 4.0 to the deposited archive

Not yet assigned; no reuse licence is implied for portal-curated metadata

ENA exposed submitted BAM and BAI files, but no FASTQ or SRA FTP links, on the audit date. 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.

Trypanosoma brucei brucei

NCBI Taxonomy:5702

J10 (MCRO/ZM/73/J10) and 1738 (MOVS/KE/70/EATRO 1738)

Modified Smart-seq2 with Nextera XT library preparation

388 · Fly-derived cells passing author QC; 46 in-vitro validation single cells are excluded

Tsetse midgut, proventriculus and salivary gland across days 21, 24 and 40

T. b. brucei 927 genome; HISAT2 2.1.0; HTSeq 0.7.1

Author-deposited Smart-seq2 integer read counts

Author fig1 UMAP coordinates

Static browser conversion and per-axis display scaling do not rerun UMAP, clustering, normalization or imputation. Optional cell-level statistics are separately labelled as portal-derived exploratory outputs.

Article: CC BY 4.0

Zenodo metadata uses “other-open”; the associated article licence is not applied to the data files

Analysis code and rendered outputs are included in the Zenodo v1.0 archive

Zenodo record uses the non-standard identifier “other-open”; inspect the source record before reuse

Not yet assigned; no reuse licence is implied for portal-curated metadata

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.

Trypanosoma brucei brucei

NCBI Taxonomy:5702

T. brucei Lister 427-derived bloodstream- and procyclic-form lines; subclone not specified in this portal passport

Chromium Single Cell 3′ v3.1

12,006 · 4,366 bloodstream-form plus 7,640 procyclic-form rows in author phase tables

Fresh and frozen replicative bloodstream and procyclic forms

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

Author-normalized non-negative fractional expression

Separate author UMAP and MNN spaces for BSF and PCF

FlatBuffer-to-static-array conversion only; no alignment, normalization, phase reassignment or recomputation

Article: CC BY 4.0

Zenodo record: CC BY 4.0

R Markdown, rendered analyses and processed objects are included in Zenodo

Zenodo 7508131: CC BY 4.0

Not yet assigned; no reuse licence is implied for portal-curated metadata

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.

Trypanosoma brucei (repository organism label)

NCBI Taxonomy:5691

Pleomorphic T. brucei EATRO 1125 AnTat 1.1 (main single-parasite RNA-seq study)

SMART-Seq v4 Ultra Low Input RNA Kit with Nextera XT

170 · 139 metacyclic/skin time-course cells plus 31 bloodstream-form cells passing author QC

Metacyclic forms, 4 h, 12 h, 24 h and 7 d skin time points, plus bloodstream forms

TREU927 release 48 plus ERCC sequences; RNASTAR 2.6.1b; featureCounts 2.0.1

139-cell normalized MCF/skin table and separate 31-cell integer BSF count table

No reusable author PCA coordinates deposited; portal provides a non-analytical sample index

Source-separated display and selection only; no PCA tracing, reconstructed embedding or matrix merging

Article: CC BY 4.0

No separate data-file licence was recorded in the GEO audit; repository terms and source authorship remain controlling

The paper mentions GitHub, but the official article pages expose no verifiable repository URL

Not verified because an official code repository URL is unresolved

Not yet assigned; no reuse licence is implied for portal-curated metadata

The 139-cell MCF/skin normalized table and 31-cell BSF integer-count table use different units and are never merged. 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.

Trypanosoma cruzi

NCBI Taxonomy:5693

Silvio X10/7 A1 (MHOM/BR/78/Silvio lineage)

Chromium Next GEM Single Cell 3′ Reagent Kit v3.1

31,065 · Valid cells retained after author quality control

Epimastigote, metacyclic, trypomastigote and amastigote lifecycle stages

Author mapping: Dm28c 2018 plus maxicircle with 3′ UTRs extended by 2,500 bp; GRCh38 was added for AMA6/24, EP/AMA120 and MIX but not SE/MT or CDT; Cell Ranger 6.0.0. The related UTR annotation asset uses TriTrypDB release 68.

Author CELL×GENE active signed scaled matrix; not raw counts

Author UMAP and PCA

CELL×GENE response decoding and display-coordinate rounding only; no rescaling of expression or reanalysis

Article: CC BY 4.0

E-MTAB-14406 data-file licence not independently verified; related UTR asset Zenodo 14229160 is CC BY 4.0

Author repository: github.com/No2Ross/TcruziAtlas; immutable code archive: Zenodo 19498217

A code-specific licence has not yet been independently verified

Not yet assigned; no reuse licence is implied for portal-curated metadata

BioStudies exposes IDF/SDRF metadata and raw-read links but no processed count matrix. 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.

Trypanosoma cruzi

NCBI Taxonomy:5693

DM28c

Chromium Next GEM Single Cell 3′ v3.1 after methanol fixation

3,151 · Final retained singlets after removing 41 doublets from 3,192 post-QC cells

Amastigotes and cell-derived trypomastigotes obtained from infected rat H9c2 myoblasts (ATCC CRL-1446), plus transitional cells

Dm28c 2018 genome, TriTrypDB release 62, combined with Dm28c maxicircle kDNA; 11,362 3′ UTRs annotated with peaks2UTR; kallisto bustools 0.51.1

Two author-deposited real-valued kallisto bustools technical matrices

Final author UMAP coordinates and post-doublet cell metadata are not deposited

Source and workflow indexing only; no reconstructed atlas or inferred final labels

eLife article: CC BY

Zenodo record: CC BY 4.0

Public GitHub workflow audited at revision 0396b4d7b3e3089b302997166e76dc69b0423d1e

A code-specific licence has not yet been independently verified

Not yet assigned; no reuse licence is implied for portal-curated metadata

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.