PBMC 3k, 10x Chromium 3' v1 (paper 4.1)
phalaena:sample:PA-S-4-1-pbmc3k
PBMC 3k from a single healthy donor, 10x Genomics Chromium 3' v1 chemistry (Zheng 2017). The v1 layout ships as RA-interleaved chunks (read-RA_*.fastq.gz) rather than pre-paired R1/R2, so the pipeline splits each chunk via RA_SPLIT into cell-barcode R1 and cDNA R2 before STARsolo. We use this sample as the canonical end-to-end verification input for the 10x v1 codepath: it runs in a fixed wall window, exercises RA_SPLIT plus STARsolo plus Scanpy, and the expected summary headlines are pinned in MANIFEST.json so a regression in cell count, mapping rate, or cluster count surfaces immediately. Roughly 3,500 cells recovered; the canonical PBMC lineage map (T cells, monocytes, B cells, NK cells) is reproducible from the run's Leiden clusters.
- kind
- sample
- organism
- Homo sapiens
- assay
- single-cell RNA sequencing, single_cell_rna_seq
- tissue
- peripheral blood
- cell_type
- peripheral blood mononuclear cell
- status
- reviewed
- ncbitaxon:9606
- tenx:pbmc3k
View PBMC 3k, 10x Chromium 3' v1 (paper 4.1) on the Phalaena Wiki