A single-cell RNA-Seq template that adapts to your lab's tissues.

This single-cell RNA-Seq template ships configured for profiling immune cell heterogeneity in human peripheral blood mononuclear cells (PBMCs) from a single healthy donor using the 10x Genomics Chromium Next GEM Single Cell 3' v3.1 chemistry, with a 10-step protocol covering PBMC isolation through Seurat-based cluster annotation. The protocol assumes target capture of 10,000 cells, NovaSeq SP flow cell sequencing at 28k reads per cell, cellranger count for alignment + UMI quantification, and Seurat v5 for QC + clustering + cell-type annotation.

Structured fields capture sample, capture, library, sequencing, and analysis metadata in typed inputs (tissue, donor, dissociation method, target cells, captured cells, doublet rate, mean reads per cell, median genes per cell, mitochondrial fraction, saturation, number of clusters), so library QC and biology outcomes are queryable across runs instead of buried in free text. The Chromium chip, GEM-X reagents, library prep kit, and sequencing flow cell link to the ELabELN inventory so lot numbers and chip-history references flow into every run record without manual entry. The spreadsheet editor captures per-cluster cell counts and assigned cell types (CD4 T, CD8 T, NK, B, Monocyte, mDC, pDC, Platelet) for cross-sample comparison.

The template is intended as a tested baseline for academic, biotechnology, and pharmaceutical labs running immune profiling, tumor microenvironment dissection, developmental atlasing, perturb-seq, or cross-condition differential abundance. Configure the tissue source, swap the chemistry (3' v3.1, 5' v2, multiome, fixed RNA), change the target cell number or sequencing depth, adjust the analysis tool (Seurat, Scanpy, Scran), or move from single-sample to multiplexed (CellPlex, HTO) or multi-modal (CITE-Seq, ATAC) by editing the capture section. ELabELN's tamper-evident audit trail captures every dissociation, every chip run, and every QC decision, so the resulting record supports reproducibility documentation, multi-PI consortium collaboration, and FDA 21 CFR Part 11 review when the lab's quality system requires it.