Standardized pipeline documentation
As part of our large-scale research projects at the Allen Institute for Immunology, we have developed multiple large-scale standardized molecular biology pipeline assays. See each subsection for additional details, methods, and tools used to implement these pipelines.
Multiplexed scRNA-seq
To profile transcription in peripheral blood mononuclear cells (PBMCs) and bone marrow mononuclear cells (BMMCs), we utilized the 10x Genomics Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 with BioLegend TotalSeq cell hashing to multiplex samples.
Plasma proteomics
To profile relative protein abundance in plasma, we utilized the Olink Explore 1536 assay. Samples were submitted to Olink in large, plate-based batches, and batches were combined for analysis by normalization based on common, cross-batch control samples.