pbmcs thawed according to 10x genomics demonstrated protocol #cg00039  (10X Genomics)

Journal: Genome Biology

Article Title: Comparative analysis of antibody- and lipid-based multiplexing methods for single-cell RNA-seq

doi: 10.1186/s13059-022-02628-8

Figure Lengend Snippet: Classification accuracy on human cells and nuclei with an overview of the experimental setup. A Overall classification accuracy (OCA) for all tested conditions and demultiplexed functions was calculated using freemuxlet demultiplexing as ground truth. SD represents variations of OCA across 4 cell lines or 3 individuals for PBMCs. B Four cancer cell lines or PBMCs were used to extract cells or nuclei to process further with the different labeling methods as indicated on the scheme. After pooling, the samples were run on a 10x Genomics Chromium platform and libraries were sequenced. LMO: lipid-modified oligonucleotides; CMO: cholesterol-modified oligonucleotides. “Pre-sort labeling”—labeling with hashing reagents followed by one wash and live/dead sorting with subsequent loading of the cells on a 10x Genomics chip. Also for these 2 PBMC samples cDNA libraries were generated using dual sample indexing (for all other samples single-sample indexing used)

Article Snippet: After the thawing as described in the PBMC sample preparation protocol from 10x Genomics (CG00039, Rev C), cells were labeled according to the adapted CITE-seq protocol [ ].

Techniques: Labeling, Modification, Generated

Journal: Genome Biology

Article Title: Comparative analysis of antibody- and lipid-based multiplexing methods for single-cell RNA-seq

doi: 10.1186/s13059-022-02628-8

Figure Lengend Snippet: Hashing of human PBMCs including SARS-CoV-2 clinical samples. Each column represents a separate hashing method or a condition (e.g., SARS-CoV-2, 2nd column). “Pre-sort labeling”—labeling with hashing reagents followed by one wash and live/dead sorting with subsequent loading of the cells on a 10x Genomics chip. Other samples undergone “classical” hashing -labeling followed by 3 washes and loading on a chip. A Hashtag-derived oligo (HTO) matrices were generated using CellRanger, followed by log-transformation and visualised on heatmaps. B MULTISeqDemux-annotated cells (HTO signal) were matched with the freemuxlet-annotated cells (gene data from 3 individuals) and visualized on the gene expression UMAP plots. Classification accuracy of every hashing method reported for each individual. C Annotation of major cell types performed using gene expression data and clustering. Classification accuracy of every hashing method reported for each cell type with SD values representing variation across 3 individuals. % mito—percentage of mitochondrial genes for each cell type

Article Snippet: After the thawing as described in the PBMC sample preparation protocol from 10x Genomics (CG00039, Rev C), cells were labeled according to the adapted CITE-seq protocol [ ].

Techniques: Labeling, Derivative Assay, Generated, Transformation Assay, Gene Expression