Single Cell Studies

The Center for Medical Genomics uses 10x Genomics Chromium Systems for single-cell analysis. The 10x system is a droplet-based scRNA-seq platform that allows genome-wide expression profiling for up to 20,000 cells at once. Using a 12-base molecular barcoding system, the unique molecular identifier (UMI) is used to directly quantify the expression level of each gene in each cell.

Single-Cell Analysis Services

The following services are supported using the 10x Genomics Chromium system:

single-cell or single nucleus RNA-seq
single-cell ATAC-seq
fixed RNA profiling or FLEX
single-cell immune profiling (with antigen specificity and cell surface proteins)
CITE-seq

Before each single-cell experiment, the center requests a project planning meeting including the PI, experimentalists (lab technician, postdocs or graduate students), core staff, and bioinformatician. In this meeting, the key experiment logistics are discussed, including cell quality assessment, experiment scheduling, expectation, analysis plan and data dissemination. The center also encourages a “dry run” before an experiment to assess the quality and quantity of the single-cell suspension.

View the checklist for single cell experiments

Single-Cell Spatial Assays

	Universal 3' Gene Expression	Universal 5' Gene Expression	Flex Gene Expression	Epi ATAC	Epi Multiome ATAC + Gene Expression
Overview	Whole transcriptome coverage	Whole transcriptome coverage	Protein coding gene coverage	Chromatin accessibility	Simultaneous messurement of gene expression and chromatin accessibility from the same nucleus
Chemistry	Reverse transcription-based	Reverse transcription-based	Probe-based
Compatible species	Agnostic	Agnostic	Human, mouse, other species with custom probes	Human, mouse, rat, non-human primate, marine, plant, insect	Human, mouse, rat, non-human primate, marine, plant, insect
Compatible sample types	Cell suspensions Nuclei suspensions Flow-sorted cells Fixed human PBMCs Fresh tissue Frozen tissue Organoids	Cell suspensions Nuclei suspensions Flow-sorted cells Fixed human PBMCs Fresh tissue Frozen tissue Organoids	Cell suspensions Nuclei suspensions Flow-sorted cells Fixed whole blood Fresh tissue Frozen tissue FFPE tissue PFA-fixed tissue Organoids	Cell suspensions Nuclei suspensions Fresh tissue Frozen tissue Organoids	Cell suspensions Nuclei suspensions Fresh tissue Frozen tissue Organoids
Multiomic capabilities	3' gene expression Cell surface protein	5' geen expression TCR & BCR sequencing Cell surface protein CRISPR screening Antigen specificity	Probe-based gene expression Cell surface protein Intracellular protein CRISPR screening	Chromatin accessibility	3' gene expression Chromatin accessibility
Throughput	Singleplex 20K cells/sample 160K cells/chip On-chip multiplexing 5K cells/sample 40K cells/chip Up to 4 samples/channel Output: 8 samples/chip Hashing/Feature barcoding 8 channels/chip 60K cells/channel 480K cells/chip	Singleplex 20K cells/sample 160K cells/chip On-chip multiplexing 5K cells/sample 40K cells/chip Up to 4 samples/channel Output: 8 samples/chip Hashing/Feature barcoding 8 channels/chip 60K cells/channel 480K cells/chip	Singleplex 20K cells/sample 160K cells/chip In-line multiplex 20K cells/sample Up to 16 samples/channel 2.56M cells/chip	Singleplex 10K nuclei/sample	Singleplex 10K nuclei/sample