Single Cell Omics

Single cell genomics allows for the high resolution assessment of hundreds to tens of thousands of individual cells, unmasking the heterogeneity of a cell population and characterizing cell types and states on a cell-by-cell basis.  Our suite of single cell technologies includes droplet-based (10x Genomics Chromium), microwell-based (BD Biosciences Rhapsody), and plate-based (via FACS) methods.  We offer many single cell transcriptomics applications, including gene expression profiling, gene & cell surface protein profiling, immune profiling, immune & cell surface protein profiling, immune profiling & antigen specificity, and gene expression CRISPR screening.  Combine single cell transcriptomics with single cell chromatin accessibility for a multi-omics approach.  Or examine copy number variation of up to 40,000 cells in parallel.  In addition to the standard services listed below, we are actively increasing our repertoire of single cell genomics offerings in this highly evolving field.  See our Research & Development page to view our latest progress.

10x Genomics Chromium System

The 10x Genomics Chromium System, powered by GemCode Technology, provides a precisely engineered reagent delivery method that enables tens of thousands of micro-reactions in parallel.  Reactions are partitioned into nanoliter-scale oil droplets, or GEMs (Gel Bead-In EMulsions), containing a single cell, nucleus, or cell bead, a Gel Bead, and reaction reagents.  Gel Beads are infused with millions of barcoded oligonucleotides with unique molecular indexes (UMIs) that allow for cell barcoding and transcript indexing.  Barcoded products are pooled for subsequent downstream reactions to create next generation sequencing libraries.  The cell barcode information is used to map reads back to their original single cell or single nucleus of origin. Single cell applications include transcriptome, genome, and epigenome sequencing.  The figure below illustrates the single cell 3’ mRNA-Seq workflow. 

3' scRNA-SEQ

The Chromium Single Cell 3’ Gene Expression Solution provides a comprehensive, scalable solution for cell characterization and gene expression profiling.  Uncover cell-to-cell gene expression variability, analyze and understand cellular heterogeneity and how it contributes to your biological system, identify rare cell types from complex biological samples, define novel cell types and cell states, and discover new biomarkers for specific cell subpopulations.  Capture from 500 – 10,000 cells per sample, with up to 8 samples in parallel.  Featuring capture rates of up to 65% with a low doublet rate of 4% for 5,000 recovered cells.   Compatible with fresh whole cells or nuclei, or frozen cells. 

3' scRNA-SEQ & CELL SURFACE PROTEIN EXPRESSION

Perform CITE-Seq (Cellular Indexing of Transcriptomes and Epitopes by Sequencing) using Feature Barcoding technology and BioLegend’s TotalSeqTM antibodies to simultaneously measure gene and cell surface protein expression in the same cell.  Furthermore, cell hashing or sample multiplexing can provide a cost-savings by allowing multiple samples to be combined into one capture.

Identify CRISPR-mediated perturbations alongside cellular transcripts using Feature Barcoding technology. Implement this improved and novel methodology to conduct high-throughput and scalable functional genetic screens in hundreds to tens of thousands of single cells simultaneously. For compatibility with Feature Barcoding technology, sgRNAs should be engineered containing one of two capture sequences found on 3’ RNA V3 gel beads.  Contact us at genomics@cshs.org for more information.

scATAC-SEQ

The Chromium Single Cell ATAC (Assay for Transposase Accessible Chromatin) Solution accelerates the understanding of the regulatory landscape of the genome.  Detect open chromatic regions in single cells with enriched signals in Transcription Start Sites (TSS) and regulatory regions to better understand gene regulatory networks upstream of gene expression.  Discover cellular heterogeneity stemming from epigenetic variability and identify cell type differences in epigenetic regulation in rare cell populations.  Profile 500 – 10,000 nuclei per channel with a recovery rate of 65%.  Investigate cell lines, primary cells, and fresh and cryopreserved samples.

scV(D)J

The Chromium Single Cell Immune Profiling Solution is a comprehensive approach to simultaneously examine the cellular context of the adaptive immune response and immune repertoires of hundreds to tens of thousands of T and B cells in human or mouse on a cell-by-cell basis.  Reveal clonality, diversity, antigen specificity, and cellular context; assemble and annotate full-length V(D)J gene sequences; pair α and β chain TCR sequences from individual T cells; and pair heavy and light chain immunoglobulin (Ig) sequences from individual B cells with full isotype resolution.  Capture from 500 – 10,000 cells per sample, with up to 8 samples in parallel.  Featuring capture rates of up to 65% with a low doublet rate of 4% for 5,000 recovered cells.   Compatible with fresh or frozen cells.

3'scV(D)J & CELL SURFACE 

PROTEIN EXPRESSION

Simultaneously measure TCR, B cell Ig, and 5’ gene expression in the same cell.

 

Perform ECCITE-Seq using BioLegend’s TotalSeqTM antibodies for simultaneous gene and cell surface protein expression or cell hashing.

Mission Bio Tapestri System

The Mission Bio Tapestriplatform is the first and only single cell multi-omics platform capable of detecting SNVs, CNVs, and protein changes simultaneously from the same cell. A two-step workflow first encapsulates a single cell together with protease, resulting in the release of the cell’s genomic DNA. Next, the cell lysate is encapsulated together with barcoding beads and reagent mix. Target amplification is achieved within the droplet, during which each amplicon is tagged with a cell barcode. The droplets are then broken to combine the amplified DNA into a single pool. Library construction is performed in bulk to add sample indices and sequencing primers, allowing for sequencing on the Illumina platform. The system is compatible with either fresh or frozen cells or tissue. An input of 100,000 cells/nuclei yields a single cell/nuclei capture of 5,000-10,000 cells/nuclei. The Tapestri platform can be used to detect rare subclones (down to 0.1%), identify true mutation co-occurance in clonal populations, resolve zygosity, andreconstruct phylogenetic lineages. Pre-designed targeted panels for hematologic and solid tumors available. Custom panels can be designed using the Tapestri Designer.