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.

scCNV

The Chromium Single Cell CNV Solution provides a comprehensive, scalable solution for cell characterization and copy number variation profiling.   Reveal the full spectrum of cellular genomes present in your sample, map clonal evolution, and identify rare clones.  Accurately call single cell CNV events at 2 Mb resolution and detect CNV events down to 100s of Kb on clusters of cells.  Capture from 250 – 5,000 cells or nuclei from cell lines, primary cells, and fresh or frozen tissue.  The Single Cell CNV Solution uses a two-step capture process that first encapsulates individual cells in a hydrogel matrix in which cells are lysed, cellular proteins are removed, and the DNA is denatured.  The second capture separately indexes the gDNA of each individual cell.

BD BIOSCIENCES RHAPSODY SINGLE CELL ANALYSIS SYSTEM

The BD Biosciences Rhapsody Single Cell Analysis System for targeted 3’ mRNA-Seq uses a 200,000+ microwell cartridge to capture a single cell, pair it with a magnetic oligonucleotide barcoded bead, and isolate the reverse transcription reaction.  The oligonucleotide barcoded beads contain a cell index, allowing beads to be pooled into a single tube for cDNA amplification and library construction.  Unique molecular indexing (UMI) of mRNA transcripts enables digital quantification of hundreds of expressed genes across tens of thousands of single cells.  Predesigned (Human Onco-BC Panel, Human Immune Response Panel, Human T-Cell Expression Panel, Mouse Immune Response Panel) or customized targeted panels help lower experimental costs compared to a whole transcriptome analysis approach.  Moreover,  sample tags can be used to combine up to 12 samples into a single capture, allowing for further cost savings.  Sample multiplexing also allows for the identity and removal of erroneous data from cell multiplets originating from separate samples.  Take a multi-omics approach and use BD AbSeq antibody-oligonucleotide conjugates for the simultaneous detection of protein and mRNA expression in a single experiment.  The figure below illustrates the BD Rhapsody mRNA-Seq workflow.

PLATE-BASED WORKFLOWS

FULL TRANSCRIPT

scRNA-SEQ

In contrast to 3’ end counting scRNA-Seq from the 10x Genomics Chromium and BD Biosciences Rhapsody systems, plate-based scRNA-Seq interrogates the full length of the mRNA transcript.  This not only allows for differential gene expression profiling, but also identification of known and novel transcript isoforms, alternative splicing events, gene fusions, and post-transcriptional modifications.  Furthermore, full transcript scRNA-Seq captures more genes, allowing one to investigate genes expressed at lower levels.  In this method, cells are FACS sorted into a 96-well PCR plate containing lysis buffer (provided by the AGCT Core), which can then be frozen to be processed at a later time.