Grant applications proposing work that will be performed by SCBL or with SCBL’s assistance do not require letters of support unless the methods that will be used are not included in SCBL’s service description in the JAX Facilities and Other Resources master document (see description below). For methods that are unusual or particularly challenging in the single cell biology field, or that were recently published, please contact the SCBL director about whether a letter of support would be appropriate.
The mission of the Single Cell Biology Laboratory (SCBL) is to develop, test, compare, validate, and make available state-of-the-art technologies to enable the molecular characterization of individual cells in isolation, in tissue, and in culture. Supported by a staff that is highly experienced in the generation and analysis of single-cell and single-nucleus data, the SCBL carries out single-cell/nucleus workflows that encompass cell and tissue dissociation; cell capture, enrichment, and isolation; molecular characterization; and the computational analysis of single-cell/nucleus data sets. Microfluidic chip-, droplet-, and plate-based single-cell/nucleus transcriptomic methods are all established in the laboratory. The Chromium X™ platform (10x Genomics) has become a key resource for work with cells/nuclei from fresh and fixed tissues as it enables preparation of sequencing libraries for up to ~20,000 single cells or nuclei, with current applications including single-cell/nucleus RNA-seq (with sample multiplexing capabilities), T- and B-cell immune repertoire sequencing, joint single-cell mRNA and cell surface protein profiling (CITE-seq), single-cell ATAC-seq, and joint single-cell RNA- and ATAC-seq. In addition, the SCBL has established the application of Chromium Single Cell Gene Expression Flex probe-based chemistry (10x Genomics) to paraformaldehyde-fixed cells/nuclei in suspension as well as nuclei isolated from formalin-fixed, paraffin-embedded (FFPE) tissues via the method of single-nuclei pathology sequencing (snPATHO-seq). The SCBL’s Chromium Connect platform (10x Genomics) enables automated single-cell/nucleus partitioning, barcoding, and library prep for selected assays. The SCBL also offers several whole-transcriptome spatial profiling assays for frozen and paraformaldehyde-fixed tissues. These assays include: Visium Spatial Gene Expression slides (10x Genomics), using either manual placement or semi-automated via the CytAssist platform (10x Genomics); Visium HD spatial Gene Expression (10x Genomics); and Curio Seeker (Curio Biosciences), which is a commercialization of the SlideSeq (v2) assay. Moreover, the SCBL offers highly multiplexed in situ profiling of gene expression via the Xenium platform (10x Genomics), which enables the subcellular localization of up to 5000 mRNAs within tissue sections. Associated SCBL equipment for spatial profiling includes a dedicated RNase-free cryostat and microtome for processing frozen and FFPE tissues, respectively. A NanoZoomer-SQ slide scanner is available for rapid and high-resolution imaging of Visium and Xenium slides (prior to or after molecular processing, respectively).
For the simultaneous localization of >10 cellular proteins at high resolution in a single imaging sample, the SCBL utilizes two platforms: 1) the PhenoCycler-Fusion System (Akoya Biosciences), which performs sequential fluorescence-based detection of up to 67 proteins in a single experiment using oligo-tagged antibodies (also known as CO-Detection by indEXing [CODEX]) and 2) the Cell DIVE (Leica), that enables detection of up to 100 proteins through cyclic detection of fluorescently labelled antibodies and is coupled with a BioAssemblyBot 200 (Advanced Solutions) to automate multiple rounds of antibody staining and imaging.
The SCBL has an established organoid screening platform equipped with robotics for automation of Matrigel/organoid dispensing, media exchange, and drug delivery (Microlab VANTAGE Liquid Handling System). This is linked by a robotic arm to an automated incubator and readout capabilities. These capabilities include the SpectraMax i3x Multi-Mode Microplate Reader (Molecular Devices) and a four-laser, four-camera Opera Phenix High-Content Screening System for confocal 3D imaging (Perkin Elmer). Additionally, the SCBL offers live imaging capabilities for functional in vitro assays and time course of 2D/3D cellular models with the Incucyte SX5 (Sartorius). In addition, the SCBL is equipped with standard laboratory equipment and workstations dedicated to tissue preparation and cell culture. The facility in Farmington is immediately adjacent to the Flow Cytometry Service and Genome Technologies Service and extensively uses equipment in these labs such as cell sorters (BD FACSAria, BD Symphony S6, Sony SH800) and Illumina® sequencers (NovaSeq X Plus, NextSeq 500, MiSeq). The SCBL is based at JAX and is accessible to the UConn/UConn Health community through a Single Cell Genomics Agreement between the two institutions.
Given the custom nature of each investigator’s project, JAX and UConn faculty can contact the SCBL to discuss service pricing.
The JAX Single Cell Biology Laboratory is a collaborative core facility with specialized expertise. Please consider the importance of our contributions to your research program; our biologists, specialists, and staff scientists may fit one or several roles of the CRediT authorship taxonomy.
Otherwise, please acknowledge the use of the JAX Single Cell Biology Laboratory in manuscripts, publications, grant applications, press releases, and presentations. Example language for the use of the Single Cell Biology Laboratory is below:
“We gratefully acknowledge the contributions of the Single Cell Biology Laboratory and Genome Technologies services at The Jackson Laboratory for expert assistance with the work described herein. These shared services are supported in part by the JAX Cancer Center (P30 CA034196).”
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