Contact: Kristin Beaumont, PhD, Associate Professor and Associate Director at kristin.beaumont@mssm.edu

Submission: Use the third section (blue) of the project submission form. Please review the Center policies before submitting. Sample submission instructions, including the shipping address, will be provided after the project is approved.

We offer a range of standard and custom single-cell and spatial transcriptomic approaches using the technologies below.

Sample Preparation for Single-Cell and Single-Nuclei Analysis

• Miltenyi gentleMACS Octo Dissociator for dissociation of tissues into single-cell suspensions
• Levitas LeviCell for live cell or nuclei enrichment before single-cell analysis
• S2 Singulator for nuclei isolation from fresh, fixed, and frozen tissue types

Single-Cell/Nuclei Analysis

• 10x Genomics Chromium: High-throughput 3′/5′ RNA sequencing of thousands to tens of thousands of single cells or nuclei. Available applications include immune profiling, CITE-seq, ATAC-seq, combined RNA/ATAC multiome analysis, and development-based assays. Standard input is at least 500,000 debris-free cells (more than 80% viable) for scRNA-seq or scATAC-seq and at least 1 million cells for CITE-seq, at 1 million cells/mL in PBS with 0.04% BSA.
• Mission Bio Tapestri: Commercial and custom targeted amplicon DNA sequencing at the single-cell level. Input requirements vary by experiment; contact the team for details.

Spatial Transcriptomics

• 10x Genomics Visium HD and Visium HD 3′: Whole-transcriptome spatial profiling of tissues up to 6.5 mm × 6.5 mm. The facility is a Certified Service Provider for these assays.
• 10x Genomics Xenium: Targeted in situ spatial transcriptomic profiling of fresh-frozen or FFPE-preserved tissue at subcellular resolution.
• Element AVITI24: Multiomic spatial profiling of cell morphology, protein expression, and gene expression, with support for perturbation analysis.
• Stellaromics: Coming soon.

Spatial transcriptomics projects generally require high-quality fresh-frozen tissue embedded in OCT or FFPE blocks. Please contact the team for assay-specific requirements.

Contact: Irene Salib at irene.salib@mssm.edu

Submission: Use the fourth section (teal) of the project submission form. Please review the Center policies before submitting. Sample submission instructions, including the shipping address, will be provided after the project is approved.

DNA microarrays are used for genome-wide characterization of gene transcription, single-nucleotide variation, copy-number variation, and cytosine methylation. The facility uses the Illumina BeadArray platform, supported by two TECAN Evo liquid-handling robots and an Illumina HiScan scanner. The facility can process up to 600 samples per week.

For platform information, visit Illumina’s HiScan page or review the specification sheet.

Human Genotyping and Methylation

The MethylationEPIC v2.0 array covers approximately 950,000 sites and can also support copy-number variant estimation. Custom-content arrays for genome-wide association studies may also be available. Please contact the team with project details for current options.

Contact: Ethan Ellis at ethan.ellis@mssm.edu

Submission: Use the first section (purple) of the project submission form. Please review the Center policies before submitting. Sample submission instructions, including the shipping address, will be provided after the project is approved.

We perform Ion Torrent sequencing on pre-existing and custom gene panels using the S5/XL system, including AmpliSeq and AmpliSeq HD panels. Frequently requested panels include:

• Oncomine Comprehensive Assay Plus: A 517-gene solid-tumor profiling panel that supports concurrent DNA and RNA analysis for SNVs, indels, CNVs, BRCA1/2 large genomic rearrangements, genomic instability, MSI, TMB, loss of heterozygosity, and gene fusions. It is FFPE compatible and accepts DNA, RNA, or matched DNA/RNA with inputs as low as 20 ng per sample type.
• Oncomine Comprehensive Assay v3: A 161-gene solid-tumor panel for SNVs, CNVs, gene fusions, and indels. It is FFPE compatible and accepts DNA, RNA, or matched DNA/RNA with inputs as low as 10 ng per sample type.
• AmpliSeq Whole Transcriptome: A gene-expression panel measuring more than 20,000 human RefSeq genes. It is FFPE compatible and accepts as little as 0.1 ng of high-quality RNA or 10 ng of FFPE RNA.

Contact: Ethan Ellis at ethan.ellis@mssm.edu

Submission: Use the second section (pink) of the project submission form. Please review the Center policies before submitting. Sample submission instructions, including the shipping address, will be provided after the project is approved.

We offer single-molecule, real-time (SMRT) sequencing on the PacBio Sequel IIe and Revio systems. SMRT sequencing combines long read lengths and high accuracy for templates ranging from approximately 500 bp to 30 kb. Applications include de novo genome assembly, full-length transcriptome profiling, targeted sequencing, and highly accurate amplicon sequencing.

Available library-preparation methods include:

• HiFi whole-genome sequencing: Highly accurate circular consensus reads for SNP and structural-variant analysis. Native preparations require at least 2 μg of high-molecular-weight genomic DNA with average fragments greater than 30 kb; a lower-input PCR-based option is available from 50 ng.
• Twist targeted sequencing: Probe-based enrichment for customizable regions of interest with haplotype-level resolution. Probe design and ordering can require up to six weeks; typical input is 2 μg of high-molecular-weight DNA.
• Isoform sequencing (Iso-Seq) with Kinnex: Full-length isoform sequencing for reference transcriptome development, alternative splicing, and promoter, exon, and UTR analysis. Typical input is at least 500 ng total RNA with RIN greater than 7 or DV200 greater than 90%.
• Single-cell Iso-Seq with 10x or ArgenTag and Kinnex: Isoform-level transcriptome analysis for individual cells. Typical input is 100 ng of unfragmented 10x or ArgenTag cDNA; tissue may also be accepted for ArgenTag preparation.
• Amplicon sequencing: High-accuracy, contiguous sequencing of DNA, cDNA, or bisulfite-treated DNA amplicons for variant phasing, haplotyping, targeted Iso-Seq, or fusion-transcript analysis. Typical input is at least 500 ng of nucleic-acid template.
• HLA genotyping: Class I and class II HLA profiling using GenDx reagents and software, with up to 96 subjects per run depending on the requested loci and throughput. Typical input is 500–2,000 ng genomic DNA per subject.

High-molecular-weight DNA and RNA extraction services are available for a range of sample types. All PacBio sequencing services include required quality control and library size selection.

PacBio Bioinformatics Services

Demultiplexing and raw-data delivery through a secure FTP link are included in the sequencing cost. Optional SMRT Link analyses are available for an additional compute fee, including:

• Circular Consensus Sequencing (CCS): Generation of HiFi reads with greater than 99.9% accuracy.
• Hierarchical Genome Assembly (HGAP): Assembly of small, haploid genomes with FASTA/FASTQ delivery.
• Microbial Assembly: Microbial genome assembly, circularization, and resolution of features such as plasmids.
• HiFi Target Enrichment: Mapping, variant calling, and haplotype phasing for targeted DNA assays.
• Base Modifications: Detection of DNA modifications and associated motifs; Revio runs include 5mC and 6mA tags by default.
• Iso-Seq and single-cell Iso-Seq: Full-length isoform prediction and cell-level transcript classification.
• Kinnex segmentation: Segmentation and adapter trimming for Kinnex concatemer reads.

Custom bioinformatics services are available upon request, including large and HiFi genome assemblies, transcriptome annotation, targeted Iso-Seq analysis, and repeat-expansion analysis.

Contact: Ethan Ellis at ethan.ellis@mssm.edu

Submission: Use the first section (purple) of the project submission form. Please review the Center policies before submitting. Sample submission instructions, including the shipping address, will be provided after the project is approved.

We offer Illumina NGS library preparation and sequencing for DNA, RNA, and epigenetic profiling. Projects may include library preparation, sequencing of user-prepared libraries, and extraction services. Pricing is based on the requested assays and sample count; contact the team for a custom estimate.

Available library-preparation methods include:

RNA Methods

• Stranded mRNA sequencing: Gene-expression analysis of polyadenylated mRNA. Compatible with species that have polyadenylated 3′ ends; not FFPE compatible. Typical input is 25 ng to 1 μg total RNA with RIN greater than 7.
• Stranded total RNA sequencing: Captures protein-coding and long noncoding RNA and supports low-yield, degraded, and FFPE samples. Input ranges from 250 pg to 1 μg for high-quality RNA, or 1 ng to 1 μg for FFPE or lower-quality RNA; minimum integrity is DV200 greater than 30%.
• Small-RNA sequencing: Analysis of small noncoding RNAs, including miRNAs. Typical input is 1 ng to 2 μg total or small-RNA-enriched RNA with RIN greater than 8.

DNA Methods

• Whole-genome sequencing: FFPE-compatible whole-genome library preparation. Typical input is 100–500 ng intact genomic DNA for human or other large genomes, or as little as 10 ng for small genomes.
• Whole-exome and targeted sequencing: Oligonucleotide-capture sequencing of coding regions or other targets. FFPE compatible; input is 10 ng to 1 μg genomic DNA, with at least 50 ng recommended for human whole-exome samples.
• Amplicon sequencing: Direct-ligation preparation for amplicons shorter than 500 bp or fragmentation-based preparation for amplicons of approximately 10–20 kb. Typical input is 1 ng per sample for small amplicons or 10 ng per sample for large amplicons.
• ChIP-seq: Library preparation from DNA recovered through chromatin immunoprecipitation. Typical input is 0.1–10 ng single- or double-stranded DNA, optimized for 200–400 bp fragments.
• ATAC-seq: Chromatin-accessibility profiling from isolated nuclei, cells, or tissue. Contact the team to coordinate handling and sample drop-off before submission.

User-Prepared Libraries

We accept user-prepared libraries for direct quality control and sequencing. Please submit more than 15 nM library in more than 20 μL of water or EDTA-free EB. Sequencing parameters and specifications can be discussed with the team.

Extractions

DNA and RNA extraction from fresh, frozen, or FFPE samples is available, along with custom extraction requests.

Quality Control Services

Submission: Use the fifth section (navy) of the project submission form. Please review the Center policies before submitting. Sample submission instructions, including the shipping address, will be provided after the project is approved.

• Qubit: Double-stranded DNA and RNA quantification in broad-range and high-sensitivity configurations.
• Agilent TapeStation and BioAnalyzer: DNA/RNA mass, integrity, and size-distribution analysis, including RIN, DIN, and DV200 measurements.
• qPCR: Quantification of specific templates, with instrumentation supporting 384-well plates.

Flow-cell selection is based on project requirements. Individual projects do not share a flow cell.

Contact: Hardik Shah at hardik.shah@mssm.edu

The facility provides bioinformatics services that translate NGS and other advanced-platform data into scientific insights. Pipelines are hosted and run on the Minerva HPC cluster. Standard services include:

• Element Biosciences AVITI and Teton CytoProfiling: Demultiplexing and visualization of CytoProfiling data.
• Takara Bio Cogent NGS Analysis Pipeline: Single-cell RNA-seq processing with expression matrices, quality metrics, clustering, and interactive reports.
• Mission Bio Tapestri Pipeline: Single-cell targeted-variant analysis with cell-by-variant genotype matrices for clonal and phylogenetic analysis.
• 10x Genomics pipelines: Cell Ranger for single-cell gene expression and immune profiling, Cell Ranger ARC for multiome RNA/ATAC analysis, and Space Ranger for spatial transcriptomics.
• RAPiD: Nextflow-based RNA-seq processing with expression matrices, differential-expression results, QC metrics, and interactive reports.
• DSeek: Nextflow-based DNA-seq alignment, quality control, variant calling, and peak calling for ATAC-seq and ChIP-seq.
• TDIsoSeq: Long-read Iso-Seq analysis with expression matrices, transcript annotation, and novel-isoform discovery.
• Custom services: Consulting and customized analysis, including reference development, differential-expression analysis, single-cell and spatial visualization, and cell-type deconvolution.