{"id":398,"date":"2018-11-07T20:12:15","date_gmt":"2018-11-07T20:12:15","guid":{"rendered":"https:\/\/www.saintjohnscancer.org\/translational-research-departments\/molecular-medicine\/current-research-topics\/next-generation-sequencing\/"},"modified":"2026-04-02T19:24:31","modified_gmt":"2026-04-02T19:24:31","slug":"genomic-sequencing-center","status":"publish","type":"page","link":"https:\/\/www.saintjohnscancer.org\/translational-research-departments\/genomic-sequencing-center\/","title":{"rendered":"Saint John\u2019s Cancer Institute Genomic Sequencing Center"},"content":{"rendered":"","protected":false},"excerpt":{"rendered":null,"protected":false},"author":2,"featured_media":0,"parent":0,"menu_order":3,"comment_status":"closed","ping_status":"closed","template":"template-front-page.php","meta":{"_acf_changed":false,"_relevanssi_hide_post":"","_relevanssi_hide_content":"","_relevanssi_pin_for_all":"","_relevanssi_pin_keywords":"","_relevanssi_unpin_keywords":"","_relevanssi_related_keywords":"","_relevanssi_related_include_ids":"","_relevanssi_related_exclude_ids":"","_relevanssi_related_no_append":"","_relevanssi_related_not_related":"","_relevanssi_related_posts":"","_relevanssi_noindex_reason":"","footnotes":""},"class_list":["post-398","page","type-page","status-publish","hentry"],"acf":{"layers":[{"acf_fc_layout":"layer_content_image","layer_label":"","layer_headline":"Next Generation Sequencing Services","layer_content":"

The Saint John\u2019s Cancer Institute Genomic Sequencing Center is an Illumina Propel-Certified sequencing provider and among a few select laboratories recognized for proficiency in Next-Generation Sequencing at the highest research industry standard. <\/p>\n

The Genomic Sequencing Center has upheld a rigorous standard of excellence in collaboration with global partners for over a decade. From direct customized consultation to high quality sequencing data generation, the Genomic Sequencing Center delivers tailored sequencing services to both internal and external research collaborators, meeting the demands of today\u2019s rapidly evolving research landscape. <\/p>\n

We welcome opportunities to provide you with an assay that fits your specific research needs. We can happily tailor sequencing needs around your budget and goals.<\/p>\n","layer_link":"","layer_img":1424,"layer_img_position":"right","layer_img_size":"cover","layer_img_is_fade":true,"layer_background_color":"","layer_id":""},{"acf_fc_layout":"layer_content_sidebar","layer_label":"","layer_headline":"","layer_intro":"","layer_content":"

General Sequencing Services<\/h2>\n
\n

Transcriptomics and Spatial Profiling<\/h3>\n
\n

mRNA-Seq (Poly-A Capture)<\/h4>\n

Accurate measurement of gene and transcript abundance, detecting both known and novel features in coding and multiple forms of noncoding RNA. Comprehensive analysis and discovery of alternative transcripts, gene fusions, and allele-specific expression.<\/p>\n

    \n
  • Acceptable Sample Format:<\/strong>FFPE, frozen tissue, cell lines, lower integrity\/quality samples.<\/li>\n
  • Minimum Input Requirement:<\/strong>1-1000 ng purified RNA.<\/li>\n<\/ul>\n

    Total RNA-Seq (rRNA Depletion)<\/h4>\n

    Analysis of the transcriptome with mRNA-focused sequencing enables characterization of gene expression, gene fusions, alternative splicing, and novel transcripts through the enrichment of polyadenylated mRNA.<\/p>\n

      \n
    • Acceptable Sample Format:<\/strong>Frozen tissue, cell lines, cell pellet.<\/li>\n
    • Minimum Input Requirement:<\/strong>25-1000 ng high-quality total RNA.<\/li>\n<\/ul>\n

      Single Cell RNA-Seq<\/h4>\n

      mRNA array offers 10X resolution at the cellular level for high-resolution analysis of gene expression at the cellular level.<\/p>\n

        \n
      • Acceptable Sample Format:<\/strong>Cells or nuclei.<\/li>\n
      • Minimum Input Requirement:<\/strong>2k-20k cells.<\/li>\n<\/ul>\n

        NanoString GeoMx Digital Spatial Profiling<\/h4>\n

        Flexible and scalable spatial analysis of microenvironments using the only automated, scalable technology capable of non-destructive profiling expression of RNA and protein across distinct tissue compartments and cell populations. Transcriptome quantification, custom markers, 18,000+ genes expression in spatial context.<\/p>\n

          \n
        • Acceptable Sample Format:<\/strong>Antibody protein, FFPE tissue sections. AOI and ROI Ab imaging based.<\/li>\n<\/ul>\n<\/div>\n

          Genomics and Epigenomics<\/h3>\n
          \n

          Whole Exome-Seq<\/h4>\n

          Targeted analysis of coding regions in the genome, providing a cost-effective alternative to whole genome sequencing. Exome sequencing captures 50 Mbp of coding exonic regions with high specificity and coverage for both human and mouse genomes..<\/p>\n

            \n
          • Acceptable Sample Format:<\/strong>FFPE, cell pellet, frozen tissue.<\/li>\n
          • Minimum Input Requirement:<\/strong>1000 ng gDNA.<\/li>\n<\/ul>\n

            CUT&RUN<\/h4>\n

            A groundbreaking strategy for ultra-sensitive genomic mapping of chromatin targets, offering a more robust approach for chromatin mapping compared to ChIP-Seq with lower cell requirements, enhanced signal-to-noise, and a streamlined workflow.<\/p>\n

              \n
            • Acceptable Sample Format:<\/strong>CUT&RUN enriched DNA: cell lines, blood, PBL.<\/li>\n
            • Minimum Input Requirement:<\/strong>0.5-5 ng CUT&RUN enriched DNA (5 ng recommended).<\/li>\n<\/ul>\n

              CUT&Tag<\/h4>\n

              Based on ChIP principles while addressing ChIP limitations, CUT&Tag investigates genomic localization of histone modifications and transcription factors to identify protein-DNA interactions or DNA binding sites for proteins of interest. Unlike ChIP-Seq, live permeabilized cells or isolated nuclei serve as starting material.<\/p>\n

                \n
              • Acceptable Sample Format:<\/strong>Freshly isolated, unfixed (i.e. native) nuclei.<\/li>\n
              • Minimum Input Requirement:<\/strong>100k nuclei per reaction recommended.<\/li>\n<\/ul>\n

                ATAC-Seq<\/h4>\n

                Simple and scalable assessment of chromatin accessibility across the genome and how it may be altered by perturbation or disease, requiring a relatively small number of cells.<\/p>\n

                  \n
                • Acceptable Sample Format:<\/strong>cfDNA\/plasma, FFPE\/frozen tissue.<\/li>\n
                • Minimum Input Requirement:<\/strong>500-2500 viable cells.<\/li>\n<\/ul>\n

                  miRNA-Seq<\/h4>\n

                  Efficient, instrument-free gene expression technology for targeted measurement of miRNA expression across various sample types, without the need for extraction. Highly reproducible results ensure precise, reliable data. <\/p>\n

                    \n
                  • Acceptable Sample Format:<\/strong>FFPE, cell lines, plasma.<\/li>\n
                  • Minimum Input Requirement:<\/strong>5 \u00b5m FFPE sections, 1k-4k cells, 13-30 \u00b5L plasma.<\/li>\n<\/ul>\n<\/div>\n

                    Instruments<\/h3>\n

                    Sequencing Platforms<\/p>\n

                    \n

                    Illumina NextSeq 2000<\/h4>\n

                    NextSeq 2000 systems simplify workflows while boasting superior performance and expanded applications for benchtop sequencing. Equipped with XLEAP-SBS chemistry and onboard informatics, NextSeq 2000 generates between 100 million-1.8 billion single reads per run. <\/p>\n

                    Illumina MiSeq<\/h4>\n

                    Ideal for small scale projects with rapid turnaround time, a single run using MiSeq can generate 1-25 million single reads in a matter of hours.<\/p><\/div>\n

                    Quality Control<\/p>\n

                    \n

                    Qubit 4 Fluorometer<\/h4>\n

                    Accurate and quick measurement of the concentration of DNA, RNA, or protein in a single sample.<\/p>\n

                    Agilent 2100 BioAnalyzer<\/h4>\n

                    An established electrophoresis solution integrating an instrument, data processing software, reagents, and a microfluidic chip specific for DNA, RNA, or protein quality control.<\/p>\n

                    Agilent TapeStation 4200<\/h4>\n

                    A high-throughput automated electrophoresis platform for fully automated, easy, and reliable quality analysis of DNA and RNA samples.\n<\/p><\/div>\n<\/div>\n

                    Sample Requirements<\/h2>\n

                    \n \n