{"id":625,"date":"2024-05-20T18:25:46","date_gmt":"2024-05-20T18:25:46","guid":{"rendered":"https:\/\/geiselmed.dartmouth.edu\/gsr\/?page_id=625"},"modified":"2026-04-28T02:37:59","modified_gmt":"2026-04-28T02:37:59","slug":"spatial-genomics","status":"publish","type":"page","link":"https:\/\/geiselmed.dartmouth.edu\/gsr\/spatial-genomics\/","title":{"rendered":"Spatial Genomics"},"content":{"rendered":"<p>The GMBSR offers a full suite of spatial genomics services in collaboration with the Pathology Shared Resource. All spatial assays include tissue sectioning, staining, imaging, and downstream library preparation where applicable.<\/p>\n<p>Use our <a href=\"https:\/\/geiselmed.dartmouth.edu\/gsr\/cost-estimator\/\">Cost Estimator Tool<\/a> for detailed project pricing.<\/p>\n<table style=\"border-collapse: separate;border-spacing: 20px;margin: 0 -20px\">\n<tbody>\n<tr>\n<td style=\"vertical-align: top;border: 1px solid #ddd;border-left: 4px solid #00693e;border-radius: 8px;padding: 24px;background: #fff\">\n<h3 style=\"margin: 0 0 4px 0;font-size: 18px;color: #333\">Visium Tissue Optimization<\/h3>\n<div style=\"font-size: 22px;font-weight: 600;color: #00693e;margin-bottom: 4px\">$1,733.66 <span style=\"font-size: 13px;font-weight: 400;color: #666\">\/ sample<\/span><\/div>\n<div style=\"font-size: 12px;color: #999;margin-bottom: 12px\">&nbsp;<\/div>\n<ul style=\"margin: 0;padding-left: 20px\">\n<li style=\"font-size: 14px;color: #555;line-height: 1.5\">Necessary step prior to performing the Visium: Fresh Frozen assay.<\/li>\n<li style=\"font-size: 14px;color: #555;line-height: 1.5\">In collaboration with Pathology, 7x10um tissue sections are cut onto Visium Tissue Optimization slides and a time course is performed to determine the optimal permeabilization time.<\/li>\n<li style=\"font-size: 14px;color: #555;line-height: 1.5\">A separate optimization run should be performed for each tissue type. It is also recommended to separately optimize healthy vs diseased samples.<\/li>\n<\/ul>\n<\/td>\n<td style=\"vertical-align: top;border: 1px solid #ddd;border-left: 4px solid #00693e;border-radius: 8px;padding: 24px;background: #fff\">\n<h3 style=\"margin: 0 0 4px 0;font-size: 18px;color: #333\">Visium Fresh Frozen<\/h3>\n<div style=\"font-size: 22px;font-weight: 600;color: #00693e;margin-bottom: 4px\">$7,004.58 <span style=\"font-size: 13px;font-weight: 400;color: #666\">\/ slide<\/span><\/div>\n<div style=\"font-size: 12px;color: #999;margin-bottom: 12px\">&nbsp;<\/div>\n<ul style=\"margin: 0;padding-left: 20px\">\n<li style=\"font-size: 14px;color: #555;line-height: 1.5\">Preparation of tissue sections for spatial transcriptomics using the 10x Genomics Visium assay for fresh frozen tissues.<\/li>\n<li style=\"font-size: 14px;color: #555;line-height: 1.5\">In collaboration with Pathology, 10um sections are cut and placed on the Visium slide (4 capture areas per slide). H&amp;E staining and imaging (20x) are performed in the Single Cell Genomics Core. Transcripts are detected using a PolyA-based approach.<\/li>\n<\/ul>\n<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<table style=\"border-collapse: separate;border-spacing: 20px;margin: 0 -20px\">\n<tbody>\n<tr>\n<td style=\"vertical-align: top;border: 1px solid #ddd;border-left: 4px solid #00693e;border-radius: 8px;padding: 24px;background: #fff\">\n<h3 style=\"margin: 0 0 4px 0;font-size: 18px;color: #333\">Visium FFPE<\/h3>\n<div style=\"font-size: 22px;font-weight: 600;color: #00693e;margin-bottom: 4px\">$9,630.74 <span style=\"font-size: 13px;font-weight: 400;color: #666\">\/ slide<\/span><\/div>\n<div style=\"font-size: 12px;color: #999;margin-bottom: 12px\">&nbsp;<\/div>\n<ul style=\"margin: 0;padding-left: 20px\">\n<li style=\"font-size: 14px;color: #555;line-height: 1.5\">Performs the 10x Genomics Visium assay on FFPE tissue sections.<\/li>\n<li style=\"font-size: 14px;color: #555;line-height: 1.5\">In collaboration with Pathology, 5um FFPE sections are cut onto standard histology slides, followed by H&amp;E staining and 40x whole-slide imaging. Whole transcriptome probes (human or mouse) are hybridized and transferred to the Visium slide using a CytAssist.<\/li>\n<li style=\"font-size: 14px;color: #555;line-height: 1.5\">Each Capture Area contains either 5,000 (6.5x6.5mm) or 14,000 (11x11mm) barcoded spots, 55 \u00b5m in diameter, providing 1-10 cells per spot resolution.<\/li>\n<\/ul>\n<\/td>\n<td style=\"vertical-align: top;border: 1px solid #ddd;border-left: 4px solid #00693e;border-radius: 8px;padding: 24px;background: #fff\">\n<h3 style=\"margin: 0 0 4px 0;font-size: 18px;color: #333\">Visium HD<\/h3>\n<div style=\"font-size: 22px;font-weight: 600;color: #00693e;margin-bottom: 4px\">$14,730.74 <span style=\"font-size: 13px;font-weight: 400;color: #666\">\/ slide<\/span><\/div>\n<div style=\"font-size: 12px;color: #999;margin-bottom: 12px\">&nbsp;<\/div>\n<ul style=\"margin: 0;padding-left: 20px\">\n<li style=\"font-size: 14px;color: #555;line-height: 1.5\">Performs the 10x Genomics Visium HD assay on tissue sections.<\/li>\n<li style=\"font-size: 14px;color: #555;line-height: 1.5\">In collaboration with Pathology, 5um FFPE sections are cut, H&amp;E stained, and imaged at 40x. Whole transcriptome probes are hybridized and transferred to the Visium slide using CytAssist (2 capture areas per slide).<\/li>\n<li style=\"font-size: 14px;color: #555;line-height: 1.5\">Visium HD slides contain ~11 million 2x2 \u00b5m barcoded squares without gaps, achieving single cell\u2013scale spatial resolution.<\/li>\n<\/ul>\n<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<table style=\"border-collapse: separate;border-spacing: 20px;margin: 0 -20px\">\n<tbody>\n<tr>\n<td style=\"vertical-align: top;border: 1px solid #ddd;border-left: 4px solid #00693e;border-radius: 8px;padding: 24px;background: #fff\">\n<h3 style=\"margin: 0 0 4px 0;font-size: 18px;color: #333\">Xenium Sample Prep<\/h3>\n<div style=\"font-size: 22px;font-weight: 600;color: #00693e;margin-bottom: 4px\">$1,212.44 <span style=\"font-size: 13px;font-weight: 400;color: #666\">\/ slide<\/span><\/div>\n<div style=\"font-size: 12px;color: #999;margin-bottom: 12px\">&nbsp;<\/div>\n<ul style=\"margin: 0;padding-left: 20px\">\n<li style=\"font-size: 14px;color: #555;line-height: 1.5\">Prepares tissue sections for the 10x Genomics Xenium assay.<\/li>\n<li style=\"font-size: 14px;color: #555;line-height: 1.5\">In collaboration with Pathology, tissue sections are cut onto Xenium slides, then probes are hybridized and ligated to their targets. Custom or off-the-shelf probe sets are available from 10x Genomics.<\/li>\n<\/ul>\n<\/td>\n<td style=\"vertical-align: top;border: 1px solid #ddd;border-left: 4px solid #00693e;border-radius: 8px;padding: 24px;background: #fff\">\n<h3 style=\"margin: 0 0 4px 0;font-size: 18px;color: #333\">Xenium<\/h3>\n<div style=\"font-size: 22px;font-weight: 600;color: #00693e;margin-bottom: 4px\">$3,949.10 <span style=\"font-size: 13px;font-weight: 400;color: #666\">\/ slide<\/span><\/div>\n<div style=\"font-size: 12px;color: #999;margin-bottom: 12px\">&nbsp;<\/div>\n<ul style=\"margin: 0;padding-left: 20px\">\n<li style=\"font-size: 14px;color: #555;line-height: 1.5\">Performs the 10x Genomics Xenium in situ assay on tissue sections.<\/li>\n<li style=\"font-size: 14px;color: #555;line-height: 1.5\">Prepared slides are loaded onto the Xenium analyzer, which amplifies and images the targets to build a spatial map of transcripts across the tissue section.<\/li>\n<\/ul>\n<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<hr \/>\n<p><img loading=\"lazy\" decoding=\"async\" class=\"alignnone wp-image-285 aligncenter\" src=\"https:\/\/geiselmed.dartmouth.edu\/gsr\/wp-content\/uploads\/sites\/28\/2019\/05\/GMBSR-logo-green-crop.png\" alt=\"\" width=\"112\" height=\"129\" srcset=\"https:\/\/geiselmed.dartmouth.edu\/gsr\/wp-content\/uploads\/sites\/28\/2019\/05\/GMBSR-logo-green-crop.png 254w, https:\/\/geiselmed.dartmouth.edu\/gsr\/wp-content\/uploads\/sites\/28\/2019\/05\/GMBSR-logo-green-crop-48x55.png 48w\" sizes=\"auto, (max-width: 112px) 100vw, 112px\" \/><\/p>\n<p style=\"text-align: center\">Prices shown reflect internal Dartmouth rates for FY2026. External users and those with large projects should contact the core directly for pricing information. Actual prices may vary based on batch size.<\/p>\n<p style=\"text-align: center\">All services provided by the GMBSR are supported by an NCI Cancer Center Support Grant (5P30CA023108) which MUST be cited in any publications or other materials using data generated in the core.<\/p>\n<p style=\"text-align: center\">Single cell sequencing services are provided through the Single Cell Genomics Core and are subsidized by a COBRE grant (P20GM130454). This grant MUST be cited in all publications and materials using single cell data generated in the core.<\/p>\n<p>Genomics Services<\/p>\n<ul>\n<li><a href=\"https:\/\/geiselmed.dartmouth.edu\/gsr\/nucleicacidextraction\/\"><span style=\"font-size: 10pt\">Nucleic Acid Extraction<\/span><\/a><\/li>\n<li><a href=\"https:\/\/geiselmed.dartmouth.edu\/gsr\/nucleic-acid-qc\/\"><span style=\"font-size: 10pt\">Nucleic Acid QC<\/span><\/a><\/li>\n<li><a href=\"https:\/\/geiselmed.dartmouth.edu\/gsr\/rna-seq\/\"><span style=\"font-size: 10pt\">RNA-seq<\/span><\/a><\/li>\n<li><a href=\"https:\/\/geiselmed.dartmouth.edu\/gsr\/dna-seq\/\"><span style=\"font-size: 10pt\">DNA-seq<\/span><\/a><\/li>\n<li><a href=\"https:\/\/geiselmed.dartmouth.edu\/gsr\/single-cell-genomics\/\"><span style=\"font-size: 10pt\">Single Cell Genomics<\/span><\/a><\/li>\n<li><a href=\"https:\/\/geiselmed.dartmouth.edu\/gsr\/spatial-genomics\/\"><span style=\"font-size: 10pt\">Spatial Genomics<\/span><\/a><\/li>\n<li><a href=\"https:\/\/geiselmed.dartmouth.edu\/gsr\/microarray\/\"><span style=\"font-size: 10pt\">Microarray<\/span><\/a><\/li>\n<li><a href=\"https:\/\/geiselmed.dartmouth.edu\/gsr\/sequencing\/\"><span style=\"font-size: 10pt\">Sequencing<\/span><\/a><\/li>\n<\/ul>\n<p>&nbsp;<\/p>\n","protected":false},"excerpt":{"rendered":"<p>The GMBSR offers a full suite of spatial genomics services in collaboration with the Pathology Shared Resource. All spatial assays include tissue sectioning, staining, imaging, and downstream library preparation where applicable. Use our Cost Estimator Tool for detailed project pricing. Visium Tissue Optimization $1,733.66 \/ sample &nbsp; Necessary step prior [\u2026] <\/p>\n<div class=\"clear\"><\/div>\n<p><a class=\"more_link clearfix\" href=\"https:\/\/geiselmed.dartmouth.edu\/gsr\/spatial-genomics\/\" rel=\"nofollow\">Read More<\/a><\/p>\n","protected":false},"author":145,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-625","page","type-page","status-publish","hentry","author-145"],"jetpack_shortlink":"https:\/\/wp.me\/PbaUZP-a5","jetpack_sharing_enabled":true,"_links":{"self":[{"href":"https:\/\/geiselmed.dartmouth.edu\/gsr\/wp-json\/wp\/v2\/pages\/625","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/geiselmed.dartmouth.edu\/gsr\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/geiselmed.dartmouth.edu\/gsr\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/geiselmed.dartmouth.edu\/gsr\/wp-json\/wp\/v2\/users\/145"}],"replies":[{"embeddable":true,"href":"https:\/\/geiselmed.dartmouth.edu\/gsr\/wp-json\/wp\/v2\/comments?post=625"}],"version-history":[{"count":9,"href":"https:\/\/geiselmed.dartmouth.edu\/gsr\/wp-json\/wp\/v2\/pages\/625\/revisions"}],"predecessor-version":[{"id":851,"href":"https:\/\/geiselmed.dartmouth.edu\/gsr\/wp-json\/wp\/v2\/pages\/625\/revisions\/851"}],"wp:attachment":[{"href":"https:\/\/geiselmed.dartmouth.edu\/gsr\/wp-json\/wp\/v2\/media?parent=625"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}