{"id":6,"date":"2018-01-19T17:12:58","date_gmt":"2018-01-19T17:12:58","guid":{"rendered":"https:\/\/lab.research.sickkids.ca\/casca\/?page_id=6"},"modified":"2025-07-31T19:17:09","modified_gmt":"2025-07-31T19:17:09","slug":"rhapsody-scrna-seq","status":"publish","type":"page","link":"https:\/\/lab.research.sickkids.ca\/casca\/rhapsody-scrna-seq\/","title":{"rendered":"Single Cell RNA Sequencing"},"content":{"rendered":"<p><div id=\"Analytical Mass Cytometry\" class=\"fusion-container-anchor\"><div class=\"fusion-fullwidth fullwidth-box fusion-builder-row-1 nonhundred-percent-fullwidth non-hundred-percent-height-scrolling\" style=\"--awb-border-radius-top-left:0px;--awb-border-radius-top-right:0px;--awb-border-radius-bottom-right:0px;--awb-border-radius-bottom-left:0px;--awb-background-color:#ffffff;--awb-flex-wrap:wrap;\" ><div class=\"fusion-builder-row fusion-row\"><div class=\"fusion-layout-column fusion_builder_column fusion-builder-column-0 fusion_builder_column_2_3 2_3 fusion-two-third fusion-column-first\" style=\"--awb-bg-blend:overlay;--awb-bg-size:cover;width:66.666666666667%;width:calc(66.666666666667% - ( ( 4% ) * 0.66666666666667 ) );margin-right: 4%;\"><div class=\"fusion-column-wrapper fusion-flex-column-wrapper-legacy\"><div class=\"fusion-text fusion-text-1\" style=\"--awb-content-alignment:justify;\"><p><strong>Single cell RNA sequencing (scRNA-seq)<\/strong>, combined with multi-omics approaches, enables simultaneous profiling of gene expression, protein, and epigenetic features at single cell resolution. This integrated analysis provides powerful insights into cellular heterogeneity, function, and lineage dynamics in both fundamental and translational research.<\/p>\n<p>Single cell multi-omics technologies are broadly applicable across immunology, oncology, neurobiology, and genetic disease research areas.<\/p>\n<p>CASCA offers the<strong> BD Rhapsody HT Xpress <\/strong>and <strong>10x Genomics Chromium X <\/strong>single cell multi-omics platforms. We offer consultation for experimental design, platform and assay selection and sample preparation optimization. We perform single cell antibody labeling (optional), cell capture and library preparation. \u00a0Sequencing is performed in partnership with <a href=\"https:\/\/tcag.ca\/\" target=\"_blank\" rel=\"noopener\">The Centre for Applied Genomics (TCAG)<\/a> at SickKids. We also provide basic downstream data analysis to assist with initial interpretation and quality assessment.<\/p>\n<p>To learn more or to obtain a quote for your project: submit a \u201cSingle Cell Multi-omics Experimental Design Consultation\u201d service request (listed in the Single Cell Multi-omics category) <a href=\"https:\/\/ca.ilab.agilent.com\/service_center\/show_external\/4205\/sickkids-centre-for-advanced-single-cell-analysis-casca\/\" target=\"_blank\" rel=\"noopener\">in iLab<\/a>.<\/p>\n<p>When choosing your platform, consider your specific experimental goals, sample type (s), and desired data output. For additional details on platform specifications, assay capabilities, and updated protocols, visit the vendor websites:<\/p>\n<ul>\n<li>BD Biosciences: <a href=\"https:\/\/scomix.bd.com\/hc\/en-us\">https:\/\/scomix.bd.com\/hc\/en-us<\/a><\/li>\n<li>10x Genomics: <a href=\"https:\/\/www.10xgenomics.com\/platforms\/chromium\">https:\/\/www.10xgenomics.com\/platforms\/chromium<\/a><\/li>\n<\/ul>\n<p style=\"text-align: center\">&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;-<\/p>\n<p style=\"text-align: center\"><strong>See table below for overview and comparison of the BD Rhapsody HT Xpress and<\/strong> <strong>10x Genomics Chromium X<\/strong><\/p>\n<\/div><div class=\"fusion-clearfix\"><\/div><\/div><\/div><div class=\"fusion-layout-column fusion_builder_column fusion-builder-column-1 fusion_builder_column_1_3 1_3 fusion-one-third fusion-column-last\" style=\"--awb-bg-blend:overlay;--awb-bg-size:cover;width:33.333333333333%;width:calc(33.333333333333% - ( ( 4% ) * 0.33333333333333 ) );\"><div class=\"fusion-column-wrapper fusion-flex-column-wrapper-legacy\"><div class=\"fusion-text fusion-text-2\"><p style=\"text-align: left\"><strong>Workflow, select image below to expand:<\/strong><\/p>\n<\/div><div class=\"fusion-image-element in-legacy-container\" style=\"--awb-caption-title-font-family:var(--h2_typography-font-family);--awb-caption-title-font-weight:var(--h2_typography-font-weight);--awb-caption-title-font-style:var(--h2_typography-font-style);--awb-caption-title-size:var(--h2_typography-font-size);--awb-caption-title-transform:var(--h2_typography-text-transform);--awb-caption-title-line-height:var(--h2_typography-line-height);--awb-caption-title-letter-spacing:var(--h2_typography-letter-spacing);\"><span class=\" fusion-imageframe imageframe-none imageframe-1 hover-type-none\"><a href=\"https:\/\/lab.research.sickkids.ca\/casca\/wp-content\/uploads\/sites\/84\/2025\/07\/ScRNAseq_Info_for_website_20250430.jpg\" class=\"fusion-lightbox\" data-rel=\"iLightbox[a6a41c9510c9ea3e563]\" data-title=\"scRNA-seq\" title=\"scRNA-seq\"><img decoding=\"async\" width=\"1280\" height=\"720\" alt=\"scRNA-seq\" src=\"https:\/\/lab.research.sickkids.ca\/casca\/wp-content\/uploads\/sites\/84\/2025\/07\/ScRNAseq_Info_for_website_20250430.jpg\" class=\"img-responsive wp-image-1483\" srcset=\"https:\/\/lab.research.sickkids.ca\/casca\/wp-content\/uploads\/sites\/84\/2025\/07\/ScRNAseq_Info_for_website_20250430-200x113.jpg 200w, https:\/\/lab.research.sickkids.ca\/casca\/wp-content\/uploads\/sites\/84\/2025\/07\/ScRNAseq_Info_for_website_20250430-400x225.jpg 400w, https:\/\/lab.research.sickkids.ca\/casca\/wp-content\/uploads\/sites\/84\/2025\/07\/ScRNAseq_Info_for_website_20250430-600x338.jpg 600w, https:\/\/lab.research.sickkids.ca\/casca\/wp-content\/uploads\/sites\/84\/2025\/07\/ScRNAseq_Info_for_website_20250430-800x450.jpg 800w, https:\/\/lab.research.sickkids.ca\/casca\/wp-content\/uploads\/sites\/84\/2025\/07\/ScRNAseq_Info_for_website_20250430-1200x675.jpg 1200w, https:\/\/lab.research.sickkids.ca\/casca\/wp-content\/uploads\/sites\/84\/2025\/07\/ScRNAseq_Info_for_website_20250430.jpg 1280w\" sizes=\"(max-width: 800px) 100vw, 600px\" \/><\/a><\/span><\/div><div class=\"accordian fusion-accordian\" style=\"--awb-border-size:1px;--awb-icon-size:13px;--awb-content-font-size:15.5px;--awb-icon-alignment:left;--awb-hover-color:#f9f9f9;--awb-border-color:rgba(100,160,200,0.24);--awb-background-color:#ffffff;--awb-divider-color:#e0dede;--awb-divider-hover-color:#e0dede;--awb-icon-color:#ffffff;--awb-title-color:#00afd8;--awb-content-color:#757575;--awb-icon-box-color:#333333;--awb-toggle-hover-accent-color:#64a0c8;--awb-title-font-family:Arial, Helvetica, sans-serif;--awb-title-font-weight:400;--awb-title-font-style:normal;--awb-title-font-size:22px;--awb-title-line-height:2.0;--awb-content-font-family:Arial, Helvetica, sans-serif;--awb-content-font-style:normal;--awb-content-font-weight:400;\"><div class=\"panel-group fusion-toggle-icon-boxed\" id=\"accordion-6-1\"><div class=\"fusion-panel panel-default panel-bbb9f459f32027014 fusion-toggle-has-divider\" style=\"--awb-title-color:#00afd8;--awb-content-color:#757575;\"><div class=\"panel-heading\"><h4 class=\"panel-title toggle\" id=\"toggle_bbb9f459f32027014\"><a aria-expanded=\"false\" aria-controls=\"bbb9f459f32027014\" role=\"button\" data-toggle=\"collapse\" data-parent=\"#accordion-6-1\" data-target=\"#bbb9f459f32027014\" href=\"#bbb9f459f32027014\"><span class=\"fusion-toggle-icon-wrapper\" aria-hidden=\"true\"><i class=\"fa-fusion-box active-icon awb-icon-minus\" aria-hidden=\"true\"><\/i><i class=\"fa-fusion-box inactive-icon awb-icon-plus\" aria-hidden=\"true\"><\/i><\/span><span class=\"fusion-toggle-heading\">Sequencing &amp; Bioinformatics<\/span><\/a><\/h4><\/div><div id=\"bbb9f459f32027014\" class=\"panel-collapse collapse \" aria-labelledby=\"toggle_bbb9f459f32027014\"><div class=\"panel-body toggle-content fusion-clearfix\">\n<p>CASCA has partnered with <a href=\"http:\/\/www.tcag.ca\/index.html\" target=\"_blank\" rel=\"noopener\">TCAG to perform Illumina sequencing .<\/a><\/p>\n<\/div><\/div><\/div><div class=\"fusion-panel panel-default panel-8d284c55c117f25ad fusion-toggle-has-divider\" style=\"--awb-title-color:#00afd8;--awb-content-color:#757575;\"><div class=\"panel-heading\"><h4 class=\"panel-title toggle\" id=\"toggle_8d284c55c117f25ad\"><a aria-expanded=\"false\" aria-controls=\"8d284c55c117f25ad\" role=\"button\" data-toggle=\"collapse\" data-parent=\"#accordion-6-1\" data-target=\"#8d284c55c117f25ad\" href=\"#8d284c55c117f25ad\"><span class=\"fusion-toggle-icon-wrapper\" aria-hidden=\"true\"><i class=\"fa-fusion-box active-icon awb-icon-minus\" aria-hidden=\"true\"><\/i><i class=\"fa-fusion-box inactive-icon awb-icon-plus\" aria-hidden=\"true\"><\/i><\/span><span class=\"fusion-toggle-heading\">Pricing Overview<\/span><\/a><\/h4><\/div><div id=\"8d284c55c117f25ad\" class=\"panel-collapse collapse \" aria-labelledby=\"toggle_8d284c55c117f25ad\"><div class=\"panel-body toggle-content fusion-clearfix\">\n<p><strong>updates in progress<\/strong><\/p>\n<\/div><\/div><\/div><\/div><\/div><div class=\"fusion-text fusion-text-3\"><p><strong>Contact <a href=\"mailto:Emily.Reddy@sickkids.ca\" target=\"_blank\" rel=\"noopener noreferrer\">Dr Emily Reddy<\/a> <\/strong>with any questions.<\/p>\n<\/div><div class=\"fusion-clearfix\"><\/div><\/div><\/div><\/div><\/div><\/div><div class=\"fusion-fullwidth fullwidth-box fusion-builder-row-2 fusion-flex-container has-pattern-background has-mask-background nonhundred-percent-fullwidth non-hundred-percent-height-scrolling\" style=\"--awb-border-radius-top-left:0px;--awb-border-radius-top-right:0px;--awb-border-radius-bottom-right:0px;--awb-border-radius-bottom-left:0px;--awb-flex-wrap:wrap;\" ><div class=\"fusion-builder-row fusion-row fusion-flex-align-items-flex-start fusion-flex-content-wrap\" style=\"max-width:1331.2px;margin-left: calc(-4% \/ 2 );margin-right: calc(-4% \/ 2 );\"><div class=\"fusion-layout-column fusion_builder_column fusion-builder-column-2 fusion_builder_column_1_1 1_1 fusion-flex-column\" style=\"--awb-bg-size:cover;--awb-width-large:100%;--awb-margin-top-large:0px;--awb-spacing-right-large:1.92%;--awb-margin-bottom-large:20px;--awb-spacing-left-large:1.92%;--awb-width-medium:100%;--awb-order-medium:0;--awb-spacing-right-medium:1.92%;--awb-spacing-left-medium:1.92%;--awb-width-small:100%;--awb-order-small:0;--awb-spacing-right-small:1.92%;--awb-spacing-left-small:1.92%;\"><div class=\"fusion-column-wrapper fusion-column-has-shadow fusion-flex-justify-content-flex-start fusion-content-layout-column\">\n<table width=\"1368\">\n<tbody>\n<tr>\n<td width=\"239\"><em><strong>Platform Overview<\/strong><\/em><\/td>\n<td width=\"534\"><strong>BD Rhapsody HT Xpress<\/strong><\/td>\n<td width=\"595\"><strong>10x Chromium X<\/strong><\/td>\n<\/tr>\n<tr>\n<td><em>Single Cell Capture<\/em><\/td>\n<td>In microwells with barcoded magnetic beads (gravity); no clogging<\/td>\n<td>In oil-emulsion droplets with barcoded gel beads (microfluidics)<\/td>\n<\/tr>\n<tr>\n<td><em>Capture Options<\/em><\/td>\n<td>8 lanes per cartridge; charged by lanes used<\/td>\n<td>8 wells per chip; charged for whole chip<\/td>\n<\/tr>\n<tr>\n<td><em>Cell Type Compatibility<\/em><\/td>\n<td>Effective for most cell types; gentle capture preserves fragile cells<\/td>\n<td>Effective for most cell types; less optimal for fragile cells<\/td>\n<\/tr>\n<tr>\n<td><em>Pre-library Capture Validation\/QC<\/em><\/td>\n<td>Integrated imaging quantifies wells with single viable cells + bead<\/td>\n<td>None<\/td>\n<\/tr>\n<tr>\n<td>\u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 &#8211;<\/td>\n<td>\u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0&#8211;<\/td>\n<td>\u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 &#8211;<\/td>\n<\/tr>\n<tr>\n<td><em><strong>Workflow Options<\/strong><\/em><\/td>\n<td><strong>BD Rhapsody HT Xpress<\/strong><\/td>\n<td><strong>10x Chromium X<\/strong><\/td>\n<\/tr>\n<tr>\n<td><em>Sample Multiplexing<\/em><\/td>\n<td>Up to 24 samples per lane<\/td>\n<td>On-chip multiplexing (3&#8217;and 5&#8242;); in-line multiplexing (Flex)<\/td>\n<\/tr>\n<tr>\n<td><em>Multiplexing Method<\/em><\/td>\n<td>Oligo-tagged antibodies bind ubiquitous surface or nuclear markers<\/td>\n<td>Lipid-modified oligos integrate into cell membranes<\/td>\n<\/tr>\n<tr>\n<td><em>Maximum # cells to load<\/em><\/td>\n<td>100,000 per lane, 800,000 per cartridge<\/td>\n<td>20,000 per sample, 160,000 per chip<\/td>\n<\/tr>\n<tr>\n<td>\u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0&#8211;<\/td>\n<td>\u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0&#8211;<\/td>\n<td>\u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0&#8211;<\/td>\n<\/tr>\n<tr>\n<td><em><strong>Assay Types<\/strong><\/em><\/td>\n<td><strong>BD Rhapsody HT Xpress<\/strong><\/td>\n<td><strong>10x Chromium X<\/strong><\/td>\n<\/tr>\n<tr>\n<td><em>mRNA WTA<\/em><\/td>\n<td>Whole Transcriptome Analysis (WTA): add link<\/td>\n<td><a href=\"https:\/\/www.10xgenomics.com\/products\/universal-three-prime-gene-expression\" target=\"_blank\" rel=\"noopener\"><b>Universal 3&#8242; Gene Expression<\/b><\/a><\/td>\n<\/tr>\n<tr>\n<td><em>Targeted Gene Expression<\/em><\/td>\n<td>~400 human or mouse genes: pre-configured or customizable<\/td>\n<td>NA<\/td>\n<\/tr>\n<tr>\n<td><em>Protein Expression<\/em><\/td>\n<td>AbSeq oligo-antibodies &#8211; surface &amp; intracellular (all assays)<\/td>\n<td>CITE-seq oligo-antibodies &#8211; surface (all assays) &amp; intracellular (Flex assay only)<\/td>\n<\/tr>\n<tr>\n<td><em>Immune Profiling<\/em><\/td>\n<td><a href=\"https:\/\/www.bdbiosciences.com\/en-ca\/products\/reagents\/single-cell-multiomics\/bd-rhapsody-tcr-bcr-next-multiomic-assays\" target=\"_blank\" rel=\"noopener\">WTA+ full-length TCRA, TCRB, TCRG, TCRD, IGHM, IGK, IGL<\/a><\/td>\n<td><a href=\"https:\/\/www.10xgenomics.com\/products\/universal-five-prime-gene-expression\" target=\"_blank\" rel=\"noopener\">5&#8242; gene expression + full-length TCRA, TCRB, IGHM, IGK, IGL<\/a><\/td>\n<\/tr>\n<tr>\n<td><em>ATACseq (nuclei)<\/em><\/td>\n<td><a href=\"https:\/\/www.bdbiosciences.com\/en-ca\/products\/reagents\/single-cell-multiomics\/bd-rhapsody-atac-seq-assays\" target=\"_blank\" rel=\"noopener\">WTA + chromatin accessability, optional sample multiplexing (up to 6 samples)<\/a><\/td>\n<td><a href=\"https:\/\/www.10xgenomics.com\/products\/epi-multiome\" target=\"_blank\" rel=\"noopener\">Chromatin accessability only or 3&#8242; gene expression + chromatin accessability<\/a><\/td>\n<\/tr>\n<tr>\n<td><em>Fixed Cell Assay<\/em><\/td>\n<td>NA<\/td>\n<td><a href=\"https:\/\/www.10xgenomics.com\/products\/flex-gene-expression\" target=\"_blank\" rel=\"noopener\">Flex: Probe-based gene expression; optional cell surface and\/or intracellular protein<\/a><\/td>\n<\/tr>\n<tr>\n<td>\u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 &#8211;<\/td>\n<td>\u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 &#8211;<\/td>\n<td>\u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0&#8211;<\/td>\n<\/tr>\n<tr>\n<td><em><strong>Data Analysis<\/strong><\/em><\/td>\n<td><strong>BD Rhapsody HT Xpress<\/strong><\/td>\n<td><strong>10x Chromium X<\/strong><\/td>\n<\/tr>\n<tr>\n<td><em>Pre-Processing<\/em><\/td>\n<td>BD pipeline (SevenBridges) &amp;<\/td>\n<td>10x pipelines (e.g., Cell Ranger, Loupe Browser)<\/td>\n<\/tr>\n<tr>\n<td><em>Analysis<\/em><\/td>\n<td>BD Cellismo data visualizaton tool, R\/Python<\/td>\n<td>R\/Python<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<\/div><\/div><\/div><\/div><div class=\"fusion-fullwidth fullwidth-box fusion-builder-row-3 nonhundred-percent-fullwidth non-hundred-percent-height-scrolling\" style=\"--awb-border-radius-top-left:0px;--awb-border-radius-top-right:0px;--awb-border-radius-bottom-right:0px;--awb-border-radius-bottom-left:0px;--awb-flex-wrap:wrap;\" ><\/div><\/p>\n","protected":false},"excerpt":{"rendered":"","protected":false},"author":2,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-6","page","type-page","status-publish","hentry"],"yoast_head":"<!-- This site is optimized with the Yoast SEO Premium plugin v27.0 (Yoast SEO v27.0) - https:\/\/yoast.com\/product\/yoast-seo-premium-wordpress\/ -->\n<title>Rhapsody scRNA-seq | CASCA | SickKids<\/title>\n<meta name=\"description\" content=\"CASCA offers services on our Becton Dickinson\u2019s Rhapsody Multi-omics platform for combined single cell RNA-Seq and protein analysis.\" \/>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, 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