Spatial Technology

YCGA offers four different platforms for spatial gene expression and Epigenetic state analysis. Spatial technologies aim to assay single cells' genomic and epigenetic information within their native tissue environment. It unravels epigenomic and transcriptomics at single-cell resolution with positional information and cell-cell interaction properties with tissue and cellular heterogeneity. YCGA is offering four different platforms: Xenium (10X Genomics), CosMx (Nanostring), CurioSeeker (Curio), and spatial ATAC-Seq (AtlasXomics)

1. Fresh frozen only
2. 10 uM section thickness
3. Cover sample section with CryoCube or Blank OCT section (30uM)
4. Deliver on dry ice.
5. Slides in mailer sealed with parafilm.
6. Place the mailer in a secondary bag with desiccant packs.
7. Samples must be processed within 4 days of sectioning.

1. Must use specialized Xenium slides.
2. Fresh Frozen
   1. 10 uM section thickness
   2. Deliver on dry ice.
3. FFPE
   1. 5 uM section thickness
   2. Deliver on wet ice or cold packs.
4. Slides in mailer sealed with parafilm.
5. Place the mailer in a secondary bag with desiccant packs.
6. Samples must be processed within 30 days of sectioning.

1. Must use only the following slides:
   1. Leica BOND Plus slides - S21.2113.A
   2. VWR Superfrost Plus Micro Slide, Premium - 48311-703
2. Fresh Frozen
   1. 5 uM section thickness (May section up to 10 uM but instrument only scans the closest 5uM of tissue)
   2. Deliver on dry ice.
3. FFPE
   1. 5 uM section thickness
   2. Deliver on wet ice or cold packs.
4. Slides in mailer sealed with parafilm.
5. Place the mailer in a secondary bag with desiccant packs.
6. Samples must be processed within 15 days of sectioning.

1. Standard 1x3” pathology slides
   1. Poly-L-Lysine (PLL) coated slides (Thermo Fisher Scientific)
   2. Superfrost Plus slides (Thermo Fisher Scientific)
2. Fresh frozen tissue only
3. 7-10 uM section thickness
4. Deliver on dry ice.
5. Slides in mailer sealed with parafilm.
6. Place the mailer in a secondary bag with desiccant packs.

Xenium is an in-situ solution for subcellular profiling hundreds of RNA targets, revealing new insights into cellular structure and function. Xenium In Situ provides highly sensitive, targeted gene expression information at subcellular resolution for hundreds of RNA targets in fresh frozen (FF) and formalin-fixed & paraffin-embedded (FFPE) tissue. Xenium is an automated in situ platform that performs successive rounds of fluorescent probe hybridization, imaging, and probe removal to generate an optical signature for each transcript. Primary analysis to decode image data to transcripts and secondary analysis to segment cells and assign transcripts is performed automatically, directly on the instrument. Data can be viewed using Xenium Explorer. The imaging area is 12 x 24 mm. Curated targeted gene panels (maximum of 2000 genes) with custom capabilities are used for transcript analysis. Imaging is done on a special slide. Slides are suitable for post-run staining, including Immunofluorescence.

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CosMx SMI is a high-plex in situ analysis platform that provides spatial transcriptomics with fresh frozen (FF) and formalin-fixed paraffin-embedded (FFPE) tissue samples at cellular and subcellular resolution. CosMx SMI enables quantification and visualization of up to 6,000 RNA with custom capabilities and 120 validated protein analytes at single-cell resolution for deeper insights leading to cell atlas, tissue phenotyping, cell-cell interactions, cellular processes, and biomarker discovery. Primary data analysis is done using the paid software AtoMX. The scannable area is 300mm2 and doesn’t need any special slide.

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CurioSeeker is an instrument-free spatial mapping tool that enables whole spatial transcriptome mapping of fresh frozen tissue using next-generation sequencing (NGS). The CurioSeeker tile preserves spatial information by capturing RNA on a monolayer of tightly packed, 10 µm beads. This doesn’t require any pre-designed or custom panel. Hence, it is amenable to a wide range of tissues and species with no optimization required. CurioSeeker is available in two different slide configurations with a scannable area of 3X3 mm and 10X10 mm, respectively.

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YCGA offers spatial Epigenomics service using the Atlasxomics platform. This platform is based on DBiT-seq. DBiT-seq combines microfluidics and Next-Generation Sequencing (NGS) to generate high-quality spatial data. We are currently offering Spatial ATAC-Seq and cut-&-tag assays on this platform.

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