The Iowa NeuroBank Core has been offering 10x Genomics' Visium Spatial Transcriptomics Service and being part of 10X's Visium Enabled Program (VEP) since 2021.
We have successfully processed brain, eye, kidney, heart, soft knee tissue, and tail bone across species (human, macaque, mouse, rabbit, and C. elegans) on various Visium platforms for internal and external investigators.
When all the samples are available, please contact the Core prior to coordinate timing of availability.
Features:
Flexible Starting Material: blocks or slides with broad range of RNA quality
Standard (6.5 mm x 6.5 mm) and larger capture area (11 mm x 11 mm) slides to get more data
The spatial resolution of Visium is based on the 2-micron squares or 55-micron spot sizes, providing an average resolution of 1 to 10 cells per spot.
Probe-based Visium platforms: The spatial barcode assigned to the spot is incorporated during cDNA synthesis and enables gene expression data to be mapped back to its location within the tissue. Fastq Data can be processed with the 10X SpaceRanger analysis software, visualized with the Loupe Browser software, and analyzed with the Partek Flow software.
Sample requirements and workflow for Spatial Gene Expression Analysis:
Fresh Frozen Tissue
Schedule a consultation meeting with us
Freshly obtained tissue should be snap frozen to prevent RNA degradation.
The recommended freezing method uses an isopentane and liquid nitrogen bath (equipment available in the Core)
RNA quality of the tissue block should be assessed prior to sectioning
Submit your frozen tissue samples for QC (RNA extraction service available in the Core)
Section your frozen blocks for tissue optimization from each new tissue type for a lab prior to scheduling a Visium GEX appointment.
Check that the morphology of the 10- µm sections is good enough for cell type annotations. This can be assessed by H&E staining on the SuperFrost Plus Slides.
Schedule a time to submit your Visium slides with frozen sections
Sample and Data Transfer for QC, library construction, sequencing, and data analysis.
FFPE and Fixed Frozen Tissue
Species Specific – only human and mouse samples currently supported
Schedule a consultation meeting with us
Submit your frozen tissue sample for QC (DV200 > 30%; percentage of fragments >200 nucleotides)
Section your FFPE blocks
Schedule a time to submit your Visium slide with FFPE sections
Deparaffinization, Staining, Imaging, Decrosslinking, CytAssist, Re-imaging, Probe Hybridization (18,000 human and 21,000 mouse genes), Ligation, Library Construction Permeabilization, cDNA Synthesis, purification, QC
Sample and Data Transfer for Sequencing and data analysis.
Important Disclaimers (Must read and accept prior to use of core)
Visium is a cutting-edge whole transcriptome spatial profiling platform. Due to its high-risk nature, we cannot guarantee a successful outcome with each Visium experiment. We also cannot guarantee any specific metrics due to the high variability of these values across tissues, species, collection methods, processing protocols, reagent batches, morphology, and RNA quality.
To prevent poor experimental outcomes, we require users to H&E stain each sample and submit the scanned images to the core. We also suggest performing RNA extraction and QC (RIN and DV200) of tissue scrolls. We can offer the QC services to analyze tissue blocks as a part of optimization and pilot study to notify the investigator prior to proceeding with the spatial omics experiment of any indications of poor tissue quality. Positive results from these t preliminary quality measures of RNA and morphology will not guarantee success, but they function to eliminate samples with a heightened risk of failure. At this point the investigator and PI will have the choice to proceed with risk or cancel the run.
