Spatial Sample guidelines
Supported tissues: Here you can find the supported protocols for FFPE and Fresh Frozen (FF) sample preparation. Alternatively, fixed tissue embedded in OCT (Fixed Frozen FXF) can also be processed but is not supported by 10X Genomics. Ensure that your FFPE tissue has been properly fixed, PFA fixation should not exceed 24 hours at 4 oC.
Tissue placement: The capture area of the Xenium slide is 10 x 22 mm. Avoid covering the fiducials with tissue as this risks failures to initiate Xenium Analyzer run. We strongly recommend to practice tissue placement on a blank slide.
Slide storage after tissue placement: After drying, slides containing FFPE tissue can be stored in a desiccator at room temperature for up to 4 weeks. Slides containing FF tissue can be stored at -80°C in a sealed slide mailer for up to 4 weeks.
Tissue slides should be free of wrinkles, folds, air bubbles or cracks.
Quality controls: When performing 5K prime Xenium, the following is required:
1. DV200 test to assess RNA integrity. This should be greater than 30%.
2. On a separate slide, perform an H&E stain and check for tissue artefacts such as: cracks, hemorrhaging and/or improper fixation.
3. On a separate slide, perform a DAPI stain and look for punctate nuclei that are clearly defined.
Supported tissues: Visium HD is a whole transcriptome probe-based gene expression assay compatible with FFPE, Fresh Frozen (FF), & Fixed Frozen tissue (FxF) sections. Here you can find the tested FFPE, FF and FxF and tissues.
Prior to section placement, draw an outline of the allowable area on the back of the blank slide to ensure downstream compatibility. Use slides recommended by 10X
Each Visium HD slide has 2 capture areas of 6.5 x 6.5 mm. When submitting samples to LGTC use a thin marker to annotate your area of interest on the back side of the tissue slide. One tissue slide is required per capture area.
Slide storage after tissue placement: After drying, slides containing FFPE tissue can be stored at 4°C in a desiccator for up to 6 months. Slides containing Fresh Frozen or Fixed frozen (FxF) can be store at -80 oC for up to 2 months.
Imaging guidelines: Follow the H&E or IF imaging guidelines accordingly. When performing IF staining optimization of the antibody concentration is required.
Quality controls:
1. DV200 test to assess RNA integrity. This should be greater than 30%. FFPE and FF kit
2. On a separate slide, perform an H&E stain and check for tissue artefacts such as: cracks, hemorrhaging and/or improper fixation (optional).
3. On a separate slide, perform a DAPI stain and look for punctate nuclei that are clearly defined (optional).
Post-Xenium Staining: H&E and IF staining are supported by 10X, samples should be stain within 3 days after the Xenium run.
Post-Xenium Visum HD: read technical note