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submission:10x_visium [2025/02/13 18:01] – [Individual Sample Information] Bioinformatics service adminsubmission:10x_visium [2025/02/14 14:53] (current) – [Overview of the Visium & Visium HD workflows] Ania Piskorz
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  10X Visium samples are processed across both the Histopathology and Genomics cores, so prior to submission, please do contact [[singlecell@cruk.cam.ac.uk|Single Cell Team]]  [[histopathology@cruk.cam.ac.uk|Histology]]  10X Visium samples are processed across both the Histopathology and Genomics cores, so prior to submission, please do contact [[singlecell@cruk.cam.ac.uk|Single Cell Team]]  [[histopathology@cruk.cam.ac.uk|Histology]]
  
-We would also recommend arranging to discuss your experimental aims with both teams by discussing this at a experimental design meeting (EDM):+We would recommend arranging to discuss your experimental aims with both teams by discussing this at a experimental design meeting (EDM):
 [[experimentaldesign@cruk.cam.ac.uk|Request EDM Here]] [[experimentaldesign@cruk.cam.ac.uk|Request EDM Here]]
-=====Overview of the Visium workflows=====+=====Overview of the Visium & Visium HD workflows===== 
 +Visium provides a whole transcriptome snapshot of gene expression across a tissue section, allowing you to identify spatial patterns of gene expression within different cell types and tissue regions. With Visium HD a significantly higher resolution is achievable essentially providing "single-cell scale" analysis by capturing gene expression data within very small, densely packed regions of a tissue section when compared to the larger spatial bins of "standard" (SD) Visium (1-10cells).  
 + 
 +{{:submission:vishd1.png?800|}} 
 {{:visium_workflow2j.png?920|}} {{:visium_workflow2j.png?920|}}
  
 =====Visium options available===== =====Visium options available=====
 ^Workflow ^Kit Used ^Slide used for submission ^Method of mRNA capture ^Spot-based array | ^Workflow ^Kit Used ^Slide used for submission ^Method of mRNA capture ^Spot-based array |
-|**Visium HD** (FFPE) \\ |Visium HD slide & Cassette, Visium HD reagent kit, Visium Human or mouse probe kit|6.5 x6.5mm section fixed on a regular superfrost slide|Whole transcriptome probe capture (Human & Mouse probe kits available)|Spot size: 2um or binned in 8uM| +|**Visium HD** (FFPE) \\ |Visium HD slide & Cassette, Visium HD reagent kit, Visium Human or mouse probe kit|6.5 x6.5mm section fixed on a regular superfrost slide|Whole transcriptome probe capture \\ (Human & Mouse probe kits available)|lawn of 2um, recommended bin size for analysis 8uM, single cell resolution| 
-|**Visium HD** (fresh frozen)\\ |Visium HD Slide & Cassette, Visium HD reagent kit, Visium Human or Mouse Probe Kit|6.5 x6.5mm section fixed on a regular superfrost slide|Whole Transcriptome probe capture (Human & Mouse probe kits avalible)|Spot size: 2um or binned in 8uM| +|**Visium HD**\\ (fresh frozen)|Visium HD Slide & Cassette, Visium HD reagent kit, Visium Human or Mouse Probe Kit|6.5 x6.5mm section fixed on a regular superfrost slide|Whole Transcriptome probe capture \\ (Human & Mouse probe kits available)|lawn of 2um, recommended bin size for analysis 8uM, single cell resolution| 
-|**Visium CytAssist**\\ (FFPE)|Visium Slide & cassette, FFPE Reagent Kit, Probe Kit|FFPE tissue section of either 11 x 11 mm or 6.5 x 6.5mm in area, fixed onto regular superfrost slide|Whole Transcriptome probe capture (Human & Mouse probe kits available)|Spot size 55um\\ 11 x 11mm 14000 spots\\ 6.5mm x 6.5mm 5000 spots| +|**Visium CytAssist**\\ (FFPE)|Visium Slide & cassette, FFPE Reagent Kit, Probe Kit|FFPE tissue section of either 11 x 11 mm or 6.5 x 6.5mm in area, fixed onto regular superfrost slide|Whole Transcriptome probe capture\\ (Human & Mouse probe kits available)|Spot size 55um\\ 11 x 11mm 14000 spots\\ 6.5mm x 6.5mm 5000 spots, average 1-10 cells resolution| 
-|**Visium CytAssist**\\ (Fresh Frozen)|Visium Slide & cassette, FFPE Reagent Kit, Probe Kit|Fresh tissue section of either 11 x 11mm or 6.5 x 6.5 mm in area, fixed onto regular superfrost slide|Whole Transcriptome probe capture (Human & Mouse probe kits available)|Spot size 55um\\ 11 x 11mm 14000 spots\\ 6.5mm x 6.5mm 5000 spots| +|**Visium CytAssist**\\ (Fresh Frozen)|Visium Slide & cassette, FFPE Reagent Kit, Probe Kit|Fresh tissue section of either 11 x 11mm or 6.5 x 6.5 mm in area, fixed onto regular superfrost slide|Whole Transcriptome probe capture \\ (Human & Mouse probe kits available)|Spot size 55um\\ 11 x 11mm 14000 spots\\ 6.5mm x 6.5mm 5000 spots, average 1-10 cells resolution| 
-|**Visium Spatial Gene Expression Manual**\\ (FFPE)|Visium Spatial Gene Expression Slide Kit, Visium FFPE Reagent Kit, Probe Kit|4 capture areas available for tissue sections 6.5 x 6.5mm in area, fixed onto a spatial gene expression slide (provided by 10X) |Whole Transcriptome probe capture (Human & Mouse probe kits available)|Spot size: each capture area has ~5000 spots| +|**Visium Spatial Gene Expression Manual**\\ (FFPE)|Visium Spatial Gene Expression Slide Kit, Visium FFPE Reagent Kit, Probe Kit|4 capture areas available for tissue sections 6.5 x 6.5mm in area, fixed onto a spatial gene expression slide\\ (**provided by 10X**) |Whole Transcriptome probe capture \\ (Human & Mouse probe kits available)|Spot size: each capture area has ~5000 spots, average 1-10 cells resolution| 
-|**Visium Spatial Gene Expression Manual**\\ (Fresh Frozen)|Visium Spatial Gene Expression Slide & Kit, Probe Kit|4 capture areas available for tissue sections 6.5 x 6.5mm in area, fixed onto a spatial gene expression slide (provided by 10X) |Poly(A) tail capture |Spot size: each capture area has ~5000 spots| +|**Visium Spatial Gene Expression Manual**\\ (Fresh Frozen)|Visium Spatial Gene Expression Slide & Kit, Probe Kit|4 capture areas available for tissue sections 6.5 x 6.5mm in area, fixed onto a spatial gene expression slide\\ (**provided by 10X**) |Poly(A) tail capture |Spot size: each capture area has ~5000 spots, average 1-10 cells resolution| 
-|**Visium CytAssist Spatial Gene & Protein Expression**|Visium Slide & Cassette, FFPE Reagent Kit, Probe Kit, Immune Cell Profiling Panel, Add on antibodies (if applicable), Visium Protein Core Reagents (CITE-Seq)|FFPE tissue section of either 6.5 x 6.5mm in area, fixed onto regular superfrost slide|Whole Transciptome probe capture (Human & Mouse probe kits available) |Spot size: 11 x 11mm 14000 spots\\ 6.5mm x 6.5mm 5000 spots|+|**Visium CytAssist Spatial Gene & Protein Expression**|Visium Slide & Cassette, FFPE Reagent Kit, Probe Kit, Immune Cell Profiling Panel, Add on antibodies (if applicable), Visium Protein Core Reagents (CITE-Seq)|FFPE tissue section of either 6.5 x 6.5mm in area, fixed onto regular superfrost slide|Whole Transciptome probe capture \\ (Human & Mouse probe kits available) |Spot size: 11 x 11mm 14000 spots\\ 6.5mm x 6.5mm 5000 spots, average 1-10 cells resolution|
  
 Make sure you provide additional H&E section or electronic version of H&E image with marked area of interest (ROI) according to the selected workflow (11 x 11mm or 6.5 x 6.5mm) to guide placement of the gasket and the alignment of the superfrost slide against the Visium slide capture array. Make sure you provide additional H&E section or electronic version of H&E image with marked area of interest (ROI) according to the selected workflow (11 x 11mm or 6.5 x 6.5mm) to guide placement of the gasket and the alignment of the superfrost slide against the Visium slide capture array.