BioMicroCenter:SpTx - Revision history

Asoberan: Remove stale pricing/workflow language from AVITI24 beta banner and pricing paragraph

2026-03-24T19:47:10Z

Remove stale pricing/workflow language from AVITI24 beta banner and pricing paragraph

← Older revision		Revision as of 19:47, 24 March 2026
Line 124:		Line 124:

	== AVITI24 CYTOPROFILING & IN SITU SEQUENCING ==		== AVITI24 CYTOPROFILING & IN SITU SEQUENCING ==
	<div style="background:#fff8e6; border-left:4px solid #c8960c; padding:8px 12px; margin-bottom:12px;">'''Beta Service — Early Access:''' The AVITI24 Teton CytoProfiling and DISS services at the BioMicro Center are operational but not yet routine~~. Parameters, pricing, and workflows are still being established~~. '''Consultation with BMC staff is required before submitting samples.'''</div>		<div style="background:#fff8e6; border-left:4px solid #c8960c; padding:8px 12px; margin-bottom:12px;">'''Beta Service — Early Access:''' The AVITI24 Teton CytoProfiling and DISS services at the BioMicro Center are operational but not yet routine. '''Consultation with BMC staff is required before submitting samples.'''</div>
	<!-- placeholder image left: AVITI24 instrument photo or Teton CytoProfiling schematic -->		<!-- placeholder image left: AVITI24 instrument photo or Teton CytoProfiling schematic -->
	<!-- replace with: [[File:AVITI24_instrument.png\|thumb\|left\|400px]] -->		<!-- replace with: [[File:AVITI24_instrument.png\|thumb\|left\|400px]] -->
Line 227:		Line 227:
	<BR><BR>		<BR><BR>
	'''Pricing'''<BR>		'''Pricing'''<BR>
	~~Pricing for AVITI24 Teton CytoProfiling and DISS is not yet finalized.~~ See [[BioMicroCenter:Pricing]] for ~~updates as~~ pricing ~~is established~~. Sequencing-only runs on the AVITI24 are charged at standard AVITI24 sequencing rates.		See [[BioMicroCenter:Pricing\|BioMicroCenter:Pricing]] → Single Cell & Spatial Services → AVITI24 for current pricing. Sequencing-only runs on the AVITI24 are charged at standard AVITI24 sequencing rates.
	<BR><BR>		<BR><BR>
	'''Service Status'''<BR>		'''Service Status'''<BR>

Slevine: /* 10X VISIUM HD */

2026-03-22T20:24:29Z

10X VISIUM HD

← Older revision		Revision as of 20:24, 22 March 2026
Line 6:		Line 6:
	{\| width="100%"		{\| width="100%"
	\|-		\|-
	\| ~~colspan~~="2" \|		\|style="width: 200px;"\|
	[[File:VisiumHD_workflow_slide.jpg\|left\|250px\|Workflow and capture areas for Visium HD]]		[[File:VisiumHD_workflow_slide.jpg\|left\|250px\|Workflow and capture areas for Visium HD]]
	<div style="clear:both; padding-top:4px; font-size:12px; color:#555;">Workflow and capture areas for Visium HD</div>		<div style="clear:both; padding-top:4px; font-size:12px; color:#555;">Workflow and capture areas for Visium HD</div>
	\|-		\|
	~~\| colspan="2"~~ \|
	[https://www.10xgenomics.com/products/visium-hd-spatial-gene-expression 10x Visium HD] is a spatial transcriptomics platform that profiles whole-transcriptome gene expression across intact tissue sections at single-cell-scale resolution. Tissue sections are processed through the CytAssist instrument, which transfers RNA complexes onto a capture slide containing a continuous array of 3,000,000 spatially barcoded 2 µm squares covering a 6.5 × 6.5 mm capture area (~0.65 cm²). Two chemistries are available: a probe-based assay for human and mouse (FF, FxF, and FFPE), and a polyA-based assay (Visium HD 3') for fresh frozen tissue from any species. H&E or immunofluorescence (IF) staining can be performed prior to processing for protein co-detection.		[https://www.10xgenomics.com/products/visium-hd-spatial-gene-expression 10x Visium HD] is a spatial transcriptomics platform that profiles whole-transcriptome gene expression across intact tissue sections at single-cell-scale resolution. Tissue sections are processed through the CytAssist instrument, which transfers RNA complexes onto a capture slide containing a continuous array of 3,000,000 spatially barcoded 2 µm squares covering a 6.5 × 6.5 mm capture area (~0.65 cm²). Two chemistries are available: a probe-based assay for human and mouse (FF, FxF, and FFPE), and a polyA-based assay (Visium HD 3') for fresh frozen tissue from any species. H&E or immunofluorescence (IF) staining can be performed prior to processing for protein co-detection.
	<BR><BR>		<BR><BR>
Line 91:		Line 90:

	=== 10X Visium HD ===		=== 10X Visium HD ===
	[[File:VisiumHD_loupe_example.jpg\|thumb\|right\|~~500px~~\|Example of FF data from Visium HD]]		[[File:VisiumHD_loupe_example.jpg\|thumb\|right\|350px\|Example of FF data from Visium HD]]

	'''FAQs for Users'''<BR>		'''FAQs for Users'''<BR>
Line 123:		Line 122:

	\|}		\|}

	== AVITI24 CYTOPROFILING & IN SITU SEQUENCING ==		== AVITI24 CYTOPROFILING & IN SITU SEQUENCING ==
	<div style="background:#fff8e6; border-left:4px solid #c8960c; padding:8px 12px; margin-bottom:12px;">'''Beta Service — Early Access:''' The AVITI24 Teton CytoProfiling and DISS services at the BioMicro Center are operational but not yet routine. Parameters, pricing, and workflows are still being established. '''Consultation with BMC staff is required before submitting samples.'''</div>		<div style="background:#fff8e6; border-left:4px solid #c8960c; padding:8px 12px; margin-bottom:12px;">'''Beta Service — Early Access:''' The AVITI24 Teton CytoProfiling and DISS services at the BioMicro Center are operational but not yet routine. Parameters, pricing, and workflows are still being established. '''Consultation with BMC staff is required before submitting samples.'''</div>

Asoberan: Stack Visium HD workflow image above intro text using full-width table row

2026-03-22T20:22:06Z

Stack Visium HD workflow image above intro text using full-width table row

← Older revision		Revision as of 20:22, 22 March 2026
Line 4:		Line 4:

	== 10X VISIUM HD ==		== 10X VISIUM HD ==
	[[File:VisiumHD_workflow_slide.jpg~~\|thumb~~\|left\|250px\|Workflow and capture areas for Visium HD]]		{\| width="100%"
			\|-
			\| colspan="2" \|
			[[File:VisiumHD_workflow_slide.jpg\|left\|250px\|Workflow and capture areas for Visium HD]]
			<div style="clear:both; padding-top:4px; font-size:12px; color:#555;">Workflow and capture areas for Visium HD</div>
			\|-
			\| colspan="2" \|
	[https://www.10xgenomics.com/products/visium-hd-spatial-gene-expression 10x Visium HD] is a spatial transcriptomics platform that profiles whole-transcriptome gene expression across intact tissue sections at single-cell-scale resolution. Tissue sections are processed through the CytAssist instrument, which transfers RNA complexes onto a capture slide containing a continuous array of 3,000,000 spatially barcoded 2 µm squares covering a 6.5 × 6.5 mm capture area (~0.65 cm²). Two chemistries are available: a probe-based assay for human and mouse (FF, FxF, and FFPE), and a polyA-based assay (Visium HD 3') for fresh frozen tissue from any species. H&E or immunofluorescence (IF) staining can be performed prior to processing for protein co-detection.		[https://www.10xgenomics.com/products/visium-hd-spatial-gene-expression 10x Visium HD] is a spatial transcriptomics platform that profiles whole-transcriptome gene expression across intact tissue sections at single-cell-scale resolution. Tissue sections are processed through the CytAssist instrument, which transfers RNA complexes onto a capture slide containing a continuous array of 3,000,000 spatially barcoded 2 µm squares covering a 6.5 × 6.5 mm capture area (~0.65 cm²). Two chemistries are available: a probe-based assay for human and mouse (FF, FxF, and FFPE), and a polyA-based assay (Visium HD 3') for fresh frozen tissue from any species. H&E or immunofluorescence (IF) staining can be performed prior to processing for protein co-detection.
	<BR><BR>		<BR><BR>
			\|}

	{\|		{\|

Asoberan: Resize images: workflow 250px, Boyer cardiomyocytes 300px

2026-03-22T20:19:01Z

Resize images: workflow 250px, Boyer cardiomyocytes 300px

← Older revision		Revision as of 20:19, 22 March 2026
Line 4:		Line 4:

	== 10X VISIUM HD ==		== 10X VISIUM HD ==
	[[File:VisiumHD_workflow_slide.jpg\|thumb\|left\|~~400px~~\|Workflow and capture areas for Visium HD]]		[[File:VisiumHD_workflow_slide.jpg\|thumb\|left\|250px\|Workflow and capture areas for Visium HD]]

	[https://www.10xgenomics.com/products/visium-hd-spatial-gene-expression 10x Visium HD] is a spatial transcriptomics platform that profiles whole-transcriptome gene expression across intact tissue sections at single-cell-scale resolution. Tissue sections are processed through the CytAssist instrument, which transfers RNA complexes onto a capture slide containing a continuous array of 3,000,000 spatially barcoded 2 µm squares covering a 6.5 × 6.5 mm capture area (~0.65 cm²). Two chemistries are available: a probe-based assay for human and mouse (FF, FxF, and FFPE), and a polyA-based assay (Visium HD 3') for fresh frozen tissue from any species. H&E or immunofluorescence (IF) staining can be performed prior to processing for protein co-detection.		[https://www.10xgenomics.com/products/visium-hd-spatial-gene-expression 10x Visium HD] is a spatial transcriptomics platform that profiles whole-transcriptome gene expression across intact tissue sections at single-cell-scale resolution. Tissue sections are processed through the CytAssist instrument, which transfers RNA complexes onto a capture slide containing a continuous array of 3,000,000 spatially barcoded 2 µm squares covering a 6.5 × 6.5 mm capture area (~0.65 cm²). Two chemistries are available: a probe-based assay for human and mouse (FF, FxF, and FFPE), and a polyA-based assay (Visium HD 3') for fresh frozen tissue from any species. H&E or immunofluorescence (IF) staining can be performed prior to processing for protein co-detection.
Line 199:		Line 199:

	=== AVITI24 Teton CytoProfiling at BMC ===		=== AVITI24 Teton CytoProfiling at BMC ===
	[[File:AVITI24_Boyer_cardiomyocytes.jpg\|thumb\|right\|~~500px~~\|Cytoprofiling of cardiomyocytes. Collaboration with the Boyer Lab.]]		[[File:AVITI24_Boyer_cardiomyocytes.jpg\|thumb\|right\|300px\|Cytoprofiling of cardiomyocytes. Collaboration with the Boyer Lab.]]

	'''About the Service'''<BR>		'''About the Service'''<BR>

Asoberan: Update image references from .png to .jpg to match uploaded files

2026-03-22T20:16:37Z

Update image references from .png to .jpg to match uploaded files

← Older revision		Revision as of 20:16, 22 March 2026
Line 4:		Line 4:

	== 10X VISIUM HD ==		== 10X VISIUM HD ==
	[[File:VisiumHD_workflow_slide.~~png~~\|thumb\|left\|400px\|Workflow and capture areas for Visium HD]]		[[File:VisiumHD_workflow_slide.jpg\|thumb\|left\|400px\|Workflow and capture areas for Visium HD]]

	[https://www.10xgenomics.com/products/visium-hd-spatial-gene-expression 10x Visium HD] is a spatial transcriptomics platform that profiles whole-transcriptome gene expression across intact tissue sections at single-cell-scale resolution. Tissue sections are processed through the CytAssist instrument, which transfers RNA complexes onto a capture slide containing a continuous array of 3,000,000 spatially barcoded 2 µm squares covering a 6.5 × 6.5 mm capture area (~0.65 cm²). Two chemistries are available: a probe-based assay for human and mouse (FF, FxF, and FFPE), and a polyA-based assay (Visium HD 3') for fresh frozen tissue from any species. H&E or immunofluorescence (IF) staining can be performed prior to processing for protein co-detection.		[https://www.10xgenomics.com/products/visium-hd-spatial-gene-expression 10x Visium HD] is a spatial transcriptomics platform that profiles whole-transcriptome gene expression across intact tissue sections at single-cell-scale resolution. Tissue sections are processed through the CytAssist instrument, which transfers RNA complexes onto a capture slide containing a continuous array of 3,000,000 spatially barcoded 2 µm squares covering a 6.5 × 6.5 mm capture area (~0.65 cm²). Two chemistries are available: a probe-based assay for human and mouse (FF, FxF, and FFPE), and a polyA-based assay (Visium HD 3') for fresh frozen tissue from any species. H&E or immunofluorescence (IF) staining can be performed prior to processing for protein co-detection.
Line 85:		Line 85:

	=== 10X Visium HD ===		=== 10X Visium HD ===
	[[File:VisiumHD_loupe_example.~~png~~\|thumb\|right\|500px\|Example of FF data from Visium HD]]		[[File:VisiumHD_loupe_example.jpg\|thumb\|right\|500px\|Example of FF data from Visium HD]]

	'''FAQs for Users'''<BR>		'''FAQs for Users'''<BR>
Line 199:		Line 199:

	=== AVITI24 Teton CytoProfiling at BMC ===		=== AVITI24 Teton CytoProfiling at BMC ===
	[[File:AVITI24_Boyer_cardiomyocytes.~~png~~\|thumb\|right\|500px\|Cytoprofiling of cardiomyocytes. Collaboration with the Boyer Lab.]]		[[File:AVITI24_Boyer_cardiomyocytes.jpg\|thumb\|right\|500px\|Cytoprofiling of cardiomyocytes. Collaboration with the Boyer Lab.]]

	'''About the Service'''<BR>		'''About the Service'''<BR>

Asoberan: Fix image filenames: remove BioMicroCenter: namespace prefix

2026-03-22T20:14:48Z

Fix image filenames: remove BioMicroCenter: namespace prefix

← Older revision		Revision as of 20:14, 22 March 2026
Line 4:		Line 4:

	== 10X VISIUM HD ==		== 10X VISIUM HD ==
	[[File~~:BioMicroCenter~~:VisiumHD_workflow_slide.png\|thumb\|left\|400px\|Workflow and capture areas for Visium HD]]		[[File:VisiumHD_workflow_slide.png\|thumb\|left\|400px\|Workflow and capture areas for Visium HD]]

	[https://www.10xgenomics.com/products/visium-hd-spatial-gene-expression 10x Visium HD] is a spatial transcriptomics platform that profiles whole-transcriptome gene expression across intact tissue sections at single-cell-scale resolution. Tissue sections are processed through the CytAssist instrument, which transfers RNA complexes onto a capture slide containing a continuous array of 3,000,000 spatially barcoded 2 µm squares covering a 6.5 × 6.5 mm capture area (~0.65 cm²). Two chemistries are available: a probe-based assay for human and mouse (FF, FxF, and FFPE), and a polyA-based assay (Visium HD 3') for fresh frozen tissue from any species. H&E or immunofluorescence (IF) staining can be performed prior to processing for protein co-detection.		[https://www.10xgenomics.com/products/visium-hd-spatial-gene-expression 10x Visium HD] is a spatial transcriptomics platform that profiles whole-transcriptome gene expression across intact tissue sections at single-cell-scale resolution. Tissue sections are processed through the CytAssist instrument, which transfers RNA complexes onto a capture slide containing a continuous array of 3,000,000 spatially barcoded 2 µm squares covering a 6.5 × 6.5 mm capture area (~0.65 cm²). Two chemistries are available: a probe-based assay for human and mouse (FF, FxF, and FFPE), and a polyA-based assay (Visium HD 3') for fresh frozen tissue from any species. H&E or immunofluorescence (IF) staining can be performed prior to processing for protein co-detection.
Line 85:		Line 85:

	=== 10X Visium HD ===		=== 10X Visium HD ===
	[[File~~:BioMicroCenter~~:VisiumHD_loupe_example.png\|thumb\|right\|500px\|Example of FF data from Visium HD]]		[[File:VisiumHD_loupe_example.png\|thumb\|right\|500px\|Example of FF data from Visium HD]]

	'''FAQs for Users'''<BR>		'''FAQs for Users'''<BR>
Line 199:		Line 199:

	=== AVITI24 Teton CytoProfiling at BMC ===		=== AVITI24 Teton CytoProfiling at BMC ===
	[[File~~:BioMicroCenter~~:AVITI24_Boyer_cardiomyocytes.png\|thumb\|right\|500px\|Cytoprofiling of cardiomyocytes. Collaboration with the Boyer Lab.]]		[[File:AVITI24_Boyer_cardiomyocytes.png\|thumb\|right\|500px\|Cytoprofiling of cardiomyocytes. Collaboration with the Boyer Lab.]]

	'''About the Service'''<BR>		'''About the Service'''<BR>

Asoberan: Add Visium HD workflow, loupe example, and AVITI24 Boyer cardiomyocyte images

2026-03-22T20:13:16Z

Add Visium HD workflow, loupe example, and AVITI24 Boyer cardiomyocyte images

← Older revision		Revision as of 20:13, 22 March 2026
Line 4:		Line 4:

	== 10X VISIUM HD ==		== 10X VISIUM HD ==
	~~<!-- placeholder image left: 10X Visium HD array diagram showing 2um spots, 6.5x6.5mm capture area, workflow overview -->~~		[[File:BioMicroCenter:VisiumHD_workflow_slide.png\|thumb\|left\|400px\|Workflow and capture areas for Visium HD]]
	~~<!-- replace with:~~ [[File:~~VisiumHD_array_diagram~~.png\|thumb\|left\|400px]] ~~-->~~

	[https://www.10xgenomics.com/products/visium-hd-spatial-gene-expression 10x Visium HD] is a spatial transcriptomics platform that profiles whole-transcriptome gene expression across intact tissue sections at single-cell-scale resolution. Tissue sections are processed through the CytAssist instrument, which transfers RNA complexes onto a capture slide containing a continuous array of 3,000,000 spatially barcoded 2 µm squares covering a 6.5 × 6.5 mm capture area (~0.65 cm²). Two chemistries are available: a probe-based assay for human and mouse (FF, FxF, and FFPE), and a polyA-based assay (Visium HD 3') for fresh frozen tissue from any species. H&E or immunofluorescence (IF) staining can be performed prior to processing for protein co-detection.		[https://www.10xgenomics.com/products/visium-hd-spatial-gene-expression 10x Visium HD] is a spatial transcriptomics platform that profiles whole-transcriptome gene expression across intact tissue sections at single-cell-scale resolution. Tissue sections are processed through the CytAssist instrument, which transfers RNA complexes onto a capture slide containing a continuous array of 3,000,000 spatially barcoded 2 µm squares covering a 6.5 × 6.5 mm capture area (~0.65 cm²). Two chemistries are available: a probe-based assay for human and mouse (FF, FxF, and FFPE), and a polyA-based assay (Visium HD 3') for fresh frozen tissue from any species. H&E or immunofluorescence (IF) staining can be performed prior to processing for protein co-detection.
Line 86:		Line 85:

	=== 10X Visium HD ===		=== 10X Visium HD ===
	~~<!-- placeholder image right: Visium HD tissue example showing spatial gene expression / clustering map from representative tissue section -->~~		[[File:BioMicroCenter:VisiumHD_loupe_example.png\|thumb\|right\|500px\|Example of FF data from Visium HD]]
	~~<!-- replace with:~~ [[File:~~VisiumHD_tissue_example~~.png\|thumb\|right\|500px]] ~~-->~~

	'''FAQs for Users'''<BR>		'''FAQs for Users'''<BR>
Line 201:		Line 199:

	=== AVITI24 Teton CytoProfiling at BMC ===		=== AVITI24 Teton CytoProfiling at BMC ===
	~~<!-- placeholder image right: example Teton output — spatial cell map with RNA/protein overlay -->~~		[[File:BioMicroCenter:AVITI24_Boyer_cardiomyocytes.png\|thumb\|right\|500px\|Cytoprofiling of cardiomyocytes. Collaboration with the Boyer Lab.]]
	~~<!-- replace with:~~ [[File:~~AVITI24_teton_example~~.png\|thumb\|right\|500px]] ~~-->~~

	'''About the Service'''<BR>		'''About the Service'''<BR>

Asoberan: Replace Ambox templates with plain HTML notice boxes (template not installed)

2026-03-22T20:07:00Z

Replace Ambox templates with plain HTML notice boxes (template not installed)

← Older revision		Revision as of 20:07, 22 March 2026
Line 121:		Line 121:

	== AVITI24 CYTOPROFILING & IN SITU SEQUENCING ==		== AVITI24 CYTOPROFILING & IN SITU SEQUENCING ==
	~~{{Ambox\|type=notice\|text~~='''Beta Service — Early Access:''' The AVITI24 Teton CytoProfiling and DISS services at the BioMicro Center are operational but not yet routine. Parameters, pricing, and workflows are still being established. '''Consultation with BMC staff is required before submitting samples.'''}}		<div style="background:#fff8e6; border-left:4px solid #c8960c; padding:8px 12px; margin-bottom:12px;">'''Beta Service — Early Access:''' The AVITI24 Teton CytoProfiling and DISS services at the BioMicro Center are operational but not yet routine. Parameters, pricing, and workflows are still being established. '''Consultation with BMC staff is required before submitting samples.'''</div>
	<!-- placeholder image left: AVITI24 instrument photo or Teton CytoProfiling schematic -->		<!-- placeholder image left: AVITI24 instrument photo or Teton CytoProfiling schematic -->
	<!-- replace with: [[File:AVITI24_instrument.png\|thumb\|left\|400px]] -->		<!-- replace with: [[File:AVITI24_instrument.png\|thumb\|left\|400px]] -->
Line 228:		Line 228:
	<BR><BR>		<BR><BR>
	'''Service Status'''<BR>		'''Service Status'''<BR>
	~~{{Ambox\|type=notice\|text~~=This service is in '''beta'''. The instrument is operational and BMC has completed initial runs, but experimental parameters are still being validated. We welcome early users willing to work collaboratively with BMC staff to establish protocols.}}		<div style="background:#fff8e6; border-left:4px solid #c8960c; padding:8px 12px; margin-top:8px;">This service is in '''beta'''. The instrument is operational and BMC has completed initial runs, but experimental parameters are still being validated. We welcome early users willing to work collaboratively with BMC staff to establish protocols.</div>

	\|}		\|}

Asoberan: Add AVITI24 Cytoprofiling & In Situ Sequencing section

2026-03-22T19:52:27Z

Add AVITI24 Cytoprofiling & In Situ Sequencing section

@@ Line 120: / Line 120: @@
 |}
-<!-- == AVITI24 IN SITU SEQUENCING ==
+== AVITI24 CYTOPROFILING & IN SITU SEQUENCING ==
-Content to be added in a future session. -->
+{{Ambox|type=notice|text='''Beta Service — Early Access:''' The AVITI24 Teton CytoProfiling and DISS services at the BioMicro Center are operational but not yet routine. Parameters, pricing, and workflows are still being established. '''Consultation with BMC staff is required before submitting samples.'''}}

Slevine: /* 10X Visium HD */

2026-03-20T15:56:27Z

10X Visium HD

← Older revision		Revision as of 15:56, 20 March 2026
Line 92:		Line 92:
	'''1) What tissues are compatible?'''<br>		'''1) What tissues are compatible?'''<br>
	Visium HD (probe-based) supports human and mouse tissues in FF, FxF, and FFPE formats. Visium HD 3' (polyA) supports fresh frozen tissue from any species. 10x Genomics maintains a [https://www.10xgenomics.com/support/spatial-gene-expression-hd/documentation/steps/tissue-prep-for-fresh-frozen/visium-hd-spatial-gene-expression-tested-tissues-fresh-frozen list of tested tissues]. Additional optimization may be required for tissues with high fat content. Consult BMC staff before starting.		Visium HD (probe-based) supports human and mouse tissues in FF, FxF, and FFPE formats. Visium HD 3' (polyA) supports fresh frozen tissue from any species. 10x Genomics maintains a [https://www.10xgenomics.com/support/spatial-gene-expression-hd/documentation/steps/tissue-prep-for-fresh-frozen/visium-hd-spatial-gene-expression-tested-tissues-fresh-frozen list of tested tissues]. Additional optimization may be required for tissues with high fat content. Consult BMC staff before starting.
	<br>		<br><br>
	'''2) How do I prepare and submit tissue?'''<br>		'''2) How do I prepare and submit tissue?'''<br>
	Tissue sectioning and H&E staining are performed by the [https://ki-sbc.mit.edu/histology Hope Babette Tang (1983) Histology Facility] at the Koch Institute. Coordinate with both the Histology Facility and BMC staff before your first submission. FF tissue should be embedded in OCT and stored at −80°C; FFPE blocks at room temperature.		Tissue sectioning and H&E staining are performed by the [https://ki-sbc.mit.edu/histology Hope Babette Tang (1983) Histology Facility] at the Koch Institute. Coordinate with both the Histology Facility and BMC staff before your first submission. FF tissue should be embedded in OCT and stored at −80°C; FFPE blocks at room temperature.
	<br>		<br><br>
	'''3) What is the resolution?'''<br>		'''3) What is the resolution?'''<br>
	Visium HD captures data at 2 µm bin resolution (single-cell scale). SpaceRanger aggregates into 8 µm and 16 µm bins for higher sensitivity by default; custom bin sizes are also supported. Cell segmentation based on H&E imaging is available in the Loupe Browser pipeline.		Visium HD captures data at 2 µm bin resolution (single-cell scale). SpaceRanger aggregates into 8 µm and 16 µm bins for higher sensitivity by default; custom bin sizes are also supported. Cell segmentation based on H&E imaging is available in the Loupe Browser pipeline.
	<br>		<br><br>
	'''4) How much sequencing is needed?'''<br>		'''4) How much sequencing is needed?'''<br>
	400–800M reads per tile is recommended for Visium HD. Sequencing is submitted separately via iLabs. Compatible platforms include NovaSeq SP, NovaSeqX, and Element AVITI. Discuss read depth with BMC staff based on your tissue type and goals.		400–800M reads per tile is recommended for Visium HD. Sequencing is submitted separately via iLabs. Compatible platforms include NovaSeq SP, NovaSeqX, and Element AVITI. Discuss read depth with BMC staff based on your tissue type and goals.
	<br>		<br><br>
	'''5) Does Visium HD require permeabilization optimization?'''<br>		'''5) Does Visium HD require permeabilization optimization?'''<br>
	No. Visium HD does not require permeabilization time optimization. For fresh frozen tissues new to the platform, a test array is available to verify tissue quality and placement before committing a full experiment.		No. Visium HD does not require permeabilization time optimization. For fresh frozen tissues new to the platform, a test array is available to verify tissue quality and placement before committing a full experiment.
	<br>		<br><br>
	'''6) Can I detect proteins alongside gene expression?'''<br>		'''6) Can I detect proteins alongside gene expression?'''<br>
	Yes. H&E or IF staining can be performed prior to CytAssist processing. Antibody panels for protein co-detection (human tissues, FFPE only) are available from 10x Genomics. Discuss your experimental design with BMC staff in advance.		Yes. H&E or IF staining can be performed prior to CytAssist processing. Antibody panels for protein co-detection (human tissues, FFPE only) are available from 10x Genomics. Discuss your experimental design with BMC staff in advance.
	<br>		<br><br>
	'''7) What analysis outputs are provided?'''<br>		'''7) What analysis outputs are provided?'''<br>
	The BMC delivers FASTQ files, aligned BAM files, the spatial feature-barcode matrix (raw and filtered at 2, 8, and 16 µm bins), and a Loupe Browser file. Downstream informatics support is available through BMC staff.		The BMC delivers FASTQ files, aligned BAM files, the spatial feature-barcode matrix (raw and filtered at 2, 8, and 16 µm bins), and a Loupe Browser file. Downstream informatics support is available through BMC staff.
	<br>		<br><br>
	'''8) Can I combine Visium HD with single-cell data?'''<br>		'''8) Can I combine Visium HD with single-cell data?'''<br>
	Yes. Visium HD data integrates with single-cell or single-nucleus RNA-seq (e.g., 10x Chromium Flex) for cell-type deconvolution. Starting from the same tissue block, nuclei can be isolated for Flex single-cell gene expression. Coordinate with BMC staff if planning a multi-modal experiment.		Yes. Visium HD data integrates with single-cell or single-nucleus RNA-seq (e.g., 10x Chromium Flex) for cell-type deconvolution. Starting from the same tissue block, nuclei can be isolated for Flex single-cell gene expression. Coordinate with BMC staff if planning a multi-modal experiment.
	<br>		<br><br>
	'''9) My gene of interest is exogenous (GFP, reporter, viral) or missing from the probe set. What are my options?'''<br>		'''9) My gene of interest is exogenous (GFP, reporter, viral) or missing from the probe set. What are my options?'''<br>
	The probe-based Visium HD assay does not capture exogenous sequences by default. Custom probes can be designed for detection — see 10x Genomics technical note CG000621. Additionally, a small fraction of endogenous genes are excluded from the standard probe sets due to predicted off-target activity: see the [https://www.10xgenomics.com/support/spatial-gene-expression-hd/documentation/steps/probe-sets/visium-human-transcriptome-probe-set-v2-1 human excluded gene list] (~2.1% of genes) and [https://www.10xgenomics.com/support/spatial-gene-expression-hd/documentation/steps/probe-sets/visium-mouse-transcriptome-probe-set-v2-0 mouse excluded gene list] (~1.8% of genes). Alternatively, the polyA-based Visium HD 3' assay captures all polyadenylated transcripts and does not require custom probes.		The probe-based Visium HD assay does not capture exogenous sequences by default. Custom probes can be designed for detection — see 10x Genomics technical note CG000621. Additionally, a small fraction of endogenous genes are excluded from the standard probe sets due to predicted off-target activity: see the [https://www.10xgenomics.com/support/spatial-gene-expression-hd/documentation/steps/probe-sets/visium-human-transcriptome-probe-set-v2-1 human excluded gene list] (~2.1% of genes) and [https://www.10xgenomics.com/support/spatial-gene-expression-hd/documentation/steps/probe-sets/visium-mouse-transcriptome-probe-set-v2-0 mouse excluded gene list] (~1.8% of genes). Alternatively, the polyA-based Visium HD 3' assay captures all polyadenylated transcripts and does not require custom probes.