BioMicroCenter:SpTx - Revision history

Slevine: /* ILLUMINA STRATAMAP SPATIAL TRANSCRIPTOME */

2026-08-13T17:16:40Z

ILLUMINA STRATAMAP SPATIAL TRANSCRIPTOME

← Older revision		Revision as of 17:16, 13 August 2026
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	\| [[File:StrataComplexity.png\|thumb\|none\|320px\|Sequencing saturation (library complexity) across StrataMap Spatial libraries]]		\| [[File:StrataComplexity.png\|thumb\|none\|320px\|Sequencing saturation (library complexity) across StrataMap Spatial libraries]]
	\|-		\|-
	\| <div style="font-size:12px; color:#555; padding-top:2px;">Data courtesy of the Spranger Lab.</div>		\| <div style="font-size:12px; color:#555; padding-top:2px;">Data courtesy of Amy Wisdom and the Spranger Lab.</div>
	\|}		\|}

Slevine at 17:12, 13 August 2026

2026-08-13T17:12:33Z

← Older revision		Revision as of 17:12, 13 August 2026
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	{{BioMicroCenter}}		{{BioMicroCenter}}

	The BioMicro Center offers ~~several~~ complementary approaches to spatial transcriptomics: [[BioMicroCenter:SpTx#ILLUMINA STRATAMAP SPATIAL TRANSCRIPTOME\|Illumina StrataMap Spatial Transcriptome]] (~~array-based~~) ~~from Illumina,~~ [[BioMicroCenter:SpTx#10X Visium HD\|10x Visium HD]] (~~array-based~~) ~~from 10x Genomics, and~~ [[BioMicroCenter:SpTx#AVITI24 In Situ Sequencing\|AVITI24 ~~in situ sequencing~~]] from Element Biosciences. The choice of method depends on your tissue type, resolution requirements, and experimental goals. We strongly encourage consultation with BMC staff prior to beginning a spatial experiment.		The BioMicro Center offers two complementary approaches to spatial transcriptomics: Microarray based platforms that capture whole genome information and are sequenced on short read sequencers inclusing [[BioMicroCenter:SpTx#ILLUMINA STRATAMAP SPATIAL TRANSCRIPTOME\|Illumina StrataMap Spatial Transcriptome]] (Fresh Frozen only) and [[BioMicroCenter:SpTx#10X Visium HD\|10x Visium HD]] (FFPE and Fresh Frozen). The Center also offers direct in situ sequencing using [[BioMicroCenter:SpTx#AVITI24 In Situ Sequencing\|AVITI24]] from Element Biosciences (Cell culture) and Singular G4X (FFPE Tissue). The choice of method depends on your tissue type, resolution requirements, and experimental goals. We strongly encourage consultation with BMC staff prior to beginning a spatial experiment.

	== ILLUMINA STRATAMAP SPATIAL TRANSCRIPTOME ==		== ILLUMINA STRATAMAP SPATIAL TRANSCRIPTOME ==

Slevine: Fix StrataMap image layout: use non-floating table so Spranger Lab credit renders directly under both images

2026-08-13T16:49:46Z

Fix StrataMap image layout: use non-floating table so Spranger Lab credit renders directly under both images

← Older revision		Revision as of 16:49, 13 August 2026
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	Illumina StrataMap Spatial Transcriptome provides array-based, whole-transcriptome spatial profiling of fresh-frozen tissue at cellular resolution.		Illumina StrataMap Spatial Transcriptome provides array-based, whole-transcriptome spatial profiling of fresh-frozen tissue at cellular resolution.
	<BR><BR>		<BR><BR>
	[[File:StrataSlide.png\|thumb\|~~right~~\|~~350px~~\|Unique transcripts per cell across a StrataMap Spatial slide containing multiple tissue sections]]		{\| style="border:none;"
	[[File:StrataComplexity.png\|thumb\|~~right~~\|~~350px~~\|Sequencing saturation (library complexity) across StrataMap Spatial libraries]]		\|-
	<div style="~~clear:both; padding-top:4px;~~ font-size:12px; color:#555;">Data courtesy of the Spranger Lab.</div>		\| [[File:StrataSlide.png\|thumb\|none\|320px\|Unique transcripts per cell across a StrataMap Spatial slide containing multiple tissue sections]]
			\|-
			\| [[File:StrataComplexity.png\|thumb\|none\|320px\|Sequencing saturation (library complexity) across StrataMap Spatial libraries]]
			\|-
			\| <div style="font-size:12px; color:#555; padding-top:2px;">Data courtesy of the Spranger Lab.</div>
			\|}

	\|}		\|}

Slevine: Add Illumina StrataMap Spatial Transcriptome section (array-based, top of page); list spatial options in intro without ordering commentary

2026-08-13T15:54:55Z

Add Illumina StrataMap Spatial Transcriptome section (array-based, top of page); list spatial options in intro without ordering commentary

@@ Line 1: / Line 1: @@
 {{BioMicroCenter}}
-The BioMicro Center supports two complementary approaches to spatial transcriptomics: [[BioMicroCenter:SpTx#10X Visium HD|10x Visium HD]] from 10x Genomics for slide-based spatial gene expression, and [[BioMicroCenter:SpTx#AVITI24 In Situ Sequencing|AVITI24 in situ sequencing]] from Element Biosciences. The choice of method depends on your tissue type, resolution requirements, and experimental goals. We strongly encourage consultation with BMC staff prior to beginning a spatial experiment.
+The BioMicro Center offers several complementary approaches to spatial transcriptomics: [[BioMicroCenter:SpTx#ILLUMINA STRATAMAP SPATIAL TRANSCRIPTOME|Illumina StrataMap Spatial Transcriptome]] (array-based) from Illumina, [[BioMicroCenter:SpTx#10X Visium HD|10x Visium HD]] (array-based) from 10x Genomics, and [[BioMicroCenter:SpTx#AVITI24 In Situ Sequencing|AVITI24 in situ sequencing]] from Element Biosciences. The choice of method depends on your tissue type, resolution requirements, and experimental goals. We strongly encourage consultation with BMC staff prior to beginning a spatial experiment.
 == 10X VISIUM HD ==
 {| width="100%"

Asoberan: Add Singular G4X in situ spatial sequencing section (beta stub)

2026-04-17T18:21:23Z

Add Singular G4X in situ spatial sequencing section (beta stub)

@@ Line 231: / Line 231: @@
 '''Service Status'''<BR>
 <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: 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
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	== 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]] -->
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	<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
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	{\| 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>
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	=== 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>
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	\|}		\|}

	== 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
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	== 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
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	== 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.
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	=== 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
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	== 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.
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	=== 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>
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	=== 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>