BioMicro Center - Recent changes [en]

BioMicroCenter

Slevine — Fri, 21 Aug 2026 19:04:22 GMT

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	[[BioMicroCenter:SingleCell\|Single Cell]] and [[BioMicroCenter:SpTx\|Spatial]]</B></BIG>		[[BioMicroCenter:SingleCell\|Single Cell]] and [[BioMicroCenter:SpTx\|Spatial]]</B></BIG>
	* 10X CHROMIUM <BR> <small> (5'RNA, 3'RNA, ATAC, multiome) </small>		* 10X CHROMIUM <BR> <small> (5'RNA, 3'RNA, ATAC, multiome) </small>
	* ~~10X VISIUM~~ <BR> <small> (~~Standard,~~ High Density) </small>		* MICROARRAY BASED <BR> <small> (10X Visium High Density, Illumina StrataMap) </small>
	* ELEMENT AVITI24 (<i>in situ</i> prep/sequencing)		* ELEMENT AVITI24 (<i>in situ</i> prep/sequencing)
	\|}		\|}

MIT:Pricing

Slevine — Mon, 17 Aug 2026 12:32:34 GMT

ARRAY BASED SPATIAL

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	\|}		\|}

	=== ~~VISIUM~~ ===		=== ARRAY BASED SPATIAL ===

	{\| class="wikitable"		{\| class="wikitable"
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	! SLIDES !! Batch Size !! [[BioMicroCenter:CoreDeps\|CORE LAB]] !! MIT !! Notes		! SLIDES !! Batch Size !! [[BioMicroCenter:CoreDeps\|CORE LAB]] !! MIT !! Notes
	\|-		\|-
	\| HD: polyA or FFPE (human/mouse only) \|\| 1 slide / 2 tiles \|\| $7,850 \|\| $8,596 \|\| Includes library generation only.		\| Illumina StrataMap \|\| 1 slide \|\| $4,550 \|\| $4,996 \|\| Includes library generation only.
			\|-
			\| 10X VisiumHD: polyA or FFPE (human/mouse only) \|\| 1 slide / 2 tiles \|\| $7,850 \|\| $8,596 \|\| Includes library generation only.
	\|-		\|-
	\| QC - FFPE Scroll \|\| per scroll \|\| $65 \|\| $71.50 \|\| RNA isolation from FFPE scroll		\| QC - FFPE Scroll \|\| per scroll \|\| $65 \|\| $71.50 \|\| RNA isolation from FFPE scroll

BioMicroCenter:Pricing

Slevine — Mon, 17 Aug 2026 12:30:09 GMT

SINGLE CELL & SPATIAL SERVICES

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	=== ~~VISIUM~~ ===		=== ARRAY BASED SPATIAL ===

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	! SLIDES !! Batch Size !! [[BioMicroCenter:FAQ#NON_MIT_USERS\|External Academic]] !! External For-Profit !! Notes		! SLIDES !! Batch Size !! [[BioMicroCenter:FAQ#NON_MIT_USERS\|External Academic]] !! External For-Profit !! Notes
	\|-		\|-
	\| HD: polyA or FFPE (hs/mm only) \|\| 1 slide / 2 tiles \|\| $9,813 \|\| $10,940 \|\| Includes library generation only.		\| Illumina StrataMap \|\| 1 slide \|\| $13,463 \|\| $15,070 \|\| Includes library prep and sequencing (25B)
			\|-
			\| VisiumHD: polyA or FFPE (hs/mm only) \|\| 1 slide / 2 tiles \|\| $9,813 \|\| $10,940 \|\| Includes library generation only.
	\|-		\|-
	\| QC - FFPE Scroll \|\| per scroll \|\| $81.25 \|\| $91 \|\| RNA isolation from FFPE scroll		\| QC - FFPE Scroll \|\| per scroll \|\| $81.25 \|\| $91 \|\| RNA isolation from FFPE scroll

BioMicroCenter:SpTx

Slevine — Thu, 13 Aug 2026 17:16:40 GMT

ILLUMINA STRATAMAP SPATIAL TRANSCRIPTOME

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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 ==
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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 Amy Wisdom and the Spranger Lab.</div>
			\|}

	\|}		\|}

File:StrataSlide.png

Slevine — Thu, 13 Aug 2026 16:47:06 GMT

Slevine uploaded File:StrataSlide.png

New page

File:StrataComplexity.png

Slevine — Thu, 13 Aug 2026 16:46:46 GMT

Slevine uploaded File:StrataComplexity.png

New page

BioMicroCenter:SpTx

Slevine — Thu, 13 Aug 2026 15:54:55 GMT

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

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 {{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%"

BioMicroCenter:BioinfoClasses

Duan — Fri, 07 Aug 2026 17:36:13 GMT

Show changes

User:Duan

Asoberan — Thu, 06 Aug 2026 14:21:47 GMT

User account Duan was created by Asoberan and password was sent by email

User:Gibcus/common.css

Gibcus — Wed, 05 Aug 2026 19:03:37 GMT

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User:Hilo1/common.css

Asoberan — Wed, 05 Aug 2026 17:09:47 GMT

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User:Toniappa/common.css

Asoberan — Wed, 05 Aug 2026 17:09:38 GMT

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User:Challee/common.css

Asoberan — Wed, 05 Aug 2026 17:09:26 GMT

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User:Cdemu/common.css

Asoberan — Wed, 05 Aug 2026 17:09:04 GMT

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User:Shebert/common.css

Asoberan — Wed, 05 Aug 2026 17:08:40 GMT

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User:Asoberan/common.css

Asoberan — Wed, 05 Aug 2026 17:07:10 GMT

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BioMicroCenter:SingleCell

Hilo1 — Tue, 28 Jul 2026 16:50:23 GMT

scRNAseq / snRNAseq

← Older revision		Revision as of 16:50, 28 July 2026
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	[https://www.10xgenomics.com/support/universal-three-prime-gene-expression/documentation/steps/sample-prep Freshly counted cells/nuclei in suspension.]		[https://www.10xgenomics.com/support/universal-three-prime-gene-expression/documentation/steps/sample-prep Freshly counted cells/nuclei in suspension.]
	\|		\|
	[https://www.10xgenomics.com/support/flex-gene-expression/documentation/steps/sample-prep Fixed cells in suspension.] Also supports ~~fresh,~~ frozen, FFPE, fixed whole blood, and flow-sorted cells.		[https://www.10xgenomics.com/support/flex-gene-expression/documentation/steps/sample-prep Fixed cells in suspension.] Also supports frozen, FFPE, fixed whole blood, and flow-sorted cells.
	\|-		\|-
	!Cell Concentration <BR><small> cells\|nuclei/uL </small>		!Cell Concentration <BR><small> cells\|nuclei/uL </small>
	\|100-~~2000~~		\|100-2,000
	\|100-~~2000~~		\|100-2,000
	\|~~100~~-~~2000~~		\|25,000-300,000 total
	\|-		\|-
	! Fraction Recovered <BR><small> est. percent of input cells captured </small>		! Fraction Recovered <BR><small> est. percent of input cells captured </small>
Line 75:		Line 75:
	\|colspan="3"\| [http://mit.edu/manoli/ Prof. Manolis Kellis]		\|colspan="3"\| [http://mit.edu/manoli/ Prof. Manolis Kellis]
	\|}		\|}

	=== CHROMATIN ===		=== CHROMATIN ===
	{\| class="wikitable" border=1		{\| class="wikitable" border=1