BioMicroCenter:SingleCell - Revision history

Asoberan: Update AVITI24 hidden comment: high-output DISS not yet released

2026-03-24T20:29:09Z

Update AVITI24 hidden comment: high-output DISS not yet released

← Older revision		Revision as of 20:29, 24 March 2026
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	<BR><BR>.		<BR><BR>.

	<!-- AVITI24 ~~IN SITU SEQUENCING~~ section ~~removed~~ - ~~content pending future update~~ -->		<!-- AVITI24 high-output DISS (whole transcriptome single cell) section pending - not yet released -->

	<!-- commenting out Seq-Well		<!-- commenting out Seq-Well

Slevine at 20:17, 17 March 2026

2026-03-17T20:17:41Z

Show changes

Slevine at 13:43, 2 September 2025

2025-09-02T13:43:52Z

← Older revision		Revision as of 13:43, 2 September 2025
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	\|}		\|}
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			[[image:Namo.jpg\|thumb\|right\|Namo (Namocell) Bio-Techne]]
	The [https://www.namocell.com/namo/ Namocell Single Cell Sorter] allows users to sort cells into plates. The sorter uses microfluidics to sort single cells in 1uL of sheath fluid into a well. The instrument uses disposable cartridges to minimize contamination. The instrument integrates well with the [[BioMicroCenter:Tecan_Freedom_Evo#TTP_LABTECH_MOSQUITO_HV\|TTP Labtech Mosquito HV]] which handles small reaction volumes. <BR><BR>		The [https://www.namocell.com/namo/ Namocell Single Cell Sorter] allows users to sort cells into plates. The sorter uses microfluidics to sort single cells in 1uL of sheath fluid into a well. The instrument uses disposable cartridges to minimize contamination. The instrument integrates well with the [[BioMicroCenter:Tecan_Freedom_Evo#TTP_LABTECH_MOSQUITO_HV\|TTP Labtech Mosquito HV]] which handles small reaction volumes. <BR><BR>
	~~[[image:Namo.jpg\|thumb\|right\|Namo (Namocell) Bio-Techne]]~~
	\|
	\|}		\|}
			<BR><BR>.


	== AVITI24 IN SITU SEQUENCING ==		== AVITI24 IN SITU SEQUENCING ==
	* coming in early 2026 *		* coming in early 2026 *

	The AVITI24 enables direct in situ sequencing of samples, allowing for very rapid characterization of single cells. Cells can be grown or placed on the AVITI24 flowcell and processed. Runs are predicted to produce a few thousand reads plus cytostaining and antibody labeling, all within a day. More information will be released soon.		The AVITI24 enables direct in situ sequencing of samples, allowing for very rapid characterization of single cells. Cells can be grown or placed on the AVITI24 flowcell and processed. Runs are predicted to produce a few thousand reads plus cytostaining and antibody labeling, all within a day. More information will be released soon.

Slevine at 13:41, 2 September 2025

2025-09-02T13:41:23Z

← Older revision		Revision as of 13:41, 2 September 2025
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	\|}		\|}

	~~<!-- 100-10k 10c/" 1b/ml -->~~


			== AVITI24 IN SITU SEQUENCING ==
			* coming in early 2026 *

			The AVITI24 enables direct in situ sequencing of samples, allowing for very rapid characterization of single cells. Cells can be grown or placed on the AVITI24 flowcell and processed. Runs are predicted to produce a few thousand reads plus cytostaining and antibody labeling, all within a day. More information will be released soon.


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	Seq-Well projects can be brought in two ways. For full service, please use the ilabs form linked on the left. At the end of the form it asks you to select several days on which the experiment can be done. The Nanowell Core will review the possible dates with you to fit it in the schedule. On that date, the core will confirm the quality of your cells prior to beginning the experiment. While 10,000 cells are typically used in a Seq-Well experiment, the core requests you plan to bring more cells - often counts from flow cytometers and other instruments are incorrect. Planning to bring more cells ensures you have the 10,000 desired. The BioMicro Center becomes involved in these projects at the exonuclease treatment step, where we take over the preparation of the library and quality control, as well as sequencing and analysis.<BR><BR>		Seq-Well projects can be brought in two ways. For full service, please use the ilabs form linked on the left. At the end of the form it asks you to select several days on which the experiment can be done. The Nanowell Core will review the possible dates with you to fit it in the schedule. On that date, the core will confirm the quality of your cells prior to beginning the experiment. While 10,000 cells are typically used in a Seq-Well experiment, the core requests you plan to bring more cells - often counts from flow cytometers and other instruments are incorrect. Planning to bring more cells ensures you have the 10,000 desired. The BioMicro Center becomes involved in these projects at the exonuclease treatment step, where we take over the preparation of the library and quality control, as well as sequencing and analysis.<BR><BR>
	Many laboratories are also using reagents from the Nanowell core to begin doing Seq-Well on their own. For these labs, we strongly recommend at least confirming the quality of the cDNA on our Advanced Analytical before continuing through library preparation. The library preparation can also be done in the BioMicro Center. Please use the standard Illumina library preparation form and note that the samples are Seq-Well. We do have all the custom primers needed for preparation and the pricing is identical to other NexteraXT preps.		Many laboratories are also using reagents from the Nanowell core to begin doing Seq-Well on their own. For these labs, we strongly recommend at least confirming the quality of the cDNA on our Advanced Analytical before continuing through library preparation. The library preparation can also be done in the BioMicro Center. Please use the standard Illumina library preparation form and note that the samples are Seq-Well. We do have all the custom primers needed for preparation and the pricing is identical to other NexteraXT preps.

	\|}		\|}
	-->		-->

Slevine at 13:15, 2 September 2025

2025-09-02T13:15:21Z

← Older revision		Revision as of 13:15, 2 September 2025
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	[[File:SingleCellOptions.png\|thumb\|right\|400px]]		[[File:SingleCellOptions.png\|thumb\|right\|400px]]
	The BioMicro Center supports a broad range of methods for single cell sequencing. The choice of method depends heavily on the type of question being asked and the source material. The methods break down into those supporting ~~[[BioMicroCenter:SingleCell#NAMOCELL_SINGLE_CELL_SORTER~~ individual cells characterized in single wells]], methods that ~~[[BioMicroCenter:SingleCell&action=submit#10x_CHROMIUM_X~~ use droplet isolation and library preparation]], and those that support rapid characterization of a modest number of transcripts using in situ sequencing (coming soon). These cell requirements for each method vary significantly so reviewing each method is valuable and we strongly encourage consultation with BMC staff prior to beginning the experiment.		The BioMicro Center supports a broad range of methods for single cell sequencing. The choice of method depends heavily on the type of question being asked and the source material. The methods break down into those supporting individual cells characterized in single wells, methods that use droplet isolation and library preparation, and those that support rapid characterization of a modest number of transcripts using in situ sequencing (coming soon). These cell requirements for each method vary significantly so reviewing each method is valuable and we strongly encourage consultation with BMC staff prior to beginning the experiment.
	<BR><BR><BR><BR><BR><BR>.		<BR><BR><BR><BR><BR><BR>.


	== 10x CHROMIUM X ==		== 10x CHROMIUM X ==
			[[File:25_10xAssays.png\|thumb\|left\|400px]]
			The BioMicro Center provides access to 10x Genomics library preparation as an assisted or a walk-up service. Added in 2023, The 10x Chromium X can handle a broad variety of methodologies now including [https://www.10xgenomics.com/solutions/single-cell/ 3', 5' and fixed RNA sequencing], [https://www.10xgenomics.com/solutions/single-cell-atac/ ATAC and multiome] <!-- [https://www.10xgenomics.com/solutions/single-cell-cnv/ CNV]. --> Dropoff for assisted service is coordinated with Center staff with at least one week's lead time. Users should bring their single cell/nuclei suspension(s) in 1.5 mL microfuge tubes in the standard buffer at or around that time. Staff works with the user to intake the initial samples and proceed through the protocol with quality control checks at the appropriate steps.
			<BR><BR>
			Chromium X usage is also offered as a walkup service. Usage may be scheduled on the iLabs calendar after training by BMC staff. This still requires at least a week's lead time before usage. You will not have permission to schedule the equipment until you have been approved by BMC staff. Reagents are stocked in the BioMicro Center and we ask that you use our reagents. This allows us to get larger bulk discounts we can pass on to our users. Please note that we do include a fraction of the instrument usage cost in the cost of the chips and will charge this cost if you use your own chips.
			<BR><BR>
			The full 10x suite of software is installed on LURIA and is integrated into our analysis package. <BR><BR>
	{\|		{\|
	\|- style="vertical-align: top;"		\|- style="vertical-align: top;"
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	=== 10X Genomics ===		=== 10X Genomics ===
	[[image:10xX.jpg\|thumb\|right\|500px\|10x Chromium X]]		[[image:10xX.jpg\|thumb\|right\|500px\|10x Chromium X]]
	The BioMicro Center provides access to 10x Genomics library preparation as an assisted or a walk-up service. Added in 2023, The 10x Chromium X can handle a broad variety of methodologies now including [https://www.10xgenomics.com/solutions/single-cell/ 3', 5' and fixed RNA sequencing], [https://www.10xgenomics.com/solutions/single-cell-atac/ ATAC and multiome] <!-- [https://www.10xgenomics.com/solutions/single-cell-cnv/ CNV]. --> Dropoff for assisted service is coordinated with Center staff with at least one week's lead time. Users should bring their single cell/nuclei suspension(s) in 1.5 mL microfuge tubes in the standard buffer at or around that time. Staff works with the user to intake the initial samples and proceed through the protocol with quality control checks at the appropriate steps.
	~~<BR><BR>~~
	Chromium X usage is also offered as a walkup service. Usage may be scheduled on the iLabs calendar after training by BMC staff. This still requires at least a week's lead time before usage. You will not have permission to schedule the equipment until you have been approved by BMC staff. Reagents are stocked in the BioMicro Center and we ask that you use our reagents. This allows us to get larger bulk discounts we can pass on to our users. Please note that we do include a fraction of the instrument usage cost in the cost of the chips and will charge this cost if you use your own chips.
	~~<BR><BR>~~
	~~The full 10x suite of software is installed on LURIA and is integrated into our analysis package. <BR><BR>~~

	FAQs for Users <BR>		FAQs for Users <BR>

Slevine at 13:03, 2 September 2025

2025-09-02T13:03:06Z

← Older revision		Revision as of 13:03, 2 September 2025
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	{{BioMicroCenter}}		{{BioMicroCenter}}

	The BioMicro Center supports ~~two technologies~~ for single cell ~~experiments~~: ~~10X libraries as walkup or as an assisted service~~, and ~~plate based methods~~ using the ~~Namocell single cell sorter~~. <BR><BR>		[[File:SingleCellOptions.png\|thumb\|right\|400px]]
			The BioMicro Center supports a broad range of methods for single cell sequencing. The choice of method depends heavily on the type of question being asked and the source material. The methods break down into those supporting [[BioMicroCenter:SingleCell#NAMOCELL_SINGLE_CELL_SORTER individual cells characterized in single wells]], methods that [[BioMicroCenter:SingleCell&action=submit#10x_CHROMIUM_X use droplet isolation and library preparation]], and those that support rapid characterization of a modest number of transcripts using in situ sequencing (coming soon). These cell requirements for each method vary significantly so reviewing each method is valuable and we strongly encourage consultation with BMC staff prior to beginning the experiment.
			<BR><BR><BR><BR><BR><BR>.


	== 10x CHROMIUM X ==		== 10x CHROMIUM X ==

172.18.0.1: /* scRNAseq / snRNAseq */

2025-08-13T16:13:54Z

scRNAseq / snRNAseq

← Older revision		Revision as of 16:13, 13 August 2025
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	\|-		\|-
	!Cell Concentration <BR><small> cells\|nuclei/uL </small>		!Cell Concentration <BR><small> cells\|nuclei/uL </small>
	\|~~700~~-~~1600~~		\|100-2000
	\|~~700~~-~~1200~~		\|100-2000
	\|~~1700~~+		\|2000+
	\|-		\|-
	! Fraction Recovered <BR><small> est. percent of input cells captured </small>		! Fraction Recovered <BR><small> est. percent of input cells captured </small>

Slevine: /* single cell RNAseq */

2025-07-23T13:20:45Z

single cell RNAseq

← Older revision		Revision as of 13:20, 23 July 2025
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	\|- style="vertical-align: top;"		\|- style="vertical-align: top;"
	\|style="width: 450px;"\|		\|style="width: 450px;"\|
	=== ~~single cell RNAseq~~ ===		=== scRNAseq / snRNAseq ===
	{\| class="wikitable" border=1		{\| class="wikitable" border=1
	!		!
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	! Fixed RNA <BR> (Flex GEM-X)		! Fixed RNA <BR> (Flex GEM-X)
	\|-		\|-
	!~~rowspan="2"\|~~INPUT		!INPUT
	\|colspan="2"\|		\|colspan="2"\|
	[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.]
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	[https://www.10xgenomics.com/support/flex-gene-expression/documentation/steps/sample-prep Fixed cells in suspension.]		[https://www.10xgenomics.com/support/flex-gene-expression/documentation/steps/sample-prep Fixed cells in suspension.]
	\|-		\|-
	\|		!Cell Concentration <BR><small> cells\|nuclei/uL </small>
	* 700-1600 cells/~~ul.~~		\|700-1600
	* ~65% ~~recovered in GEMS~~		\|700-1200
	* 500-20,000/lane		\|1700+
	* 8% doublet @ 20k		\|-
	\|		! Fraction Recovered <BR><small> est. percent of input cells captured </small>
	* 700-1200 cells/ul.		\| ~65%
	* ~60% recovered in GEMS		\| ~60%
	* 500-5,000/lane		\| ~50%
	* 7.5% doublet @ 5k		\|-
	\|		! Target recovery <BR> <small> multiply by recovery for input </small>
	* 1700+ cells/ul		\| 500-20,000/lane
	* ~50% recovered in GEMS		\| 500-5,000/lane
	* 500-10,000/sample		\| 500-10,000/sample
	* 8% doublet @ 10k		\|-
	* HUMAN/MOUSE ONLY!		! Expected doublet rate @ Max load
			\| 8%
			\| 7.5%
			\| 8% doublet @ 10k
	\|-		\|-
	!Multiplexing		!Multiplexing
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	\|		\|
	Additional genes [https://www.10xgenomics.com/support/flex-gene-expression/documentation/steps/experimental-design-and-planning/custom-probe-design-for-visium-spatial-gene-expression-and-chromium-single-cell-gene-expression-flex require new probes.]		Additional genes [https://www.10xgenomics.com/support/flex-gene-expression/documentation/steps/experimental-design-and-planning/custom-probe-design-for-visium-spatial-gene-expression-and-chromium-single-cell-gene-expression-flex require new probes.]
			\|-
			! KEY NOTES
			\|
			\|
			\| Human/Mouse only
	\|-		\|-
	!SUBMISSION FORMS		!SUBMISSION FORMS

Slevine: /* CHROMATIN */

2025-07-22T15:50:44Z

CHROMATIN

← Older revision		Revision as of 15:50, 22 July 2025
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	\|-		\|-
	! Multiplexing		! Multiplexing
	\| ~~rowspan~~ =2 \| Not available		\| colspan =2 \| Not available
	\|-		\|-
	!SUBMISSION FORMS		!SUBMISSION FORMS

Slevine: /* CHROMATIN */

2025-07-22T15:50:16Z

CHROMATIN

← Older revision		Revision as of 15:50, 22 July 2025
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	\|-		\|-
	! Input		! Input
	\| ~~rowspan~~ =2 \|		\| colspan=2 \|
	* 160-8,000 nuclei/uL		* 160-8,000 nuclei/uL
	* 50% estimated recovery		* 50% estimated recovery
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	\|-		\|-
	!SUBMISSION FORMS		!SUBMISSION FORMS
	\|colspan="3"\| ASSISTED - [https://mit.ilabsolutions.com/service_item/new/3381?spt_id=12903 ilabs] WALKUP - [https://mit.ilabsolutions.com/equipment/380963 Calendar]		\|colspan="2"\| ASSISTED - [https://mit.ilabsolutions.com/service_item/new/3381?spt_id=12903 ilabs] WALKUP - [https://mit.ilabsolutions.com/equipment/380963 Calendar]
	\|-		\|-
	!DELIVERY		!DELIVERY
	\|colspan="3"\| FASTQ, BAM, 10X QC, loupe file		\|colspan="2"\| FASTQ, BAM, 10X QC, loupe file
	\|}		\|}