BioMicroCenter:Element Sequencing - Revision history

Asoberan: Redirect to consolidated BioMicroCenter:ShortRead page

2026-04-21T00:52:00Z

Redirect to consolidated BioMicroCenter:ShortRead page

← Older revision		Revision as of 00:52, 21 April 2026
Line 1:		Line 1:
	~~== Element Sequencing ==~~		#REDIRECT [[BioMicroCenter:ShortRead]]
	~~The Center currently hosts an AVITI24 platform from [https://www.elementbiosciences.com/ Element Biosciences].~~
	~~AVITI24 platform supports both sequencing and cytoprofiling. For most sequencing needs, the Center will use Element's Freestyle chemistry kits.~~
	{\|
	\|
	~~{\| class="wikitable" border=1~~
	~~!width=100\|Service~~
	~~!width=250\|Element Sequencing~~
	\|-
	~~\|SUBMISSION \|\| Illumina OR Element libraries~~
	\|-
	~~\|MIN VOLUME \|\| 15 uL~~
	\|-
	~~\|MIN CONCENTRATION \|\| 2 nM~~
	\|-
	~~\|INCLUDED SERVICES~~
	\|
	* Quality Control:Fragment Analyzer and qPCR
	* Element Sequencing
	* Demultiplexing
	\|-
	~~\|ADDITIONAL SERVICES \|\|~~
	* Quality Control
	* Element library preperation
	\|-
	~~\|DATA FORMATS~~
	\|
	*FASTQ (stored 1 year)
	\|-
	~~\|QUALITY CONTROL~~
	\|
	* [https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ FASTQC]
	* Basic run metrics (alignment rate, complexity)
	* Basic RNAseq metrics (where applicable)
	* Basic paired end metrics (where applicable)
	* Contamination checks
	\|-
	~~\|PRICING \|\|~~ [[BioMicroCenter:~~Pricing#SINGULAR_G4\|LINK~~]]
	\|-
	~~\|SUBMISSION~~
	\|
	* MIT - [https://mit.ilabsolutions.com/service_item/new/3381?spt_id=3863 ilabs]
	\|-
	\|}
	~~\| valign='top' \|~~
	{\|
	~~=== ANCHORS ===~~
	Element supports both Illumina anchors (P5/P7) using 'Freestyle' chemistry and and Element Anchors (SP5/SP27) for 'Adept' chemistry. For runs in the BMC, P5/P7 anchored library (Illumina) are preferred. Element Adept libraries (SP5/SP27) require a 5'-phosphate on the forward end in order to circularize and sequence. <BR><BR>
	~~=== INDEXING ===~~
	Compared to an Illumina platform, AVITI24 reads are similar in read direction to Illumina's Forward Strand workflow for Dual Indexed Libraries. Indexes are read from antisense primers to the forward and reverse reads with the P7 side read first (index 1). Indexes are therefore antisense to the ordered oligos in traditional chemistry. Index sequences should be provided AS READ and not as ordered. <BR>
	* Custom primer submission: 70 uL at 100 uM for Read 1, all other reads require 40 uL at 100 uM.
	* Custom primers must be compatible with TruSeq, Nextera, TruSeq, smRNA and Element sequencing primers
	~~===SINGLE LANE ===~~
	~~Each lane of the AVITI24 can be loaded independently. Flowcells require both lanes to be filled to be run.~~
	~~Custom primers must be designed to not interfere with other user's samples.~~
	~~All other requests require a full flowcell. 300PE kits only have a single lane.~~

	~~=== MINIMUM READS ===~~
	~~Minimum reads per lane are guaranteed if:~~
	*the BMC has performed quality control,
	*the samples have high diversity, especially within the first 5 bases of read 1, and
	*submitted libraries are at least 2 nM.

	\|}
	\|}

	~~== The AVITI24 Platform ==~~
	~~{\| class="wikitable" border=1~~
	~~!width=100\|~~
	~~!width=250\| AVITI24~~
	~~!width=150\| NOTES~~
	\|-
	~~\|'''SEQUENCER'''\|\|[[Image:Element_AVITI.jpg\|center\|200px]]\|\|~~
	\|-
	~~\| '''READS/FLOWCELL'''<BR> Low number is minimum per lane for standard P5/P7 libraries.\|\|~~
	* 250M HQ read pairs (150 for PE300)
	\|-
	~~\|'''RUN TIME'''\|\|~~
	* 75 PE 24 hours
	* 150 PE 38 hours
	* 300 PE 60 hours
	\|-
	~~\|'''KITS AVAILABLE'''\|\|~~
	* 2x75 Cloudbreak FS High
	* 2x150 Cloudbreak FS High
	* 2x300 Cloudbreak FS High
	~~\|\| - Single end supported <br> - each kit comes with 34 additional cycles~~
	\|-
	~~\|'''KEY NOTES'''\|\|~~
	* 4-color chemistry
	* Random flow cell
	* 2-lanes per flow cell (1 for 300PE)
	* Q40+ > 80%
	* Low-binding surface chemistry
	\|-
	~~\|'''THANKS TO'''\|\|~~
	* Element Biosciences / Scott Ritterbush
	\|}


	The AVITI24 can run 2 flow cells per run, each hosting 2 independently-addressable lanes. Both lanes are washed with the same reagents. Element currently offers kits with 150 and 300 cycles, both supporting 2 lanes, as well as a 600 cycle kit that supports a single lane. Index hopping rates are similar to non-patterned Illumina, limiting the need for UDI's. The AVITI24 can also perform direct in sample sequencing which includes spatial imaging of RNA, proteins, phospho-proteins, and cell morphology using [https://www.elementbiosciences.com/products/aviti24/cytoprofiling/ Teton chemistry] for cytoprofiling.


	~~<!-- hidden~~
	~~== Cytoprofiling with AVITI24 ==~~

	~~[[Image:DISS_example.jpg\|thumb\|right\|200px\|Example of Teton imaging from Element Biosciences website]]~~

	A user can optimize the assay before attempting a Teton Run. This test will require an optimization kit. Optimization is similar to creating a slide for a Teton run. The standard steps of coating (or not) that slide, loading and culturing cells prior to fixing are all similar. Instead of running the optimization slide on the AVITI24, the optimization slide should be inspected with a fluorescence objective. This process requires a separate kit from the actual slide kits.

	~~[[Image:OptimizationSlide.jpg\|thumb\|middle\|Lamason Lab Slide provided from Element Biosciences]]~~

	Users can pick up a 1- or 12-well Teton Slide kit from the Center. Currently, Poly-L-Lysine-coated and uncoated slide kits are available. Uncoated slides must be coated as laid out in the protocol and users should ensure that cell fixation is ideal for one of the possible coatings which are not PLL (currently: Collagen, Fibronectin, Gelatin, Laminin, Matrigel). Cells are loaded and cultured for the desired amount of time on coated slides. Cells are fixed and the Teton Slide may be stored at 2-8C for up to 30 days or may be run immediately on the AVITI24.

	For a Teton Run, cells are washed in the appropriate Cell Paint reagents for a fixed panel or custom panel cytoprofiling assay. A single Teton slide can be used to infer Morphology, RNA within the cells, Protein and also direct in situ sequencing up to 100nt which is not robust enough for transcriptomics, but is sufficient for investigating CRISPR or TCR or other short sequences of interest.

	~~-->~~

Slevine: /* Element Sequencing */

2025-07-20T15:56:10Z

Element Sequencing

← Older revision		Revision as of 15:56, 20 July 2025
Line 3:		Line 3:
	AVITI24 platform supports both sequencing and cytoprofiling. For most sequencing needs, the Center will use Element's Freestyle chemistry kits.		AVITI24 platform supports both sequencing and cytoprofiling. For most sequencing needs, the Center will use Element's Freestyle chemistry kits.
	{\|		{\|
			\|
	{\| class="wikitable" border=1		{\| class="wikitable" border=1
	!width=100\|Service		!width=100\|Service
Line 42:		Line 43:
	\|-		\|-
	\|}		\|}
			\| valign='top' \|
			{\|
			=== ANCHORS ===
			Element supports both Illumina anchors (P5/P7) using 'Freestyle' chemistry and and Element Anchors (SP5/SP27) for 'Adept' chemistry. For runs in the BMC, P5/P7 anchored library (Illumina) are preferred. Element Adept libraries (SP5/SP27) require a 5'-phosphate on the forward end in order to circularize and sequence. <BR><BR>
			=== INDEXING ===
			Compared to an Illumina platform, AVITI24 reads are similar in read direction to Illumina's Forward Strand workflow for Dual Indexed Libraries. Indexes are read from antisense primers to the forward and reverse reads with the P7 side read first (index 1). Indexes are therefore antisense to the ordered oligos in traditional chemistry. Index sequences should be provided AS READ and not as ordered. <BR>
			* Custom primer submission: 70 uL at 100 uM for Read 1, all other reads require 40 uL at 100 uM.
			* Custom primers must be compatible with TruSeq, Nextera, TruSeq, smRNA and Element sequencing primers
			===SINGLE LANE ===
			Each lane of the AVITI24 can be loaded independently. Flowcells require both lanes to be filled to be run.
			Custom primers must be designed to not interfere with other user's samples.
			All other requests require a full flowcell. 300PE kits only have a single lane.

	P5/P7 anchored library (Illumina) is preferred. Element Adept libraries (SP5/SP27) require a 5'-phosphate on the forward end in order to circularize and sequence. Compared to an Illumina platform, AVITI24 reads are similar in read direction to Illumina's Forward Strand workflow for Dual Indexed Libraries.		=== MINIMUM READS ===

	Minimum reads per lane are guaranteed if:		Minimum reads per lane are guaranteed if:
	*the BMC has performed quality control,		*the BMC has performed quality control,
Line 50:		Line 62:
	*submitted libraries are at least 2 nM.		*submitted libraries are at least 2 nM.

	~~===Lane-by-lane Notes===~~		\|}
	*The wait is variable		\|}
	*Custom primers must be compatible with TruSeq, Nextera, TruSeq, smRNA and Element sequencing primers

	~~All other requests require a full flowcell. 300PE kits only have a single lane.~~

	* Min custom primer submission: 70 uL at 100 uM for Read 1, all other reads require 40 uL at 100 uM.

	== The AVITI24 Platform ==		== The AVITI24 Platform ==

Slevine at 02:34, 20 June 2025

2025-06-20T02:34:03Z

← Older revision		Revision as of 02:34, 20 June 2025
Line 43:		Line 43:
	\|}		\|}

	Illumina ~~library~~ is preferred. Element libraries require a 5'-phosphate on the forward end in order to circularize and sequence. Compared to an Illumina platform, AVITI24 reads are similar in read direction to Illumina's Forward Strand workflow for Dual Indexed Libraries.		P5/P7 anchored library (Illumina) is preferred. Element Adept libraries (SP5/SP27) require a 5'-phosphate on the forward end in order to circularize and sequence. Compared to an Illumina platform, AVITI24 reads are similar in read direction to Illumina's Forward Strand workflow for Dual Indexed Libraries.

	Minimum reads per lane are guaranteed if:		Minimum reads per lane are guaranteed if:
Line 66:		Line 66:
	\|'''SEQUENCER'''\|\|[[Image:Element_AVITI.jpg\|center\|200px]]\|\|		\|'''SEQUENCER'''\|\|[[Image:Element_AVITI.jpg\|center\|200px]]\|\|
	\|-		\|-
	\| '''READS/FLOWCELL'''<BR> Low number is minimum per lane for standard ~~Illumina~~ libraries.\|\|		\| '''READS/FLOWCELL'''<BR> Low number is minimum per lane for standard P5/P7 libraries.\|\|
	* ~~300M~~ HQ read pairs ~~PF/flowcell~~		* 250M HQ read pairs (150 for PE300)
	\|-		\|-
	\|'''RUN TIME'''\|\|		\|'''RUN TIME'''\|\|
Line 79:		Line 79:
	* 2x300 Cloudbreak FS High		* 2x300 Cloudbreak FS High
	\|\| - Single end supported <br> - each kit comes with 34 additional cycles		\|\| - Single end supported <br> - each kit comes with 34 additional cycles
	\|-
	~~\|'''KNOWN APPLICATIONS'''\|\|~~
	* Whole Genome Sequencing
	* RNA Sequencing
	* 16S
	* Single-cell
	* Target Sequencing and Enrichment
	* Metagenomics
	\|-		\|-
	\|'''KEY NOTES'''\|\|		\|'''KEY NOTES'''\|\|
	* 4-color chemistry		* 4-color chemistry
	* Random flow cell		* Random flow cell
	* 2-lanes per flow cell		* 2-lanes per flow cell (1 for 300PE)
	* Q40+ > 80%		* Q40+ > 80%
	* Low-binding surface chemistry		* Low-binding surface chemistry
	* Adept Workflow for adaptation of Illumina libraries
	\|-		\|-
	\|'''THANKS TO'''\|\|		\|'''THANKS TO'''\|\|
	* Element Biosciences		* Element Biosciences / Scott Ritterbush
	\|}		\|}
	Aviti24 circularizes linear Element or Illumina libraries onboard, and then performs rolling circle amplification to generate thousands of copies of the original template on a single strand. The strand is then packaged up into a polony. These polonies are washed with a complex of primers, polymerase, and dye-labelled avidites. Avidites are multivalent-nucleotide-ligands on dye labeled cores capable of binding to multiple sites to form a polymerase–polymer–nucleotide complex within a polony. After an imaging step, the avidites are washed away and the growing read strand incorporates a single nucleotide that is reversibly blocked on the 3' end. The polonies are again loaded with avidites, repeating the process over many cycles.

	The AVITI24 can run 2 flow cells per run, each hosting 2 independently-addressable lanes. Both lanes are washed with the same reagents. Element currently offers kits with 150 and 300 cycles, both supporting 2 lanes, as well as a 600 cycle kit that supports a single lane. Index hopping rates are ~~virtually nil~~, limiting the need for UDI's. The AVITI24 can also perform direct in sample sequencing which includes spatial imaging of RNA, proteins, phospho-proteins, and cell morphology using [https://www.elementbiosciences.com/products/aviti24/cytoprofiling/ Teton chemistry] for cytoprofiling.
			The AVITI24 can run 2 flow cells per run, each hosting 2 independently-addressable lanes. Both lanes are washed with the same reagents. Element currently offers kits with 150 and 300 cycles, both supporting 2 lanes, as well as a 600 cycle kit that supports a single lane. Index hopping rates are similar to non-patterned Illumina, limiting the need for UDI's. The AVITI24 can also perform direct in sample sequencing which includes spatial imaging of RNA, proteins, phospho-proteins, and cell morphology using [https://www.elementbiosciences.com/products/aviti24/cytoprofiling/ Teton chemistry] for cytoprofiling.

Hilo1 at 21:04, 9 June 2025

2025-06-09T21:04:57Z

← Older revision		Revision as of 21:04, 9 June 2025
Line 104:		Line 104:


			<!-- hidden
	== Cytoprofiling with AVITI24 ==		== Cytoprofiling with AVITI24 ==

Line 116:		Line 116:

	For a Teton Run, cells are washed in the appropriate Cell Paint reagents for a fixed panel or custom panel cytoprofiling assay. A single Teton slide can be used to infer Morphology, RNA within the cells, Protein and also direct in situ sequencing up to 100nt which is not robust enough for transcriptomics, but is sufficient for investigating CRISPR or TCR or other short sequences of interest.		For a Teton Run, cells are washed in the appropriate Cell Paint reagents for a fixed panel or custom panel cytoprofiling assay. A single Teton slide can be used to infer Morphology, RNA within the cells, Protein and also direct in situ sequencing up to 100nt which is not robust enough for transcriptomics, but is sufficient for investigating CRISPR or TCR or other short sequences of interest.

			-->

Hilo1: /* Cytoprofiling with AVITI24 */

2025-06-09T21:03:55Z

Cytoprofiling with AVITI24

← Older revision		Revision as of 21:03, 9 June 2025
Line 107:		Line 107:
	== Cytoprofiling with AVITI24 ==		== Cytoprofiling with AVITI24 ==

	[[Image:DISS_example.jpg\|right\|200px\|Example of Teton imaging]]		[[Image:DISS_example.jpg\|thumb\|right\|200px\|Example of Teton imaging from Element Biosciences website]]

	A user can optimize the assay before attempting a Teton Run. This test will require an optimization kit. Optimization is similar to creating a slide for a Teton run. The standard steps of coating (or not) that slide, loading and culturing cells prior to fixing are all similar. Instead of running the optimization slide on the AVITI24, the optimization slide should be inspected with a fluorescence objective. This process requires a separate kit from the actual slide kits.		A user can optimize the assay before attempting a Teton Run. This test will require an optimization kit. Optimization is similar to creating a slide for a Teton run. The standard steps of coating (or not) that slide, loading and culturing cells prior to fixing are all similar. Instead of running the optimization slide on the AVITI24, the optimization slide should be inspected with a fluorescence objective. This process requires a separate kit from the actual slide kits.

	[[Image:OptimizationSlide.jpg\|middle\|Lamason Lab ~~Optimization~~ Slide]]		[[Image:OptimizationSlide.jpg\|thumb\|middle\|Lamason Lab Slide provided from Element Biosciences]]

	Users can pick up a 1- or 12-well Teton Slide kit from the Center. Currently, Poly-L-Lysine-coated and uncoated slide kits are available. Uncoated slides must be coated as laid out in the protocol and users should ensure that cell fixation is ideal for one of the possible coatings which are not PLL (currently: Collagen, Fibronectin, Gelatin, Laminin, Matrigel). Cells are loaded and cultured for the desired amount of time on coated slides. Cells are fixed and the Teton Slide may be stored at 2-8C for up to 30 days or may be run immediately on the AVITI24.		Users can pick up a 1- or 12-well Teton Slide kit from the Center. Currently, Poly-L-Lysine-coated and uncoated slide kits are available. Uncoated slides must be coated as laid out in the protocol and users should ensure that cell fixation is ideal for one of the possible coatings which are not PLL (currently: Collagen, Fibronectin, Gelatin, Laminin, Matrigel). Cells are loaded and cultured for the desired amount of time on coated slides. Cells are fixed and the Teton Slide may be stored at 2-8C for up to 30 days or may be run immediately on the AVITI24.

	For a Teton Run, cells are washed in the appropriate Cell Paint reagents for a fixed panel or custom panel cytoprofiling assay. A single Teton slide can be used to infer Morphology, RNA within the cells, Protein and also direct in situ sequencing up to 100nt which is not robust enough for transcriptomics, but is sufficient for investigating CRISPR or TCR or other short sequences of interest.		For a Teton Run, cells are washed in the appropriate Cell Paint reagents for a fixed panel or custom panel cytoprofiling assay. A single Teton slide can be used to infer Morphology, RNA within the cells, Protein and also direct in situ sequencing up to 100nt which is not robust enough for transcriptomics, but is sufficient for investigating CRISPR or TCR or other short sequences of interest.

Hilo1: /* Cytoprofiling with AVITI24 */

2025-06-09T21:01:09Z

Cytoprofiling with AVITI24

← Older revision		Revision as of 21:01, 9 June 2025
Line 109:		Line 109:
	[[Image:DISS_example.jpg\|right\|200px\|Example of Teton imaging]]		[[Image:DISS_example.jpg\|right\|200px\|Example of Teton imaging]]

	A user ~~must~~ optimize the assay before attempting a Teton Run. This test will require an optimization kit. Optimization is similar to creating a slide for a Teton run. The standard steps of coating (or not) that slide, loading and culturing cells prior to fixing are all similar. Instead of running the optimization slide on the AVITI24, the optimization slide should be inspected with a fluorescence objective. This process requires a separate kit from the actual slide kits.		A user can optimize the assay before attempting a Teton Run. This test will require an optimization kit. Optimization is similar to creating a slide for a Teton run. The standard steps of coating (or not) that slide, loading and culturing cells prior to fixing are all similar. Instead of running the optimization slide on the AVITI24, the optimization slide should be inspected with a fluorescence objective. This process requires a separate kit from the actual slide kits.

	[[Image:OptimizationSlide.jpg\|middle\|Lamason Lab Optimization Slide]]		[[Image:OptimizationSlide.jpg\|middle\|Lamason Lab Optimization Slide]]

Hilo1: /* Cytoprofiling with AVITI24 */

2025-06-09T20:55:18Z

Cytoprofiling with AVITI24

← Older revision		Revision as of 20:55, 9 June 2025
Line 109:		Line 109:
	[[Image:DISS_example.jpg\|right\|200px\|Example of Teton imaging]]		[[Image:DISS_example.jpg\|right\|200px\|Example of Teton imaging]]

	A user must optimize the assay before attempting a ~~full~~ Teton Run. This will require coating (or not) a slide, loading and culturing cells ~~and inspecting~~ the ~~quality with an~~ optimization ~~kit~~, ~~which is~~ a separate kit from the actual slide kits.		A user must optimize the assay before attempting a Teton Run. This test will require an optimization kit. Optimization is similar to creating a slide for a Teton run. The standard steps of coating (or not) that slide, loading and culturing cells prior to fixing are all similar. Instead of running the optimization slide on the AVITI24, the optimization slide should be inspected with a fluorescence objective. This process requires a separate kit from the actual slide kits.

	[[Image:OptimizationSlide.jpg\|middle\|Lamason Lab Optimization Slide]]		[[Image:OptimizationSlide.jpg\|middle\|Lamason Lab Optimization Slide]]

	Users can pick up a 1- or 12-well Teton Slide kit from the Center. Currently, Poly-L-Lysine-coated and uncoated slide kits are available. Uncoated slides must be coated ~~for~~ cell fixation. Cells are loaded and cultured for the desired amount of time on coated slides. ~~Once cells~~ are fixed, the Teton Slide may be stored at 2-8C for up to 30 days ~~prior to Cytoprofiling~~ on the AVITI24.		Users can pick up a 1- or 12-well Teton Slide kit from the Center. Currently, Poly-L-Lysine-coated and uncoated slide kits are available. Uncoated slides must be coated as laid out in the protocol and users should ensure that cell fixation is ideal for one of the possible coatings which are not PLL (currently: Collagen, Fibronectin, Gelatin, Laminin, Matrigel). Cells are loaded and cultured for the desired amount of time on coated slides. Cells are fixed and the Teton Slide may be stored at 2-8C for up to 30 days or may be run immediately on the AVITI24.

	~~Cells~~ are washed in the appropriate Cell Paint reagents for a fixed panel or custom panel cytoprofiling assay.		For a Teton Run, cells are washed in the appropriate Cell Paint reagents for a fixed panel or custom panel cytoprofiling assay. A single Teton slide can be used to infer Morphology, RNA within the cells, Protein and also direct in situ sequencing up to 100nt which is not robust enough for transcriptomics, but is sufficient for investigating CRISPR or TCR or other short sequences of interest.

	A single Teton slide can be used to infer Morphology, RNA within the cells, Protein and also direct in situ sequencing up to 100nt which is not robust enough for transcriptomics, but is sufficient for investigating CRISPR or TCR or other short sequences of interest.

Hilo1: /* Cytoprofiling with AVITI24 */

2025-06-09T20:47:53Z

Cytoprofiling with AVITI24

← Older revision		Revision as of 20:47, 9 June 2025
Line 111:		Line 111:
	A user must optimize the assay before attempting a full Teton Run. This will require coating (or not) a slide, loading and culturing cells and inspecting the quality with an optimization kit, which is a separate kit from the actual slide kits.		A user must optimize the assay before attempting a full Teton Run. This will require coating (or not) a slide, loading and culturing cells and inspecting the quality with an optimization kit, which is a separate kit from the actual slide kits.

	[[Image:OptimizationSlide.jpg\|middle~~\|200px~~\|Lamason Lab Optimization Slide]]		[[Image:OptimizationSlide.jpg\|middle\|Lamason Lab Optimization Slide]]

	Users can pick up a 1- or 12-well Teton Slide kit from the Center. Currently, Poly-L-Lysine-coated and uncoated slide kits are available. Uncoated slides must be coated for cell fixation. Cells are loaded and cultured for the desired amount of time on coated slides. Once cells are fixed, the Teton Slide may be stored at 2-8C for up to 30 days prior to Cytoprofiling on the AVITI24.		Users can pick up a 1- or 12-well Teton Slide kit from the Center. Currently, Poly-L-Lysine-coated and uncoated slide kits are available. Uncoated slides must be coated for cell fixation. Cells are loaded and cultured for the desired amount of time on coated slides. Once cells are fixed, the Teton Slide may be stored at 2-8C for up to 30 days prior to Cytoprofiling on the AVITI24.

Hilo1: /* Cytoprofiling with AVITI24 */

2025-06-09T20:47:42Z

Cytoprofiling with AVITI24

← Older revision		Revision as of 20:47, 9 June 2025
Line 110:		Line 110:

	A user must optimize the assay before attempting a full Teton Run. This will require coating (or not) a slide, loading and culturing cells and inspecting the quality with an optimization kit, which is a separate kit from the actual slide kits.		A user must optimize the assay before attempting a full Teton Run. This will require coating (or not) a slide, loading and culturing cells and inspecting the quality with an optimization kit, which is a separate kit from the actual slide kits.

			[[Image:OptimizationSlide.jpg\|middle\|200px\|Lamason Lab Optimization Slide]]

	Users can pick up a 1- or 12-well Teton Slide kit from the Center. Currently, Poly-L-Lysine-coated and uncoated slide kits are available. Uncoated slides must be coated for cell fixation. Cells are loaded and cultured for the desired amount of time on coated slides. Once cells are fixed, the Teton Slide may be stored at 2-8C for up to 30 days prior to Cytoprofiling on the AVITI24.		Users can pick up a 1- or 12-well Teton Slide kit from the Center. Currently, Poly-L-Lysine-coated and uncoated slide kits are available. Uncoated slides must be coated for cell fixation. Cells are loaded and cultured for the desired amount of time on coated slides. Once cells are fixed, the Teton Slide may be stored at 2-8C for up to 30 days prior to Cytoprofiling on the AVITI24.
Line 116:		Line 118:

	A single Teton slide can be used to infer Morphology, RNA within the cells, Protein and also direct in situ sequencing up to 100nt which is not robust enough for transcriptomics, but is sufficient for investigating CRISPR or TCR or other short sequences of interest.		A single Teton slide can be used to infer Morphology, RNA within the cells, Protein and also direct in situ sequencing up to 100nt which is not robust enough for transcriptomics, but is sufficient for investigating CRISPR or TCR or other short sequences of interest.

	~~[[Image:OptimizationSlide.jpg\|left\|200px\|Lamason Lab Optimization Slide]]~~

Hilo1: /* Cytoprofiling with AVITI24 */

2025-06-09T20:47:11Z

Cytoprofiling with AVITI24

← Older revision		Revision as of 20:47, 9 June 2025
Line 108:		Line 108:

	[[Image:DISS_example.jpg\|right\|200px\|Example of Teton imaging]]		[[Image:DISS_example.jpg\|right\|200px\|Example of Teton imaging]]

			A user must optimize the assay before attempting a full Teton Run. This will require coating (or not) a slide, loading and culturing cells and inspecting the quality with an optimization kit, which is a separate kit from the actual slide kits.

	Users can pick up a 1- or 12-well Teton Slide kit from the Center. Currently, Poly-L-Lysine-coated and uncoated slide kits are available. Uncoated slides must be coated for cell fixation. Cells are loaded and cultured for the desired amount of time on coated slides. Once cells are fixed, the Teton Slide may be stored at 2-8C for up to 30 days prior to Cytoprofiling on the AVITI24.		Users can pick up a 1- or 12-well Teton Slide kit from the Center. Currently, Poly-L-Lysine-coated and uncoated slide kits are available. Uncoated slides must be coated for cell fixation. Cells are loaded and cultured for the desired amount of time on coated slides. Once cells are fixed, the Teton Slide may be stored at 2-8C for up to 30 days prior to Cytoprofiling on the AVITI24.
Line 114:		Line 116:

	A single Teton slide can be used to infer Morphology, RNA within the cells, Protein and also direct in situ sequencing up to 100nt which is not robust enough for transcriptomics, but is sufficient for investigating CRISPR or TCR or other short sequences of interest.		A single Teton slide can be used to infer Morphology, RNA within the cells, Protein and also direct in situ sequencing up to 100nt which is not robust enough for transcriptomics, but is sufficient for investigating CRISPR or TCR or other short sequences of interest.

			[[Image:OptimizationSlide.jpg\|left\|200px\|Lamason Lab Optimization Slide]]