Editing BioMicroCenter:Element Sequencing (section)

== 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.


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== 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.

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