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| == Element Sequencing ==
| | #REDIRECT [[BioMicroCenter:ShortRead]] |
| The Center currently hosts an AVITI24 platform from [https://www.elementbiosciences.com/ Element Biosciences].
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| AVITI24 platform supports both sequencing and cytoprofiling. For most sequencing needs, the Center will use Element's Freestyle chemistry kits.
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| {|
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| {| class="wikitable" border=1
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| !width=100|Service
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| !width=250|Element Sequencing
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| |-
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| |SUBMISSION || Illumina OR Element libraries
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| |-
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| |MIN VOLUME || 15 uL
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| |MIN CONCENTRATION || 2 nM
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| |INCLUDED SERVICES
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| * Quality Control:Fragment Analyzer and qPCR
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| * Element Sequencing
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| * Demultiplexing
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| |-
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| |ADDITIONAL SERVICES ||
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| * Quality Control
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| * Element library preperation
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| |DATA FORMATS
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| *FASTQ (stored 1 year)
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| |QUALITY CONTROL
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| * [https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ FASTQC]
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| * Basic run metrics (alignment rate, complexity)
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| * Basic RNAseq metrics (where applicable)
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| * Basic paired end metrics (where applicable)
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| * Contamination checks
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| |-
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| |PRICING || [[BioMicroCenter:Pricing#SINGULAR_G4|LINK]]
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| |SUBMISSION
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| * MIT - [https://mit.ilabsolutions.com/service_item/new/3381?spt_id=3863 ilabs]
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| |-
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| |}
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| == The AVITI24 Platform ==
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| {| class="wikitable" border=1
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| !width=100|
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| !width=250| AVITI24
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| !width=150| NOTES
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| |'''SEQUENCER'''||[[Image:Element_AVITI.jpg|center|200px]]||
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| | '''READS/FLOWCELL'''<BR> Low number is minimum per lane for standard Illumina libraries.||
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| * 300M HQ read pairs PF/flowcell
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| |'''RUN TIME'''||
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| * 75 PE 24 hours
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| * 150 PE 38 hours
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| * 300 PE 60 hours
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| |-
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| |'''KITS AVAILABLE'''||
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| * 2x75 Cloudbreak FS High
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| * 2x150 Cloudbreak FS High
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| * 2x300 Cloudbreak FS High
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| || - Single end supported <br> - each kit comes with 34 additional cycles
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| |'''KNOWN APPLICATIONS'''||
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| * Whole Genome Sequencing
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| * RNA Sequencing
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| * 16S
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| * Single-cell
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| * Target Sequencing and Enrichment
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| * Metagenomics
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| |-
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| |'''KEY NOTES'''||
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| * 4-color chemistry
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| * Patterned flow cell
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| * 2-lanes per flow cell
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| * Q40+ > 80%
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| * Low-binding surface chemistry
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| * Adept Workflow for adaptation of Illumina libraries
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| |-
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| |'''THANKS TO'''||
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| * Element Biosciences
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| |}
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| 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.
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| 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.
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