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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.
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=== 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.


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.
=== 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,
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*submitted libraries are at least 2 nM.
*submitted libraries are at least 2 nM.


===Lane-by-lane Notes===
|}
*The wait is variable
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*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 ==
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  |'''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'''||
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* 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.




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


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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.
-->

Latest revision as of 15:56, 20 July 2025

Element Sequencing[edit]

The Center currently hosts an AVITI24 platform from Element Biosciences. AVITI24 platform supports both sequencing and cytoprofiling. For most sequencing needs, the Center will use Element's Freestyle chemistry kits.

Service 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
  • FASTQC
  • Basic run metrics (alignment rate, complexity)
  • Basic RNAseq metrics (where applicable)
  • Basic paired end metrics (where applicable)
  • Contamination checks
PRICING LINK
SUBMISSION

ANCHORS[edit]

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.

INDEXING[edit]

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.

  • 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[edit]

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[edit]

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[edit]

AVITI24 NOTES
SEQUENCER
READS/FLOWCELL
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
- 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 Teton chemistry for cytoprofiling.


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