Editing BioMicroCenter:Element Sequencing (section)

== Element Sequencing ==
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.
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  !width=100|Service 
  !width=250|Element Sequencing
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  |SUBMISSION || Illumina OR Element libraries
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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
* Element Sequencing 
* Demultiplexing
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  |ADDITIONAL SERVICES ||
* Quality Control
* 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]
* Basic run metrics (alignment rate, complexity)
* Basic RNAseq metrics (where applicable)
* Basic paired end metrics (where applicable)
* Contamination checks
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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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=== 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.

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