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Which 10x Genomics library types are compatible with sequencing on the Element AVITI™ System?

Question: Which 10x Genomics library types are compatible with sequencing on the Element AVITI™ System?

Answer: As part of the 10x Genomics Compatible Partner Program, the library types below have been verified as compatible with sequencing on the Element AVITI System, after processing with the Element Adept™ Library Compatibility Kit.

  • Single Cell Gene Expression
    • Gene Expression: 3’ v3.1
  • Single Cell Immune Profiling
    • Gene Expression: 5’ v2
    • V(D)J: 5’ v2
  • Single Cell Gene Expression Flex
    • Gene Expression*
  • Visium Spatial Gene Expression for Fresh Frozen

The library types below have not been tested nor validated by 10x Genomics for sequencing on the Element AVITI System. Please reach out directly to Element Biosciences with questions regarding sequencing these library types on AVITI:

  • Single Cell Gene Expression
    • Gene Expression: 3’ HT, 3’ v4
    • Cell Surface Protein: 3’ v3.1, 3’ HT, 3’v4
    • Cell Multiplexing: 3’v3.1, 3’ HT
    • 3’ CRISPR: 3’ v3.1, 3’ HT
  • Single Cell Immune Profiling
    • Gene Expression: 5’ HT, 5’ v3
    • V(D)J: 5’ HT, 5’ v3
    • Cell Surface Protein: 5’ v2, 5’ HT, 5’ v3
    • 5’ CRISPR: 5’ v2, 5’ HT, 5’v3
  • Single Cell Gene Expression Flex
    • Cell Surface Protein
  • Single Cell ATAC
  • Single Cell Multiome ATAC + Gene Expression
    • Gene Expression
    • ATAC
  • Visium Spatial Gene Expression for FFPE*
  • Visium CytAssist Spatial Gene and Protein Expression
    • Gene Expression*
    • Protein
  • Visium HD Spatial Gene Expression*

* indicates that the 10x Genomics library construction uses Dual Index Plate TS, which requires custom primers for sequencing on the AVITI (see below).

Element workflows

1) Element Adept Library Compatibility Workflow

  • The compatibility testing mentioned above was performed with libraries processed using the Element Adept Library Compatibility Kit, which adapts linear libraries prepared with third-party kits for sequencing on the Element AVITI System. The Adept Standard Protocol uses the Element Adept Library Compatibility Kit v1.1 to circularize up to 24 reactions. The protocol starts with denaturing a linear library into single strands. The library is then annealed to splint oligos, which introduce the Element surface primer binding sequences. A ligation reaction circularizes the library, followed by enzymatic digestion for cleanup.

2) Element Cloudbreak Freestyle Workflow

  • The Element Cloudbreak Freestyle sequencing kit enables circularization on the flow cell, with direct loading of linear third-party libraries, and eliminates the need for library conversion steps before sequencing. The library types that were tested with the Adept workflow (see list above) were also tested by Element with the Cloudbreak Freestyle workflow. Please reach out to Element for further information. 10x Genomics has not verified compatibility of the Cloudbreak Freestyle workflow.

Custom sequencing primers needed for Dual Index TS plate

When sequencing 10x Genomics libraries processed using the Element Adept Library Compatibility workflow or the Cloudbreak Freestyle workflow, the standard AVITI sequencing primers are compatible with Illumina TruSeq and Nextera sequences and therefore would be compatible with 10x Genomics Dual Index TT, NT, TN or NN plates. If using 10x Genomics Dual Index TS plate, custom sequencing primers would be required. Please reach out to Element (support@elembio.com) for further guidance regarding custom primer design.

To determine which 10x Genomics Dual Index plate is used for a particular 10x Genomics library type, refer to this linked article (here), as well as the relevant library preparation User Guide.

Data analysis

For suggestions for running 10x Genomics software pipelines see this article: I have sequenced my 10x Genomics libraries on the Element AVITI System. Will my FASTQ files be compatible for software analysis?

Additional resources

Testing of the 10x Genomics library types in the verified list above was performed as part of the 10x Genomics Compatible Partner Program. However, 10x Genomics is not able to provide troubleshooting guidance for adapting 10x libraries for AVITI compatibility, or guidance regarding sequencing configurations, library pooling, or data analysis using Element workflows. 10x Genomics cannot guarantee success with these downstream workflows nor offer any replacements or goodwill reagents for troubleshooting Element workflows. Please reach out to Element (support@elembio.com) for assistance with troubleshooting Element workflows.

 

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