Please follow the step-by-step instruction in the PDF document.

Select the appropriate Magnis protocol from the protocol menu for your NGS application. If you are not certain which protocol to use for your Magnis run, please consult with your local field application scientist to choose the proper protocol.

1. Protocol SSEL-RNA-XTHS2-ILM

   This protocol is designed and optimized to automate the SureSelect XT HS2 RNA workflow on the Magnis NGS Prep system including on-deck cDNA conversion. Output libraries are ready to use with downstream Illumina sequencing platforms, including high-throughput sequencing platforms using patterned flow cells. Users can choose to start from either samples of intact RNA or FFPE samples.

   This protocol is compatible with the following Magnis SureSelect XT HS2 RNA reagent kits, which contain pre-aliquoted capture probes on the probe plate:

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   Part Number	Description
   G9751C	Magnis SureSelect XT HS2, RNA, Tier 1 (1 - 499kb), Illumina, 32
   G9751D	Magnis SureSelect XT HS2, RNA, Tier 1 (1 - 499kb), Illumina, 96
   G9752C	Magnis SureSelect XT HS2, RNA, Tier 2 (0.5-2.9Mb), Illumina, 32
   G9752D	Magnis SureSelect XT HS2, RNA, Tier 2 (0.5-2.9Mb), Illumina, 96
   G9753C	Magnis SureSelect XT HS2, RNA, Tier 3 (3-5.9Mb), Illumina, 32
   G9753D	Magnis SureSelect XT HS2, RNA, Tier 3 (3-5.9Mb), Illumina, 96
   G9754C	Magnis SureSelect XT HS2 RNA, Tier 4 (6-11.9Mb), Illumina, 32
   G9754D	Magnis SureSelect XT HS2, RNA, Tier 4 (6 11.9Mb), Illumina, 96
   G9755C	Magnis SureSelect XT HS2, RNA, Tier 5 (12-24Mb), Illumina, 32
   G9755D	Magnis SureSelect XT HS2, RNA, Tier 5 (12-24Mb), Illumina, 96
   G9756C	Magnis SureSelect XT HS2, RNA, 24-50Mb, Illumina, 32
   G9756D	Magnis SureSelect XT HS2, RNA, 24-50Mb, Illumina, 96
   G9773C	Magnis SureSelect XT HS2, RNA, Exome V7, Illumina, 32
   G9773D	Magnis SureSelect XT HS2, RNA, Exome V7, Illumina, 96
   G9774C	Magnis SureSelect XT HS2, RNA, Exome V8, Illumina, 32
   G9774D	Magnis SureSelect XT HS2, RNA, Exome V8, Illumina, 96
   G9777C	Magnis SureSelect Cancer CGP, XT HS2 RNA, Illumina, 32
   G9777D	Magnis SureSelect Cancer CGP, XT HS2 RNA, Illumina, 96

   
    
2. Protocol SSEL-DNA-XTHS2-ILM

   This protocol is designed and optimized to automate the SureSelect XT HS2 DNA workflow on the Magnis NGS Prep System. Output libraries are ready to use with downstream Illumina sequencing platforms, including high-throughput sequencing platforms using patterned flow cells. Users can choose to either start from gDNA using the on-deck enzymatic fragmentation or to start from DNA that is already sheared by a Covaris.

   This protocol is compatible with the following Magnis SureSelect XT HS2 DNA reagent kits, which contain pre-aliquoted capture probes in the probe plate:

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   Part Number	Description
   G9751A	Magnis SSEL XT HS2, DNA, Tier 1, ILM, 32
   G9751B	Magnis SSEL XT HS2, DNA, Tier 1, ILM, 96
   G9752A	Magnis SSEL XT HS2, DNA, Tier 2, ILM, 32
   G9752B	Magnis SSEL XT HS2, DNA, Tier 2, ILM, 96
   G9753A	Magnis SSEL XT HS2, DNA, Tier 3, ILM, 32
   G9753B	Magnis SSEL XT HS2, DNA, Tier 3, ILM, 96
   G9754A	Magnis SSEL XT HS2, DNA, Tier 4, ILM, 32
   G9754B	Magnis SSEL XT HS2, DNA, Tier 4, ILM, 96
   G9755A	Magnis SSEL XT HS2, DNA, Tier 5, ILM, 32
   G9755B	Magnis SSEL XT HS2, DNA, Tier 5, ILM, 96
   G9756A	Magnis SSEL XT HS2, DNA, 24-50Mb, ILM, 32
   G9756B	Magnis SSEL XT HS2, DNA, 24-50Mb, ILM, 96
   G9773A	Magnis SSEL XT HS2, DNA,HuExon V7,ILM 32
   G9773B	Magnis SSEL XT HS2, DNA,HuExon V7,ILM 96
   G9774A	Magnis SSEL XT HS2, DNA,HuExon V8,ILM 32
   G9774B	Magnis SSEL XT HS2, DNA,HuExon V8,ILM 96
   G9776A	Magnis SSEL XTHS2, DNA, TumorMap, ILM 32
   G9776B	Magnis SSEL XTHS2, DNA, TumorMap, ILM 96

   
    
3. Protocol SSEL XTHS-RevB-ILM

   This protocol is compatible with SureSelect XT HS Rev B labeled Magnis kits, output libraries are ready to use with downstream Illumina sequencing platforms. This protocol supports optimal hybridization conditions for most SureSelect XT HS custom probes and SureSelect Human Exome V7 and Exome V8.

   This protocol is compatible with following Magnis reagent kit part numbers:

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   Part Number	Description
   G9731C	Magnis SSEL XT HS, Tier 1, Rev B, ILM, 32
   G9731D	Magnis SSEL XT HS, Tier 1, Rev B, ILM, 96
   G9732C	Magnis SSEL XT HS, Tier 2, Rev B, ILM, 32
   G9732D	Magnis SSEL XT HS, Tier 2, Rev B, ILM, 96
   G9733C	Magnis SSEL XT HS, Tier 3, Rev B, ILM, 32
   G9733D	Magnis SSEL XT HS, Tier 3, Rev B, ILM, 96
   G9734C	Magnis SSEL XT HS, Tier 4, Rev B, ILM, 32
   G9734D	Magnis SSEL XT HS, Tier 4, Rev B, ILM, 96
   G9735C	Magnis SSEL XT HS, Tier 5, Rev B, ILM, 32
   G9735D	Magnis SSEL XT HS, Tier 5, Rev B, ILM, 96
   G9736C	Magnis SSEL XT HS, SOW, Rev B, ILM, 32
   G9736D	Magnis SSEL XT HS, SOW, Rev B, ILM, 96
   G9771C	Magnis SSEL XT HS, HuExon V7, RevB, ILM, 32
   G9771D	Magnis SSEL XT HS, HuExon V7, RevB, ILM, 96
   G9772C	Magnis SSEL XT HS, HuExon V8, RevB, ILM, 32
   G9772D	Magnis SSEL XT HS, HuExon V8, RevB, ILM, 96

   
    
4. Protocol LT-SSEL XTHS-RevB-ILM

   This protocol is compatible with SureSelect XT HS Rev B labeled Magnis kits, output libraries are ready to use with downstream Illumina sequencing platforms. If you are running SureSelectXT HS-Illumina protocol on your Magnis, Agilent recommends this protocol when switching to Rev B labeled reagent kits to maintain current performance. This protocol is also recommended when using legacy XT custom probes.

   This protocol is compatible with the following Magnis reagent kit part numbers:

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   Part Number	Description
   G9731C	Magnis SSEL XT HS, Tier 1, Rev B, ILM, 32
   G9731D	Magnis SSEL XT HS, Tier 1, Rev B, ILM, 96
   G9732C	Magnis SSEL XT HS, Tier 2, Rev B, ILM, 32
   G9732D	Magnis SSEL XT HS, Tier 2, Rev B, ILM, 96
   G9733C	Magnis SSEL XT HS, Tier 3, Rev B, ILM, 32
   G9733D	Magnis SSEL XT HS, Tier 3, Rev B, ILM, 96
   G9734C	Magnis SSEL XT HS, Tier 4, Rev B, ILM, 32
   G9734D	Magnis SSEL XT HS, Tier 4, Rev B, ILM, 96
   G9735C	Magnis SSEL XT HS, Tier 5, Rev B, ILM, 32
   G9735D	Magnis SSEL XT HS, Tier 5, Rev B, ILM, 96

   
    
5. Protocol SSEL-RNA-XTHS2-EPIS-ILM

   This protocol is designed and optimized to automate the SureSelect XT HS2 RNA workflow for Magnis reagent kit G9750D (Magnis SSEL XT HS2 RNA, No Probe, ILMN, 96 rxns). In this protocol, the user starts from total RNA and self-fills each of the 8 wells with the same or different SureSelect target capture probes in each run. Output libraries are ready to use with downstream Illumina sequencing platforms, including high-throughput sequencing platforms using patterned flow cells.

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   Part Number	Description
   G9750D	Magnis SSEL XT HS2 RNA, No Probe, ILMN, 96 Rxns

   
    
6. Protocol SSEL-DNA-XTHS2-EPIS-ILM

   This protocol is designed and optimized to automate the SureSelect XT HS2 DNA workflow for Magnis reagent kit G9750B (Magnis SSEL XT HS2 DNA, No Probe, ILMN, 96 rxns). In this protocol, the user self-fills each of the 8 wells with the same or different SureSelect target capture probes in each run. Output libraries are ready to use with downstream Illumina sequencing platforms, including high-throughput sequencing platforms using patterned flow cells. Users can choose to either start from gDNA using the on-deck enzymatic fragmentation or to start from DNA that is already sheared by a Covaris.

   DOWNLOAD

   Part Number	Description
   G9750B	Magnis SSEL XT HS2 DNA, No Probe, ILMN, 96 Rxns

   
    
7. Protocol SSEL-XTHS-RevB-EPIS-ILM

   This protocol is designed and optimized for Magnis reagent kit G9730D (Magnis SSEL XT HS, No Probe, Rev B, ILMN, 96 rxns). In this protocol, the user self-fills each of the 8 wells with same or different SureSelect target capture probes in each run. Output libraries are ready to use with downstream Illumina sequencing platforms. This protocol supports optimal hybridization conditions for most SureSelect XT HS custom probes and SureSelect Human Exome V7 and Exome V8.

   DOWNLOAD
   
    
8. Protocol LT-SSEL-XTHS-RevB-EPIS-ILM

   This protocol is designed and optimized for Magnis kit G9730D (Magnis SureSelect XT HS, No probe, Rev B, ILMN, 96 rxns). In this protocol, the user self-fills each of the 8 wells with same or different SureSelect target capture probes in each run. Output libraries are ready to use with downstream Illumina sequencing platforms. If you are using Magnis reagent kit G9730B (Magnis SureSelect XT HS, No probe, ILMN, 96 rxns) on Magnis, Agilent recommends this protocol when switching to Magnis reagent kit G9730D reagent kits to maintain current performance. This protocol is also recommended when using legacy SureSelect XT custom probes.

   DOWNLOAD

For Research Use Only. Not for use in diagnostic procedures.