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High-throughput workflow for the genotypic characterization of transposon insertion library variants v2
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This is a workflow for the genotypic characterization of transposon library variants. It has been developed using an open-source Opentrons OT-2 robot, BLASTN for genomic annotations and modular sub-protocols (e.g., PCR sample preparation, OT-2 volume transfer, OT-2 counter selection, etc) that can be used for other tasks, thus providing a general-purpose pipeline. All steps follow a 96-well plate format for high-throughput analysis. The protocol is described for the characterization of transposon library variants generated with SEVA-Sib pBAMD1-x and pBLAM1-x plasmid sets that follow Standard European Vector Architecture (SEVA, https://seva-plasmids.com) and can be amplified with the standard PS1-PS6 primers. However, it can be adapted for other transposon systems. Changes from previous version: - This version references updated OT-2 automation protocols which now follow the standardized LAP format (https://www.laprepo.com). - Genotyping is performed with a new ad hoc python package to annotate genomic reads and identify the transposon insertion sites.
Springer Science and Business Media LLC
Title: High-throughput workflow for the genotypic characterization of transposon insertion library variants v2
Description:
This is a workflow for the genotypic characterization of transposon library variants.
It has been developed using an open-source Opentrons OT-2 robot, BLASTN for genomic annotations and modular sub-protocols (e.
g.
, PCR sample preparation, OT-2 volume transfer, OT-2 counter selection, etc) that can be used for other tasks, thus providing a general-purpose pipeline.
All steps follow a 96-well plate format for high-throughput analysis.
The protocol is described for the characterization of transposon library variants generated with SEVA-Sib pBAMD1-x and pBLAM1-x plasmid sets that follow Standard European Vector Architecture (SEVA, https://seva-plasmids.
com) and can be amplified with the standard PS1-PS6 primers.
However, it can be adapted for other transposon systems.
Changes from previous version: - This version references updated OT-2 automation protocols which now follow the standardized LAP format (https://www.
laprepo.
com).
- Genotyping is performed with a new ad hoc python package to annotate genomic reads and identify the transposon insertion sites.
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