multiplex PCR amplicon sequencing of TiLV_Nk - SRA

SRX20019090: multiplex PCR amplicon sequencing of TiLV_Nk
1 OXFORD_NANOPORE (MinION) run: 25,098 spots, 12.5M bases, 11.2Mb downloads

Design: Two sets of multiplex RT-PCR products were combined as a template for library preparation using the ligation sequencing kit (SQK-LSK109) and the native barcoding expansion 1-12 kit (EXP-NBD104) were used according to the Oxford Nanopore Technologies (ONT) standard protocols adapted for the Flongle flow cell. We used 250 ng PCR products for each sample (BCxx-BCxx), one unique native barcode (BC) per sample and washed the library of pooled barcoded samples with the Short Fragment Buffer (SFB) just before the elution step at the end of the protocol. DNA concentrations were determined between each step using the Qubit assay. The prepared TiLV library was loaded as per the standard protocol onto a Flongle flow cell (FLO-FLG106) for multiplex RT-PCR. Flongle flow cell was fitted to a Flongle adapter (FLGIntSP) for MinION.

Submitted by: WorldFish

Study: Tilapinevirus tilapiae Raw sequence reads

PRJNA957495 • SRP433472 • All experiments • All runs

show Abstracthide Abstract

TiLV is an important viral pathogen affecting Tilapia species worldwide. It causes significant impacts on production, livelihood and food security. Development of rapid diagnostic tools to generate genomic data for fine epidemiology and surveillance are needed.This is the first study to explore the usage of singleplex and multiplex RT-PCR enrichment approaches coupled with Nanopore amplicon based sequencing to obtain whole genome of the virusThis work was undertaken as part of the CGIAR Research Program on Fish Agri-Food Systems (FISH) led by WorldFish, the CGIAR Big Data Platform Inspire Challenge 2019 led by CIAT and IFPRI and is supported by contributors to the CGIAR Trust Fund: https://www.cgiar.org/funders/.

Sample:

SAMN34257321 • SRS17360746 • All experiments • All runs

Organism: Tilapia lake virus

Library:

Name: Nk

Instrument: MinION

Strategy: AMPLICON

Source: VIRAL RNA

Selection: RT-PCR

Layout: SINGLE

Runs: 1 run, 25,098 spots, 12.5M bases, 11.2Mb

Run	# of Spots	# of Bases	Size	Published
SRR24222688	25,098	12.5M	11.2Mb	2023-04-20

ID:: 27416800

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