High-throughput Viral Amplicon Sequencing

The mHVRs for TEDa2cl4 were amplified according to the protocol and primers proposed in [33 (link)]. Amplicons were then purified using the magnetic beads Agencourt AMPure XP-PCR Purification (Beckman Genomics, USA). The concentration of the purified amplicons was controlled using Qubit Fluorometer 2.0 (Invitrogen, USA). The library was validated using the Fragment Analyzer system (Advanced Analytical Technologies, USA). The library was sequenced on an Illumina MiSeq using a 500 cycle v2 kit (Illumina, San Diego, USA). The mHVR reads from TEV55cl1 and PalDa20cl3 were previously published in [33 (link)].

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Rusman F., Floridia-Yapur N., Ragone P.G., Diosque P, & Tomasini N. (2020). Evidence of hybridization, mitochondrial introgression and biparental inheritance of the kDNA minicircles in Trypanosoma cruzi I. PLoS Neglected Tropical Diseases, 14(1), e0007770.

Publication 2020

Qubit Fluorometer 2.0 Fragment Analyzer system 500 cycle v2 kit

Library Primers

Corresponding Organization : Consejo Nacional de Investigaciones Científicas y Técnicas

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Variable analysis

independent variables

Primers used for amplification of mHVRs for TEDa2cl4 as proposed in [33]
Magnetic beads Agencourt AMPure XP-PCR Purification used for amplicon purification
Illumina MiSeq sequencing platform used with a 500 cycle v2 kit

dependent variables

Concentration of purified amplicons measured using Qubit Fluorometer 2.0
Library validation using the Fragment Analyzer system

control variables

MHVR reads from TEV55cl1 and PalDa20cl3 previously published in [33]

controls

Positive control: mHVR reads from TEV55cl1 and PalDa20cl3 previously published in [33]
Negative control: Not explicitly mentioned

Annotations

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