Título

Adapterama I: universal stubs and primers for 384 unique dual-indexed or 147,456 combinatorially-indexed Illumina libraries (iTru

&

iNext)

Autor

Travis Glenn

Troy Kieran

Jon Sanders

NATALIA JULIANA BAYONA VASQUEZ

John Finger

Todd Pierson

Swarnali Louha

FRANCISCO JAVIER GARCIA DE LEON

MIGUEL ANGEL DEL RIO PORTILLA

Nivel de Acceso

Acceso Abierto

Referencia de publicación

URL/URL: https://peerj.com/articles/7755/

doi: DOI: 10.7717/peerj.7755

ISSN/ISSN: 21678359

Resumen o descripción

"Massively parallel DNA sequencing offers many benefits, but major inhibitory cost factors include: (1) start-up (i.e., purchasing initial reagents and equipment); (2) buyin (i.e., getting the smallest possible amount of data from a run); and (3) sample preparation. Reducing sample preparation costs is commonly addressed, but start-up and buy-in costs are rarely addressed. We present dual-indexing systems to address all three of these issues. By breaking the library construction process into universal, re-usable, combinatorial components, we reduce all costs, while increasing the number of samples and the variety of library types that can be combined within runs. We accomplish this by extending the Illumina TruSeq dual-indexing approach to 768 (384 C 384) indexed primers that produce 384 unique dual-indexes or 147,456 (384 _ 384) unique combinations. We maintain eight nucleotide indexes, with many that are compatible with Illumina index sequences. We synthesized these indexing primers, purifying them with only standard desalting and placing small aliquots in replicate plates. In qPCR validation tests, 206 of 208 primers tested passed (99% success). We then created hundreds of libraries in various scenarios. Our approach reduces startup and per-sample costs by requiring only one universal adapter that works with indexed PCR primers to uniquely identify samples. Our approach reduces buy-in costs because: (1) relatively few oligonucleotides are needed to produce a large number of indexed libraries; and (2) the large number of possible primers allows researchers to use unique primer sets for different projects, which facilitates pooling of simples during sequencing. Our libraries make use of standard Illumina sequencing primers and index sequence length and are demultiplexed with standard Illumina software, thereby minimizing customization headaches. In subsequent Adapterama papers, we use these same primers with different adapter stubs to construct amplicon and restriction-site associated DNAlibraries, but their use can be expanded to any type of library sequenced on Illumina platforms."

Editor

PeerJ

Fecha de publicación

2019

Tipo de publicación

Artículo

Versión de la publicación

Versión publicada

Formato

application/pdf

Fuente

PeerJ

Idioma

Inglés

Repositorio Orígen

Repositorio Institucional CIBNOR

Descargas

269

Comentarios



Necesitas iniciar sesión o registrarte para comentar.