Real-time DNA barcoding in a remote rainforest using nanopore sequencing, bioRxiv, 2017-09-16

AbstractAdvancements in portable scientific instruments provide promising avenues to expedite field work in order to understand the diverse array of organisms that inhabit our planet. Here we tested the feasibility for in situ molecular analyses of endemic fauna using a portable laboratory fitting within a single backpack, in one of the world’s most imperiled biodiversity hotspots the Ecuadorian Chocó rainforest. We utilized portable equipment, including the MinION DNA sequencer (Oxford Nanopore Technologies) and miniPCR (miniPCR), to perform DNA extraction, PCR amplification and real-time DNA barcode sequencing of reptile specimens in the field. We demonstrate that nanopore sequencing can be implemented in a remote tropical forest to quickly and accurately identify species using DNA barcoding, as we generated consensus sequences for species resolution with an accuracy of >99% in less than 24 hours after collecting specimens. In addition, we generated sequence information at Universidad Tecnológica Indoamérica in Quito for the recently re-discovered Jambato toad Atelopus ignescens, which was thought to be extinct for 28 years, a rare species of blind snake Trilepida guayaquilensis, and two undescribed species of Dipsas snakes. In this study we establish how mobile laboratories and nanopore sequencing can help to accelerate species identification in remote areas (especially for species that are difficult to diagnose based on characters of external morphology), be applied to local research facilities in developing countries, and rapidly generate information for species that are rare, endangered and undescribed, which can potentially aid in conservation efforts.

biorxiv evolutionary-biology 100-200-users 2017

Massive Mining of Publicly Available RNA-seq Data from Human and Mouse, bioRxiv, 2017-09-15

RNA-sequencing (RNA-seq) is currently the leading technology for genome-wide transcript quantification. While the volume of RNA-seq data is rapidly increasing, the currently publicly available RNA-seq data is provided mostly in raw form, with small portions processed non- uniformly. This is mainly because the computational demand, particularly for the alignment step, is a significant barrier for global and integrative retrospective analyses. To address this challenge, we developed all RNA-seq and ChIP-seq sample and signature search (ARCHS4), a web resource that makes the majority of previously published RNA-seq data from human and mouse freely available at the gene count level. Such uniformly processed data enables easy integration for downstream analyses. For developing the ARCHS4 resource, all available FASTQ files from RNA-seq experiments were retrieved from the Gene Expression Omnibus (GEO) and aligned using a cloud-based infrastructure. In total 137,792 samples are accessible through ARCHS4 with 72,363 mouse and 65,429 human samples. Through efficient use of cloud resources and dockerized deployment of the sequencing pipeline, the alignment cost per sample is reduced to less than one cent. ARCHS4 is updated automatically by adding newly published samples to the database as they become available. Additionally, the ARCHS4 web interface provides intuitive exploration of the processed data through querying tools, interactive visualization, and gene landing pages that provide average expression across cell lines and tissues, top co-expressed genes, and predicted biological functions and protein-protein interactions for each gene based on prior knowledge combined with co-expression. Benchmarking the quality of these predictions, co-expression correlation data created from ARCHS4 outperforms co-expression data created from other major gene expression data repositories such as GTEx and CCLE.ARCHS4 is freely accessible at <jatsext-link xmlnsxlink=httpwww.w3.org1999xlink ext-link-type=uri xlinkhref=httpamp.pharm.mssm.eduarchs4>httpamp.pharm.mssm.eduarchs4<jatsext-link>

biorxiv bioinformatics 200-500-users 2017

 

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