共查询到20条相似文献,搜索用时 250 毫秒
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Courtney N. Passow Thomas J. Y. Kono Bethany A. Stahl James B. Jaggard Alex C. Keene Suzanne E. McGaugh 《Molecular ecology resources》2019,19(2):456-464
RNA sequencing is a popular next‐generation sequencing technique for assaying genome‐wide gene expression profiles. Nonetheless, it is susceptible to biases that are introduced by sample handling prior gene expression measurements. Two of the most common methods for preserving samples in both field‐based and laboratory conditions are submersion in RNAlater and flash freezing in liquid nitrogen. Flash freezing in liquid nitrogen can be impractical, particularly for field collections. RNAlater is a solution for stabilizing tissue for longer‐term storage as it rapidly permeates tissue to protect cellular RNA. In this study, we assessed genome‐wide expression patterns in 30‐day‐old fry collected from the same brood at the same time point that were flash‐frozen in liquid nitrogen and stored at ?80°C or submerged and stored in RNAlater at room temperature, simulating conditions of fieldwork. We show that sample storage is a significant factor influencing observed differential gene expression. In particular, genes with elevated GC content exhibit higher observed expression levels in liquid nitrogen flash‐freezing relative to RNAlater storage. Further, genes with higher expression in RNAlater relative to liquid nitrogen experience disproportionate enrichment for functional categories, many of which are involved in RNA processing. This suggests that RNAlater may elicit a physiological response that has the potential to bias biological interpretations of expression studies. The biases introduced to observed gene expression arising from mimicking many field‐based studies are substantial and should not be ignored. 相似文献
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De novo transcriptome assembly and identification of genes associated with feed conversion ratio and breast muscle yield in domestic ducks
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Feng Zhu Jian‐Ming Yuan Zhen‐He Zhang Jin‐Ping Hao Yu‐ze Yang Shen‐Qiang Hu Fang‐Xi Yang Lu‐Jiang Qu Zhuo‐Cheng Hou 《Animal genetics》2015,46(6):636-645
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A. R. Pérez‐Porro D. Navarro‐Gómez M. J. Uriz G. Giribet 《Molecular ecology resources》2013,13(3):494-509
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Josefa Gómez‐Maldonado Isabelle Lesur Noe Fernández‐Pozo Marina Rueda‐López Dario Guerrero‐Fernández Vanessa Castro‐Rodríguez Hicham Benzekri Rafael A. Cañas María‐Angeles Guevara Andreia Rodrigues Pedro Seoane Caroline Teyssier Alexandre Morel François Ehrenmann Grégoire Le Provost Céline Lalanne Céline Noirot Christophe Klopp Isabelle Reymond Angel García‐Gutiérrez Jean‐François Trontin Marie‐Anne Lelu‐Walter Celia Miguel María Teresa Cervera Francisco R. Cantón Christophe Plomion Luc Harvengt Concepción Avila M. Gonzalo Claros Francisco M. Cánovas 《Plant biotechnology journal》2014,12(3):286-299
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Danielle A. Schmidt Nathan R. Campbell Purnima Govindarajulu Karl W. Larsen Michael A. Russello 《Molecular ecology resources》2020,20(1):114-124
Minimally invasive sampling (MIS) is widespread in wildlife studies; however, its utility for massively parallel DNA sequencing (MPS) is limited. Poor sample quality and contamination by exogenous DNA can make MIS challenging to use with modern genotyping‐by‐sequencing approaches, which have been traditionally developed for high‐quality DNA sources. Given that MIS is often more appropriate in many contexts, there is a need to make such samples practical for harnessing MPS. Here, we test the ability for Genotyping‐in‐Thousands by sequencing (GT‐seq), a multiplex amplicon sequencing approach, to effectively genotype minimally invasive cloacal DNA samples collected from the Western Rattlesnake (Crotalus oreganus), a threatened species in British Columbia, Canada. As there was no previous genetic information for this species, an optimized panel of 362 SNPs was selected for use with GT‐seq from a de novo restriction site‐associated DNA sequencing (RADseq) assembly. Comparisons of genotypes generated within and among RADseq and GT‐seq for the same individuals found low rates of genotyping error (GT‐seq: 0.50%; RADseq: 0.80%) and discordance (2.57%), the latter likely due to the different genotype calling models employed. GT‐seq mean genotype discordance between blood and cloacal swab samples collected from the same individuals was also minimal (1.37%). Estimates of population diversity parameters were similar across GT‐seq and RADseq data sets, as were inferred patterns of population structure. Overall, GT‐seq can be effectively applied to low‐quality DNA samples, minimizing the inefficiencies presented by exogenous DNA typically found in minimally invasive samples and continuing the expansion of molecular ecology and conservation genetics in the genomics era. 相似文献
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