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RNA-seq

RNA-SEQ applied to the peacock blenny Salaria pavo: unveiling the gene networks and signalling pathways behind phenotypic plasticity in a littoral fish

RNA-SEQ applied to the peacock blenny Salaria pavo: unveiling the gene networks and signalling pathways behind phenotypic plasticity in a littoral fish

... of RNA-Seq data available from these studies, one way forward would be to do a comparative analysis, controlling for developmental factors, so that the shared genetic modules underlying the different ...

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RNA-Seq analysis of the Sclerotinia homoeocarpa--creeping bentgrass pathosystem.

RNA-Seq analysis of the Sclerotinia homoeocarpa--creeping bentgrass pathosystem.

... A better understanding of the molecular interactions between S. homoeocarpa and creeping bentgrass will be essential for the development of more sustainable and practical management strategies, including the use of plant ...

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A statistical method for the detection of alternative splicing using RNA-seq.

A statistical method for the detection of alternative splicing using RNA-seq.

... We randomly selected 20 false positive (FP) and several false negative (FN) splicing junctions for experimental validation by RT-PCR followed by Sanger sequencing (Table S2). False positive splicing junctions refer to ...

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Comparação de metodologias para identificação de genes diferencialmente expressos em experimentos de RNA-Seq de suínos

Comparação de metodologias para identificação de genes diferencialmente expressos em experimentos de RNA-Seq de suínos

... Apesar de útil, a técnica de microarray utilizada nesse estudo, apresenta algumas limitações quando comparada ao novo método sequenciamento de RNA em larga escala (RNA-Seq). Dentre essas limitações, ...

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Análise do transcriptoma de folhas de cana-de-açúcar submetidas à prolongada limitação hídrica usando RNA-Seq

Análise do transcriptoma de folhas de cana-de-açúcar submetidas à prolongada limitação hídrica usando RNA-Seq

... the RNA-Seq ...the RNA-Seq method were generated over a billion sequences, which allowed to obtain a total of 177,509 and 185,153 transcripts sequences for the tolerant and sensitive ...

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Identifying stably expressed genes from multiple RNA-Seq data sets

Identifying stably expressed genes from multiple RNA-Seq data sets

... In this paper, we identify stably expressed genes from RNA-Seq data sets based on a numerical measure—the sum of three variance components estimated from a mixed-effect model. For microarray data, there ...

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Assessing pseudogene expression during neural differentiation by RNA-Seq

Assessing pseudogene expression during neural differentiation by RNA-Seq

... of RNA is converted to cDNA fragments (library preparation) with adaptors attached to one or both ends, and the sequenced (Wang et ...engaged RNA polymerases by nuclear run-on RNA molecules (Core et ...

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Getting the most out of RNA-seq data analysis

Getting the most out of RNA-seq data analysis

... experiments with biological replicates, these methods were later modified to accommodate analysis of unreplicated experiments as well, but their performance relative to ASC, GFOLD and NOISeq remains unclear. We did not ...

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Identification of serum microRNA biomarkers for tuberculosis using RNA-seq.

Identification of serum microRNA biomarkers for tuberculosis using RNA-seq.

... [24,25]. RNA-seq is a more effective method for identifying significant changes in the levels of microRNAs between healthy people and individuals with active disease and for identifying microRNAs with ...

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MÉTODO DE IDENTIFICAÇÃO DE GENES TAXONOMICAMENTE RESTRITOS EM DADOS DE RNA-SEQ EM ORGANISMO NÃO MODELO

MÉTODO DE IDENTIFICAÇÃO DE GENES TAXONOMICAMENTE RESTRITOS EM DADOS DE RNA-SEQ EM ORGANISMO NÃO MODELO

... Black pepper (Piper nigrum) is a biotechnologically interesting plant, research target for both metabolism exploration and improvement related to phytopathological problems, in addition to understanding the evolution of ...

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Systematically differentiating functions for alternatively spliced isoforms through integrating RNA-seq data.

Systematically differentiating functions for alternatively spliced isoforms through integrating RNA-seq data.

... Integrating large-scale functional genomic data has significantly accelerated our understanding of gene functions. However, no algorithm has been developed to differentiate functions for isoforms of the same gene using ...

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RNA-Seq reveals leaf cuticular wax-related genes in Welsh onion.

RNA-Seq reveals leaf cuticular wax-related genes in Welsh onion.

... and to identify the important genes that play key roles in wax synthesis in the Welsh onion. The high-throughput sequencing results will also reveal other pathways that are related to wax synthesis and will identify a ...

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Identification of potential target genes of USP22 via ChIP-seq and RNA-seq analysis in HeLa cells

Identification of potential target genes of USP22 via ChIP-seq and RNA-seq analysis in HeLa cells

... To further investigate the regulation of target gene ex- pression by USP22, HeLa cells were infected with control lentivirus or lentivirus for USP22-specific shRNA expres- sion. Western blot analysis indicated that ...

8

ANOVA-like differential expression (ALDEx) analysis for mixed population RNA-Seq.

ANOVA-like differential expression (ALDEx) analysis for mixed population RNA-Seq.

... At least one other RNA-Seq analysis method, baySeq[53], has used a Bayesian framework to estimate the likelihood of differential gene expression. There are several differences between the Bayesian methods ...

15

AuPairWise: A Method to Estimate RNA-Seq Replicability through Co-expression.

AuPairWise: A Method to Estimate RNA-Seq Replicability through Co-expression.

... accessible RNA-seq experiments where we define an experiment as a set of ...83 RNA-seq experiments from the Gemma database [40] that were processed using RSEM ...

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Compacting and correcting Trinity and Oases RNA-Seq de novo assemblies

Compacting and correcting Trinity and Oases RNA-Seq de novo assemblies

... these RNA-Seq assembly problems but several software packages have been proven to generate contig sets comprising most of the expressed transcripts correctly ...

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Número de repetições na identificação de genes diferencialmente expressos em experimentos de RNA-Seq

Número de repetições na identificação de genes diferencialmente expressos em experimentos de RNA-Seq

... (RNA- Seq). De modo geral, as metodologias de RNA-Seq se caracterizam pela conversão de RNA em uma biblioteca de fragmentos de cDNA, de forma que cada molécula pode ser sequenciada por ...

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RNA-Seq gene profiling--a systematic empirical comparison.

RNA-Seq gene profiling--a systematic empirical comparison.

... of RNA-seq data analysis methods: one on the performance of several spliced alignment programs by focusing on the quality of the alignments [16]; the second study evaluated computational methods for ...

10

Bioinformatics analyses and approaches to RNA-Seq Data

Bioinformatics analyses and approaches to RNA-Seq Data

... total RNA was depleted with the Ribo-Zero Low Input Gold Kit (Human/Mouse/Rat) from Epicentre using 500-1000 ng of starting ...sample. RNASeq libraries were prepared from the enriched material using ...

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Análise de dados de RNA-Seq com diferentes números de fatores e repetições

Análise de dados de RNA-Seq com diferentes números de fatores e repetições

... fragmentos de cDNA de tamanho entre 35 a 300 pares de bases (pb) são selecionados e colocados para serem ampliados por PCR (conjunto de reações químicas que multiplica a quantidade de material genético disponível em uma ...

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