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[PDF] Top 20 De novo assembly of the perennial ryegrass transcriptome using an RNA-Seq strategy.

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De novo assembly of the perennial ryegrass transcriptome using an RNA-Seq strategy.

De novo assembly of the perennial ryegrass transcriptome using an RNA-Seq strategy.

... independently using the Trinity pipeline (release 2013- 02-25) with the following settings; Inchworm: -K –L 25; Chrysalis: -min_glue 2 -glue_factor ...1000000. The de novo assembled ... See full document

13

De Novo Transcriptome Assembly of the Chinese Swamp Buffalo by RNA Sequencing and SSR Marker Discovery.

De Novo Transcriptome Assembly of the Chinese Swamp Buffalo by RNA Sequencing and SSR Marker Discovery.

... to the Bubalus genus of the Bovidae family, is an economically significant livestock that has been used as dairy, meat, and source of draught power ...swamps. The domestic water ... See full document

20

De novo transcriptome sequencing of the Octopus vulgaris hemocytes using Illumina RNA-Seq technology: response to the infection by the gastrointestinal parasite Aggregata octopiana.

De novo transcriptome sequencing of the Octopus vulgaris hemocytes using Illumina RNA-Seq technology: response to the infection by the gastrointestinal parasite Aggregata octopiana.

... through the skin and mantle muscle behind the head to withdraw hemolymph with a disposable syringe (1 ml) inserted directly into the cephalic ...milliliter of hemolymph from each octopus was ... See full document

15

De novo assembly of the common bean transcriptome using short reads for the discovery of drought-responsive genes.

De novo assembly of the common bean transcriptome using short reads for the discovery of drought-responsive genes.

... one of the most important food legumes, far ahead of other ...legumes. The average grain yield of the common bean worldwide is much lower than its potential yields, primarily due ... See full document

10

De novo transcriptome assembly for the tropical grass Panicum maximum Jacq.

De novo transcriptome assembly for the tropical grass Panicum maximum Jacq.

... quarter of total production ...in the species breeding objectives ...Currently, the breeding of tropical forage grasses such as ...on the assessment and selection of natural ... See full document

10

Use of a capture-based pathogen transcript enrichment strategy for RNA-Seq analysis of the Francisella tularensis LVS transcriptome during infection of murine macrophages.

Use of a capture-based pathogen transcript enrichment strategy for RNA-Seq analysis of the Francisella tularensis LVS transcriptome during infection of murine macrophages.

... has the ability to infect multiple cell types and exist within multiple intracellular compartments during infection of the ...host. The requirements for survival and proliferation during ... See full document

12

De novo transcriptome assembly and the putative biosynthetic pathway of steroidal sapogenins of Dioscorea composita.

De novo transcriptome assembly and the putative biosynthetic pathway of steroidal sapogenins of Dioscorea composita.

... veal the biosynthesis of the active ...in transcriptome deep sequencing technology and bioinformatics have opened a new avenue for such ...with the conventional methods for gene cloning ... See full document

18

De Novo Assembly and Characterization of Early Embryonic Transcriptome of the Horseshoe Crab Tachypleus tridentatus.

De Novo Assembly and Characterization of Early Embryonic Transcriptome of the Horseshoe Crab Tachypleus tridentatus.

... understand the molecular mechanisms underlying the embryonic development of ...for the first time the de novo transcriptome assembly for ...stage using ... See full document

18

European sea bass (Dicentrarchus labrax) skin and scale transcriptomes

European sea bass (Dicentrarchus labrax) skin and scale transcriptomes

... appendages, the mineralized scales, are important organs for protection and homeostasis, but little is known about their specific transcript or protein ...used RNA-seq to generate ... See full document

10

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

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

... number of diverse samples (Danio rerio multi samples: Dd) and one simulated dataset (Danio rerio simulated: ...Ds). The simulated reads have been produced using rsem-simulate-reads (version ...2011). ... See full document

22

Getting the most out of RNA-seq data analysis

Getting the most out of RNA-seq data analysis

... Despite the microarray’s analytical maturity, RNA-seq, which is based on next- generation sequencing technology—is set to become the method of choice for current and future gene ... See full document

20

A powerful method for transcriptional profiling of specific cell types in eukaryotes: laser-assisted microdissection and RNA sequencing.

A powerful method for transcriptional profiling of specific cell types in eukaryotes: laser-assisted microdissection and RNA sequencing.

... linear RNA amplification method and the emerging RNA-Seq ...cells of Arabidopsis thaliana from which only around 50 are formed within a flower, each of them individually enclosed ... See full document

13

Transcriptome sequencing and De Novo analysis of Youngia japonica using the illumina platform.

Transcriptome sequencing and De Novo analysis of Youngia japonica using the illumina platform.

... Sequencing The mRNA-seq library was constructed using an mRNA-Seq Sample Preparation Kit (Cat# RS-930-1001, Illumina ...following the manufacturer’s instructions. The ... See full document

10

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

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

... disease, the predominate disease on highly-maintained ...understanding of the molecular interactions between ...in the de novo assembly of ...obtained using ... See full document

13

De novo assembly and transcriptome analysis of the rubber tree (Hevea brasiliensis) and SNP markers development for rubber biosynthesis pathways.

De novo assembly and transcriptome analysis of the rubber tree (Hevea brasiliensis) and SNP markers development for rubber biosynthesis pathways.

... is the primary source of natural rubber that is native to the Amazon ...rainforest. The singular properties of natural rubber make it superior to and competitive with synthetic rubber ... See full document

14

De Novo Assembly of Coding Sequences of the Mangrove Palm (Nypa fruticans) Using RNA-Seq and Discovery of Whole-Genome Duplications in the Ancestor of Palms.

De Novo Assembly of Coding Sequences of the Mangrove Palm (Nypa fruticans) Using RNA-Seq and Discovery of Whole-Genome Duplications in the Ancestor of Palms.

... in the Old World from Ceylon, the Gan- ges Delta, Burma, and the Malay Peninsula through Indonesia to New Guinea and the Solomon Islands, northward to the Philippines and Ryukyu ... See full document

15

A Comparison between Transcriptome Sequencing and 16S Metagenomics for Detection of Bacterial Pathogens in Wildlife.

A Comparison between Transcriptome Sequencing and 16S Metagenomics for Detection of Bacterial Pathogens in Wildlife.

... limitation of the approaches performed here is the accuracy level of the taxo- nomic assignation; to some extent, RNA-Seq allows taxa classification at a species level ... See full document

21

Transcriptome analysis of immature xylem in the Chinese fir at different developmental phases

Transcriptome analysis of immature xylem in the Chinese fir at different developmental phases

... to the Coniferopsida ...clarifying the functions of the relevant pathways in Chinese ...results using samples from different cultivation phases identified a much larger number of ... See full document

21

Characterization of FUS mutations in amyotrophic lateral sclerosis using RNA-Seq.

Characterization of FUS mutations in amyotrophic lateral sclerosis using RNA-Seq.

... influenced the spliceosome, but the R522G mutation also altered genes involved in ribosomal processes, mismatch repair, and DNA ...analysis of skipped exons revealed that both FUS mutants affected ... See full document

8

Comparative Transcriptome Analysis Reveals the Influence of Abscisic Acid on the Metabolism of Pigments, Ascorbic Acid and Folic Acid during Strawberry Fruit Ripening.

Comparative Transcriptome Analysis Reveals the Influence of Abscisic Acid on the Metabolism of Pigments, Ascorbic Acid and Folic Acid during Strawberry Fruit Ripening.

... 20 using the NGS QC toolkit [28], were removed from the raw ...assembling the resulting clean reads with the Trinity program [29] and optimizing by TGICL ...aligned using BLASTx ... See full document

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