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[PDF] Top 20 RNA CoMPASS: a dual approach for pathogen and host transcriptome analysis of RNA-seq datasets.

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RNA CoMPASS: a dual approach for pathogen and host transcriptome analysis of RNA-seq datasets.

RNA CoMPASS: a dual approach for pathogen and host transcriptome analysis of RNA-seq datasets.

... High-throughput RNA sequencing (RNA-seq) has become an instrumental assay for the analysis of multiple aspects of an organism’s ...the analysis of a biological ... See full document

9

Simultaneous RNA-seq analysis of a mixed transcriptome of rice and blast fungus interaction.

Simultaneous RNA-seq analysis of a mixed transcriptome of rice and blast fungus interaction.

... the host plant and its fungal pathogen simultaneously, we developed a workflow to analyze the mixed transcriptome of rice and blast fungus that was obtained from infected rice ... See full document

15

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.

... up-regulation of oxyR, fur, and a diguanylate cyclase (DGC) (FTL_1218) after 8 hours of infection (Table ...oxyR and fur transcriptional regulators have been shown to promote formation ... See full document

12

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.

... identification of pathogens in animal reservoirs has relied on individual case- by-case strategies, which are based on species-specific detection tests such as real-time quanti- tative PCR (qPCR), DNA arrays or ... See full document

21

Mining SNPs in extracellular vesicular transcriptome of Trypanosoma cruzi: a step closer to early diagnosis of neglected Chagas disease

Mining SNPs in extracellular vesicular transcriptome of Trypanosoma cruzi: a step closer to early diagnosis of neglected Chagas disease

... One of the newest and strongest members of intercellular communicators, the Extracellular vesicles (EVs) and their enclosed RNAs; Extracellular RNAs (exRNAs) have been acknowledged as putative ... See full document

16

Variation in RNA-Seq transcriptome profiles of peripheral whole blood from healthy individuals with and without globin depletion.

Variation in RNA-Seq transcriptome profiles of peripheral whole blood from healthy individuals with and without globin depletion.

... male and 3 female) were collected into PAXgene Blood RNA tubes (PreAnalytiX GmbH– BD Biosciences, Mississauga, ON, Canada) and BD vacutainer plastic EDTA tubes (BD ...samples and 1 EDTA blood ... See full document

11

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

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

... row of Figure 5 shows a plot of the between- condition fold change (M) ...majority of the plasmid-associated transcripts, circled in black, are clear outliers on the within-condition ...value ... See full document

15

R-seqQI: RNA-Seq Quality Indicator

R-seqQI: RNA-Seq Quality Indicator

... process of RNA splicing involves primarily three types of sequences, represented in figure 4: splice-donors, occurring in the region where the 3’ end of an exon connects to the 5’ end ... See full document

137

Bioinformatics analyses and approaches to RNA-Seq Data

Bioinformatics analyses and approaches to RNA-Seq Data

... makes RNA-Seq particularly useful for non-model organisms with genomic sequences that are yet to be ...determined. RNA-Seq can reveal the precise location of transcription boundaries, ... See full document

48

Pseudo-messenger RNA: phantoms of the transcriptome.

Pseudo-messenger RNA: phantoms of the transcriptome.

... mammalian transcriptome harbours shadowy entities that resist classification and ...pseudo–messenger RNA to be RNA molecules that resemble protein-coding mRNA, but cannot encode full-length ... See full document

11

Heterogeneous Effects of Direct Hypoxia Pathway Activation in Kidney Cancer.

Heterogeneous Effects of Direct Hypoxia Pathway Activation in Kidney Cancer.

... calling and ranked on the vertical axis according to signal ...maps of these sites (±5kb on horizontal axis) showing ChIP-seq read density for the indicated HIF subunits were generated for both the ... See full document

19

De novo transcriptome and small RNA analyses of two amorphophallus species.

De novo transcriptome and small RNA analyses of two amorphophallus species.

... one of the most important glucomannan crops worldwide. The breeding and genomic researches are largely limited by the genetic basis of ...lengths of 430 nt in A. konjac and 119,678 ... See full document

12

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

... centrifugation and protein quantification, the supernatants were reacted with anti-USP22 (2 mg), anti- GCN5 (2 mg) or negative control IgG (2 mg, Santa Cruz Biotechnology, Santa Cruz, USA) for 12 h with ...h ... See full document

8

Mining RNA-seq data for infections and contaminations.

Mining RNA-seq data for infections and contaminations.

... context of both metatran- scriptomics and metagenomics are missing genome sequences for the species/strains in the sample, which may result in misalign- ments of reads to related species or ... See full document

12

RNA-seq analysis of the Quercus suber root response to drought

RNA-seq analysis of the Quercus suber root response to drought

... variety of environmental ...variety of advance response mechanisms to cope with the challenges facing a sessile ...development and yield. Abiotic stress, that can consist of drought, salinity, ... See full document

134

Transcriptome analysis of Pseudomonas aeruginosa PAO1 grown at both body and elevated temperatures

Transcriptome analysis of Pseudomonas aeruginosa PAO1 grown at both body and elevated temperatures

... the RNA polymerase core enzyme gene rpoD was upregulated during heat ...work of Aramaki & Fujita (1999). The expression of rpoD, together with other sigma factors such as rpoH and rpoB ... See full document

19

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

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

... hsa-miR-486-5p and hsa-miR-376c all target NFAT5 (nuclear factor of activated T-cells 5) (http:// ...proliferation and induces apoptosis in endometriotic stromal cells [34] and is associated ... See full document

7

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

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

... experimental and simulated data sets with different characteristics ...length and sequencing depth). In the absence of knowledge of the ‘ground truth’ in real RNAseq data sets, we used ... 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

... deletion and polyA/T ...self-chimera and removes them by splitting contigs in parts or removing duplicated chimeric ...bl2seq and keeps only matches having an identity greater or equal to ...60% ... See full document

22

Evaluating the Stability of RNA-Seq Transcriptome Profiles and Drug-Induced Immune-Related Expression Changes in Whole Blood.

Evaluating the Stability of RNA-Seq Transcriptome Profiles and Drug-Induced Immune-Related Expression Changes in Whole Blood.

... stability of rat whole blood expression obtained from RNA sequencing (RNA-seq) and assess changes in whole blood transcriptome profiles in experiments replicated over ... See full document

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