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RNA-Seq analysis

Tìm thấy 13+ kết quả cho từ khóa "RNA-Seq analysis"

RNA-Seq analysis of blood meal induced gene-expression changes in Aedes aegypti ovaries

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Among the genes tested, although the level of expression change does not match with that of the RNA-Seq analysis, the overall trend (over or under- expression) remained the same in both RT-qPCR and RNA-Seq analyses. Among the 10 genes tested, we in- cluded OBP46, an odorant-binding protein, to confirm that OBPs were differentially expressed following a blood meal in ovaries. Most of the DEGs on day 3 returned to the non- significant level at later time points.

Small RNA-seq analysis of single porcine blastocysts revealed that maternal estradiol-17beta exposure does not affect miRNA isoform (isomiR) expression

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One of the strands or sometimes both represents the functional mature miRNA form that is incorporated in the RNA-induced silencing complex (RISC). MiRBase is one of the databases for miRNA sequences. The first universal steps of the RNA- seq analysis starting with quality control up to adapter clipping are needed for every FastQ file analysis.

RNA-seq analysis of galaninergic neurons from ventrolateral preoptic nucleus identifies expression changes between sleep and wake

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Another set of genes that showed highly consistent changes between VLPO-Gal neurons and other brain re- gions were cold-inducible RNA-binding proteins (Cirbp and Rbm3). Interestingly, a subset of genes were regulated between sleep and wake in the opposite direction in VLPO-Gal when compared to our previously published RNA-seq analysis of mPFC [20].

RNA-Seq analysis of differentially expressed genes relevant to innate and adaptive immunity in cecropin P1 transgenic rainbow trout (Oncorhynchus mykiss)

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How- ever, due to the inherited disadvantages associated with the cDNA microarray study, as mentioned in the Intro- duction, a confirmation study via a second experimental approach is required in order to provide a more solid evidence to support our hypothesis, and thus RNA-Seq analysis was adopted in this study [14]..

RNA-Seq based transcriptome analysis during bovine viral diarrhoea virus (BVDV) infection

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To further understand the mechanisms by which BVDV overcomes the host cell innate immune response and provide more clues for further understanding the BVDV-host interaction, in this descriptive study, we conducted a investigation of differentially expressed genes (DEGs) of the host during BVDV infection by RNA-Seq analysis.. Results: Our analysis identified and 1877 DEGs in the comparison groups mock vs. MDBK cells infected with BVDV post 2 h (MBV2h), mock vs. MBV6h, mock vs.

Choice of library size normalization and statistical methods for differential gene expression analysis in balanced two-group comparisons for RNA-seq studies

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RNA-seq: High-throughput RNA sequencing. RSEM: RNA-seq by expectation- maximization. RNA-Seq: a revolutionary tool for transcriptomics. RNA-seq: from technology to biology. De novo assembly and analysis of RNA-seq data. New gene models and alternative splicing in the maize pathogen Colletotrichum graminicola revealed by RNA-Seq analysis. SNP discovery in the bovine milk transcriptome using RNA-Seq technology.. Reliable identification of genomic variants from RNA-seq data.

Plant stress RNA-seq Nexus: A stress-specific transcriptome database in plant cells

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Plant stress RNA-Seq dataset collection. The annotation for the RNA-Seq datasets regarding plant stress was collected from NCBI GEO [21], and RNA-Seq reads were downloaded from the SRA [22].. Each dataset has several stress-specific subsets that con- tain a group of RNA-Seq samples of plants treated with. We only retained the datasets that had a reference transcriptome for subsequent RNA-Seq analysis. Stress-specific differentially expressed transcripts.

BALLI: Bartlett-adjusted likelihood-based linear model approach for identifying differentially expressed genes with RNA-seq data

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ReCount: a multi-experiment resource of analysis-ready RNA-seq gene count datasets. RNA-seq analysis for detecting quantitative trait-associated genes

Systematic identification and validation of the reference genes from 60 RNA-Seq libraries in the scallop Mizuhopecten yessoensis

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Similar results are also reported for housekeeping or reference genes identified by genome-wide analysis in other organisms, such as humans [54], mice [13], and maize [55]. The results of RNA-Seq were validated by RT-qPCR for 6 candidate and 6 commonly used reference genes.. 3 Evaluation of the reference gene candidates and reported reference genes based on RNA-seq analysis. reference genes being more stable than most of the trad- itionally used reference genes.

Expression analysis of lung miRNAs responding to ovine VM virus infection by RNA-seq

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Additional file 1: PCA analysis of the 12 samples used in the RNA-seq analysis. The samples were obtained from different commercial flocks in the routine of the Veterinary Faculty (University of Zaragoza) in the framework of the national research project ref. The complete experimental procedure was approved and licensed by the Ethical Committee of the University of Zaragoza (ref: PI09/10)..

Dual RNA-seq transcriptome analysis of caecal tissue during primary Eimeria tenella infection in chickens

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Results: Dual RNA-seq analysis revealed time-dependent changes in both host and parasite gene expression during the course of the infection. Hence, the development of new sustainable control methods is demanded by the industry, but will require a better understanding of the biology of Eimeria infection in the chicken host.. https://doi.org/10.1186/s . evidence of the immune pathways.

Identification and characterization of SSR, SNP and InDel molecular markers from RNA-Seq data of guar (Cyamopsis tetragonoloba, L. Taub.) roots

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Identification and characterization of SSR, SNP and InDel molecular markers from RNA-Seq data of guar (Cyamopsis. Hence, the present work was done to enrich the molecular markers resource of guar by identifying high quality SSR, SNP and InDel markers from the RNA-Seq data of the roots of two guar varieties.. Results: We carried out RNA-Seq analysis of the roots of two guar varieties, namely, RGC-1066 and M-83.

CAMPAREE: A robust and configurable RNA expression simulator

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Assessing the prevalence of mycoplasma contamination in cell culture via a survey of NCBI ’ s RNA-seq archive. STAR: ultrafast universal RNA-seq aligner. Near-optimal probabilistic RNA- seq quantification. Differential analyses for RNA-seq:. A comparative study of RNA-seq analysis strategies. Benchmarking differential expression analysis tools for RNA-Seq: normalization-based vs

RNA-Seq analysis of Clerodendrum inerme (L.) roots in response to salt stress

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RNA-Seq analysis of Clerodendrum inerme (L.) roots in response to salt stress. inerme to salt stress.. inerme in response to salt stress.

RNA-Seq analysis reveals transcript diversity and active genes after common cutworm (Spodoptera litura Fabricius) attack in resistant and susceptible wild soybean lines

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The early- and late-induction time points in the two accessions in- dicated by the expression patterns of two typical genes (LOX7 and VSP β ) were chosen for the transcriptome analysis by RNA-Seq. The functional analysis of a down-regulated phosphate transporter gene showed specific susceptibility in the overexpression transgenic soybean plants.

RNA-seq analysis provides insights into cold stress responses of Xanthomonas citri pv. citri

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In order to investigate the effect of low temperature on Xcc, RNA-Seq of Xcc was carried out at different tem- peratures. The Q20 value of Xcc grown at 28 °C and 15 °C remained as 96.69 and 96.97%, respectively whereas the genome of Xcc was used as reference (NC_. 5) and results indicated acceptable quality of Xcc RNA sequencing..

Stability of methods for differential expression analysis of RNA-seq data

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Conclusion: Empirical results support that AUCOR can effectively rank the DE methods in terms of stability for given RNA-seq datasets. In addition, we explore how biological or technical factors from experiments and data analysis affect the stability of DE methods. In the past few years, dozens of DE analysis meth- ods have been proposed in three mainstream strategies:.

BaRTv1.0: An improved barley reference transcript dataset to determine accurate changes in the barley transcriptome using RNA-seq

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Pipeline de- scribing the algorithm to compare HR-RT-PCR and RNA-seq alternatively spliced transcript proportions and correlations.. HR RT-PCR: High resolution RT- PCR. RNA-seq: RNA-sequencing. PR-F and MB assembled the RNA- seq data. JF, GS and CS identified the AS genes and performed the HR RT- PCR screening and analysis of the data. PR-F, C-DM, JWSB, RZ, WG and CS performed the detailed analysis of the RNA-seq and HR RT-PCR data. BaRTv1.0 and BaRTv1.0 – QUASI are available as .fasta and.

Genome-wide transcriptome analysis using RNA-Seq reveals a large number of differentially expressed genes in a transient MCAO rat model

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We performed a genome-wide analysis of the transcrip- tome via RNA-Seq in the subcortical structures of the rat brain that contained the ischemic focus and the penumbra region under the conditions of the tMCAO model.. An analysis of the expression of 20 genes by real-time RT – PCR confirmed the RNA-Seq results.

Comparison of RNA isolation methods on RNA-Seq: Implications for differential expression and meta-analyses

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Comparison of RNA isolation methods on RNA-Seq: implications for differential. In this study, we examined the effects of RNA isolation method as a possible source of batch effects in RNA- seq design..