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Search Results: 1 - 10 of 3573 matches for " RNA-seq "
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Evaluation of RNA-Seq software in gene expression quantification  [PDF]
Yan Ji, Ziliang Qian, Jia Wei
Journal of Biomedical Science and Engineering (JBiSE) , 2013, DOI: 10.4236/jbise.2013.64059

High-throughput RNA sequencing (RNA-Seq) promises a complete annotation and quantification of all genes and their isoforms across samples. Because sequencing reads from this new technology are shorter than transcripts from which they are derived, expression estimation with RNA-Seq requires increasingly complex computational methods. In recent years, a number of expression quantification methods have been published from both public and commercial sources. Here we presented an overview of these attempts on quantifying gene expression. We then defined a set of criteria and compared the performance of several programs based on these criteria, and we further provided advices on selecting suitable tools for different biological applications.

Targeting miRNAs in Osteoblast Differentiation under Malnutrition Conditions  [PDF]
Yuying Wang, Rui He, Liangjun Zhong
Journal of Biosciences and Medicines (JBM) , 2018, DOI: 10.4236/jbm.2018.65012
Abstract: Aims: Previous studies reported that reduced bone formation was identified in fasting adult female mice compared with the ad libitum control group. An increasing number of studies have shown that miRNAs contribute to bone homeostasis. Unfortunately, there are minor concerns about the underlying mechanisms in osteoblastic differentiation under malnutrition conditions. Methods: We investigated microRNAs (miRNAs) in osteoblastic differentiation under malnutrition conditions using high-throughput bioinformatics approaches. To screen for targeted microRNAs, sequences were quantified by aligning reads to miRbase using miRDeep2 software. Unadjusted p-values were calculated using the Student’s t-test. Genes with a p-value of <0.05 and log 2FC (fold change) ≥ 1 were considered differentially expressed genes (DEGs). DEGs were submitted to Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses, respectively. Results: They were mainly enriched in biological process terms type and biological pathways, respectively. Particularly, we evaluated seven microRNAs, mir-494 3p, mir-466, mir-455, mir-708, mir-298, mir-92 and mir-224, which likely play roles in osteoblastogenesis in fasting adult mice. Conclusion: To our knowledge, this is the first study on the expression pattern of miRNA in osteoblasts of malnourished adult mice. These targeting miRNAs may provide a potential therapeutic approach to treat osteoporosis.
Isoform Inference From RNA-Seq Samples Based on Gene Structures on Chromosomes  [PDF]
Yan Ji, Jia Wei
Journal of Biosciences and Medicines (JBM) , 2013, DOI: 10.4236/jbm.2013.11001
Abstract: The emerging RNA-Seq technology makes it possible to infer splicing variants from millions of short sequence reads. Here we present a method to identify isoforms by their specific signatures on chromosomes including both exons and junctions. By applying this method to a RNA-Seq dataset of gastric cancer, we showed that our method is more accurate and sensitive than other isoform inference tools such as RSEM and Cufflinks. By constructing a network from gene list identified by our method but missed by other tools, we found that some cancer-related genes enriched in network modules have significant implications for cancer drug discovery.
Transcriptome Analysis of Drought Induced Stress in Chenopodium quinoa  [PDF]
Joshua A. Raney, Derrick J. Reynolds, David B. Elzinga, Justin Page, Joshua A. Udall, Eric N. Jellen, Alejandro Bonfacio, Daniel J. Fairbanks, Peter J. Maughan
American Journal of Plant Sciences (AJPS) , 2014, DOI: 10.4236/ajps.2014.53047

Quinoa (Chenopodium quinoa Willd.) is a halophytic, allotetraploid grain crop of the Amaranthaceae family with impressive drought tolerance, nutritional content and an increasing worldwide market. Here we report the results of an RNA-seq transcriptome analysis of Chenopodium quinoa using four water treatments (field capacity to drought) on the varietiesIngapirca (representing valley ecotypes) and Ollague (representing Altiplano Salares ecotypes). Physiological results, including growth rate, photosynthetic rate, stomatal conductance, and stem water potential, support the earlier findings that the Altiplano Salares ecotypes display greater tolerance to drought-like stress conditions than the valley ecotypes. cDNA libraries from root tissue samples for each variety × treatment combination were sequenced using Illumina Hi-Seq technology in an RNA-seq experiment. De novo assembly of the transcriptome generated 20,337 unique transcripts. Gene expression analysis of the RNA-seq data identified 462 putative gene products that showed differential expression based on treatment, and 27 putative gene products differentially expressed based on variety × treatment, including significant expression

Transcriptome Analysis of Ten-DPA Fiber in an Upland Cotton (Gossypium hirsutum) Line with Improved Fiber Traits from Phytochrome A1 RNAi Plants  [PDF]
Qing Miao, Peng Deng, Sukumar Saha, Johnie N. Jenkins, Chuan-Yu Hsu, Ibrokhim Y. Abdurakhmonov, Zabardast T. Buriev, Alan Pepper, Din-Pow Ma
American Journal of Plant Sciences (AJPS) , 2017, DOI: 10.4236/ajps.2017.810172
Abstract: Silencing phytochrome A1 gene (PHYA1) by RNA interference in Upland cotton (Gossypium hirsutum L. cv. Coker 312) had generated PHYA1 RNAi lines with improved fiber quality (longer, stronger and finer fiber). To reveal molecular mechanisms that govern fiber development with positive fiber traits, a study of global gene expression profiling of 10-DPA fibers in a PHYA1 RNAi line and its parent Coker 312 was conducted by high-throughput RNA sequencing. A comparative analysis of transcriptomes between the two lines had identified 142 genes that were differentially expressed in the 10-DPA fiber of the RNAi line. Gene Ontology analysis showed that these differentially expressed genes were mainly involved in metabolic pathways, heterocyclic/organic cyclic compound binding and multiple enzyme activities, and cell structures which were reported to play important roles in fiber development. Twenty-eight KEGG pathways were mapped for the 142 genes, and the pathways related to glycolysis/gluconeogenesis and pyruvate metabolism were the most abundant and followed by cytochrome P450-involved pathways, suggesting that fiber improvement could be through the regulation of proteins involved in cytochrome P450 pathways. Genes encoding WRKY transcription factors, sucrose synthase, xyloglucan endotransglucosylase hydrolase, udp-glucuronate: xylan alpha-glucuronosyltransferase, and genes involved in lipid
Baculovirus Induced Transcripts in Hemocytes from the Larvae of Heliothis virescens
Jonathan E. Breitenbach,Kent S. Shelby,Holly J.R. Popham
Viruses , 2011, DOI: 10.3390/v3112047
Abstract: Using RNA-seq digital difference expression profiling methods, we have assessed the gene expression profiles of hemocytes harvested from Heliothis virescens that were challenged with Helicoverpa zea single nucleopolyhedrovirus (HzSNPV). A?reference transcriptome of hemocyte-expressed transcripts was assembled from 202?million 42-base tags by combining the sequence data of all samples, and the assembled sequences were then subject to BLASTx analysis to determine gene identities. We used the fully sequenced HzSNPV reference genome to align 477,264 Illumina sequence tags from infected hemocytes in order to document expression of HzSNPV genes at early points during infection. A comparison of expression profiles of control insects to those lethally infected with HzSNPV revealed differential expression of key cellular stress response genes and genes involved in lipid metabolism. Transcriptional regulation of specific insect hormones in baculovirus-infected insects was also altered. A number of transcripts bearing homology to retroviral elements that were detected add to a growing body of evidence for extensive invasion of errantiviruses into the insect genome. Using this method, we completed the first and most comprehensive gene expression survey of both baculoviral infection and host immune defense in lepidopteran larvae.
The bench scientist's guide to statistical analysis of RNA-Seq data
Craig R Yendrek, Elizabeth A Ainsworth, Jyothi Thimmapuram
BMC Research Notes , 2012, DOI: 10.1186/1756-0500-5-506
Abstract: When comparing statistical tools, the negative binomial distribution-based methods, edgeR and DESeq, respectively identified 11,995 and 11,317 differentially expressed genes from an RNA-seq dataset generated from soybean leaf tissue grown in elevated O3. However, the number of genes in common between these two methods was only 10,535, resulting in 2,242 genes determined to be differentially expressed by only one method. Upon analysis of the non-significant genes, several limitations of these analytic tools were revealed, including evidence for overly stringent parameters for determining statistical significance of differentially expressed genes as well as increased type II error for high abundance transcripts.Because of the high variability between methods for determining differential expression of RNA-Seq data, we suggest using several bioinformatics tools, as outlined here, to ensure that a conservative list of differentially expressed genes is obtained. We also conclude that despite these analytical limitations, RNA-Seq provides highly accurate transcript abundance quantification that is comparable to qRT-PCR.As a method for characterizing global changes in transcription, RNA-Seq is an attractive option because of the ability to quantify differences in mRNA abundance in response to various treatments and diseases, as well as to detect alternative splice variants and novel transcripts [1]. Compared to microarray techniques, RNA-Seq eliminates the need for prior species-specific sequence information and overcomes the limitation of detecting low abundance transcripts. In addition, early studies have demonstrated that RNA-Seq is very reliable in terms of technical reproducibility [2]. As a result, biologists studying an array of model and non-model organisms are beginning to utilize RNA-Seq analysis with ever growing frequency [3-7]. However, without experience using bioinformatics methods, the large number of choices available to analyze differential expression can
Using RNA-seq to determine the transcriptional landscape and the hypoxic response of the pathogenic yeast Candida parapsilosis
Alessandro Guida, Claudia Lindst?dt, Sarah L Maguire, Chen Ding, Desmond G Higgins, Nicola J Corton, Matthew Berriman, Geraldine Butler
BMC Genomics , 2011, DOI: 10.1186/1471-2164-12-628
Abstract: We used next generation sequencing (RNA-seq) to determine the transcriptional profile of C. parapsilosis growing in several conditions including different media, temperatures and oxygen concentrations. We identified 395 novel protein-coding sequences that had not previously been annotated. We removed > 300 unsupported gene models, and corrected approximately 900. We mapped the 5' and 3' UTR for thousands of genes. We also identified 422 introns, including two introns in the 3' UTR of one gene. This is the first report of 3' UTR introns in the Saccharomycotina. Comparing the introns in coding sequences with other species shows that small numbers have been gained and lost throughout evolution. Our analysis also identified a number of novel transcriptional active regions (nTARs). We used both RNA-seq and microarray analysis to determine the transcriptional profile of cells grown in normoxic and hypoxic conditions in rich media, and we showed that there was a high correlation between the approaches. We also generated a knockout of the UPC2 transcriptional regulator, and we found that similar to C. albicans, Upc2 is required for conferring resistance to azole drugs, and for regulation of expression of the ergosterol pathway in hypoxia.We provide the first detailed annotation of the C. parapsilosis genome, based on gene predictions and transcriptional analysis. We identified a number of novel ORFs and other transcribed regions, and detected transcripts from approximately 90% of the annotated protein coding genes. We found that the transcription factor Upc2 role has a conserved role as a major regulator of the hypoxic response in C. parapsilosis and C. albicans.Candida species are the causative agents of 8-10% of hospital-acquired bloodstream infections worldwide [1]. Candida albicans remains the most common, but other species (such as Candida tropicalis, Candida parapsilosis and Candida glabrata) are increasing in frequency. C. parapsilosis is currently the second most co
Transcriptome of the adult female malaria mosquito vector Anopheles albimanus
Jesus Martinez-Barnetche, Rosa E Gómez-Barreto, Marbella Ovilla-Mu?oz, Juan Téllez-Sosa, David E García-López, Rhoel R Dinglasan, Ceereena Ubaida Mohien, Robert M MacCallum, Seth N Redmond, John G Gibbons, Antonis Rokas, Carlos M Machado, Febe Cazares-Raga, Lilia González-Cerón, Salvador Hernández-Martínez, Mario H Rodríguez-Lopez
BMC Genomics , 2012, DOI: 10.1186/1471-2164-13-207
Abstract: We sequenced the transcriptome of the An. albimanus adult female. By combining Sanger, 454 and Illumina sequences from cDNA libraries derived from the midgut, cuticular fat body, dorsal vessel, salivary gland and whole body, we generated a single, high-quality assembly containing 16,669 transcripts, 92% of which mapped to the An. darlingi genome and covered 90% of the core eukaryotic genome. Bidirectional comparisons between the An. gambiae, An. darlingi and An. albimanus predicted proteomes allowed the identification of 3,772 putative orthologs. More than half of the transcripts had a match to proteins in other insect vectors and had an InterPro annotation. We identified several protein families that may be relevant to the study of Plasmodium-mosquito interaction. An open source transcript annotation browser called GDAV (Genome-Delinked Annotation Viewer) was developed to facilitate public access to the data generated by this and future transcriptome projects.We have explored the adult female transcriptome of one important New World malaria vector, An. albimanus. We identified protein-coding transcripts involved in biological processes that may be relevant to the Plasmodium lifecycle and can serve as the starting point for searching targets for novel control strategies. Our data increase the available genomic information regarding An. albimanus several hundred-fold, and will facilitate molecular research in medical entomology, evolutionary biology, genomics and proteomics of anopheline mosquito vectors. The data reported in this manuscript is accessible to the community via the VectorBase website (http://www.vectorbase.org/Other/AdditionalOrganisms/ webcite).
Transcriptome analysis at four developmental stages of grape berry (Vitis vinifera cv. Shiraz) provides insights into regulated and coordinated gene expression
Sweetman Crystal,Wong Darren CJ,Ford Christopher M,Drew Damian P
BMC Genomics , 2012, DOI: 10.1186/1471-2164-13-691
Abstract: Background Vitis vinifera berry development is characterised by an initial phase where the fruit is small, hard and acidic, followed by a lag phase known as veraison. In the final phase, berries become larger, softer and sweeter and accumulate an array of organoleptic compounds. Since the physiological and biochemical makeup of grape berries at harvest has a profound impact on the characteristics of wine, there is great interest in characterising the molecular and biophysical changes that occur from flowering through veraison and ripening, including the coordination and temporal regulation of metabolic gene pathways. Advances in deep-sequencing technologies, combined with the availability of increasingly accurate V. vinifera genomic and transcriptomic data, have enabled us to carry out RNA-transcript expression analysis on a global scale at key points during berry development. Results A total of 162 million 100-base pair reads were generated from pooled Vitis vinifera (cv. Shiraz) berries sampled at 3-weeks post-anthesis, 10- and 11-weeks post-anthesis (corresponding to early and late veraison) and at 17-weeks post-anthesis (harvest). Mapping reads from each developmental stage (36-45 million) onto the NCBI RefSeq transcriptome of 23,720 V. vinifera mRNAs revealed that at least 75% of these transcripts were detected in each sample. RNA-Seq analysis uncovered 4,185 transcripts that were significantly upregulated at a single developmental stage, including 161 transcription factors. Clustering transcripts according to distinct patterns of transcription revealed coordination in metabolic pathways such as organic acid, stilbene and terpenoid metabolism. From the phenylpropanoid/stilbene biosynthetic pathway at least 46 transcripts were upregulated in ripe berries when compared to veraison and immature berries, and 12 terpene synthases were predominantly detected only in a single sample. Quantitative real-time PCR was used to validate the expression pattern of 12 differentially expressed genes from primary and secondary metabolic pathways. Conclusions In this study we report the global transcriptional profile of Shiraz grapes at key stages of development. We have undertaken a comprehensive analysis of gene families contributing to commercially important berry characteristics and present examples of co-regulation and differential gene expression. The data reported here will provide an invaluable resource for the on-going molecular investigation of wine grapes.
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