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https://www.readbyqxmd.com/read/28110034/transcriptome-profiles-of-the-clam-meretrix-petechialis-hepatopancreas-in-response-to-vibrio-infection
#1
Fengjuan Jiang, Xin Yue, Hongxia Wang, Baozhong Liu
Microbial diseases have received much attention due to their enormous destruction of aquaculture, and Vibrio parahaemolyticus is one of the main pathogens that cause bacterial disease in the clam Meretrix petechialis. To better understand the molecular mechanisms of the immune response to Vibrio in M. petechialis, RNA-Seq was applied to explore global expression changes of hepatopancreas from this clam after Vibrio challenge. There were 199,318,966 clean reads obtained by Illumina sequencing, which were further assembled into 214,577 transcripts, and then 147,255 unigenes with an N50 of 1393 bp were identified...
January 18, 2017: Fish & Shellfish Immunology
https://www.readbyqxmd.com/read/28109476/a-three-lncrna-signature-derived-from-the-atlas-of-ncrna-in-cancer-tanric-database-predicts-the-survival-of-patients-with-head-and-neck-squamous-cell-carcinoma
#2
Wei Cao, Jian-Nan Liu, Zeqi Liu, Xu Wang, Ze-Guang Han, Tong Ji, Wan-Tao Chen, Xin Zou
OBJECTIVE: Long non-coding RNAs (lncRNAs) have important biological functions and can be used as prognostic biomarkers in cancer. To identify a lncRNA prognostic signature for head and neck squamous cell carcinoma (HNSCC). METHOD: We analysed RNA-seq data derived from the TANRIC database to identify a lncRNA prognostic signature model using the orthogonal partial least squares discrimination analysis (OPLS-DA) and 1.5-fold expression change criterion methods. The prognosis prediction model based on the lncRNA signatures and clinical parameters were evaluated using the 5-fold cross validation method...
February 2017: Oral Oncology
https://www.readbyqxmd.com/read/28109431/proteogenomics-recycling-public-data-to-improve-genome-annotations
#3
A McAfee, L J Foster
Massively parallel sequencing is revealing species genomes faster than ever before, but the value of the raw sequence is limited unless the genes can be accurately annotated. This is typically achieved using gene prediction algorithms which, despite continual improvement, still require substantial verification and refinement. For example, in silico methods struggle with annotating splice isoforms accurately and empirical methods are needed to refine and verify the initial bioinformatic gene predictions. RNA-seq is an excellent way to confirm exon-exon boundaries and transcript termini, while mass spectrometry (MS) offers definitive proof that a gene is translated and a secondary means of confirming exon expression, protein termini, and posttranslational modifications...
2017: Methods in Enzymology
https://www.readbyqxmd.com/read/28109426/wgcna-application-to-proteomic-and-metabolomic-data-analysis
#4
G Pei, L Chen, W Zhang
Progresses in mass spectrometric instrumentation and bioinformatics identification algorithms made over the past decades allow quantitative measurements of relative or absolute protein/metabolite amounts in cells in a high-throughput manner, which has significantly expedited the exploration into functions and dynamics of complex biological systems. However, interpretation of high-throughput data is often restricted by the limited availability of suitable computational methods and enough statistical power. While many computational methodologies have been developed in the past decades to address the issue, it becomes clear that network-focused rather than individual gene/protein-focused strategies would be more appropriate to obtain a complete picture of cellular responses...
2017: Methods in Enzymology
https://www.readbyqxmd.com/read/28108965/transcriptomic-and-hormone-analyses-reveal-mechanisms-underlying-petal-elongation-in-chrysanthemum-morifolium-jinba
#5
Jingjing Wang, Haibin Wang, Lian Ding, Aiping Song, Feng Shen, Jiafu Jiang, Sumei Chen, Fadi Chen
Auxin regulates chrysanthemum petal elongation by promoting cell elongation. Transcriptomic analysis shows that auxin signal transduction may connect with other transcription factors by TCPs to regulate chrysanthemum petal elongation. As an ornamental species, Chrysanthemum morifolium has high ornamental and economic value. Petal size is the primary factor that influences the ornamental value of chrysanthemum, but the mechanism underlying the development of C. morifolium petals remains unclear. In our study, we tracked the growth of petals and found that the basal region of 'Jinba' petals showed a higher elongation rate, exhibiting rapid cell elongation during petal growth...
January 20, 2017: Plant Molecular Biology
https://www.readbyqxmd.com/read/28108964/heme-oxygenase-1-defects-lead-to-reduced-chlorophyll-in-brassica-napus
#6
Lixia Zhu, Zonghui Yang, Xinhua Zeng, Jie Gao, Jie Liu, Bin Yi, Chaozhi Ma, Jinxiong Shen, Jinxing Tu, Tingdong Fu, Jing Wen
We previously described a Brassica napus chlorophyll-deficient mutant (ygl) with yellow-green seedling leaves and mapped the related gene, BnaC.YGL, to a 0.35 cM region. However, the molecular mechanisms involved in this chlorophyll defect are still unknown. In this study, the BnaC07.HO1 gene (equivalent to BnaC.YGL) was isolated by the candidate gene approach, and its function was confirmed by genetic complementation. Comparative sequencing analysis suggested that BnaC07.HO1 was lost in the mutant, while a long noncoding-RNA was inserted into the promoter of the homologous gene BnaA07...
January 20, 2017: Plant Molecular Biology
https://www.readbyqxmd.com/read/28108803/the-genome-sequence-of-a-novel-rna-virus-in-adelphocoris-suturalis
#7
Xinlian Li, Pengjun Xu, Xianming Yang, He Yuan, Lizhen Chen, Yanhui Lu
The complete genome of a novel virus found in Adelphocoris suturalis was determined by RNA-seq and named Adelphocoris suturalis-associated virus 1 (ASV1). ASV1 has a single-stranded RNA genome of 10,845 nucleotides in length and contains five putative open reading frames (ORFs). ORF1 encodes a polypeptide of 2592 amino acids (aa) and contains four conserved domains: a viral RNA methyltransferase domain, an FtsJ-like methyltransferase domain, a viral RNA helicase domain and an RNA-dependent RNA polymerase domain...
January 20, 2017: Archives of Virology
https://www.readbyqxmd.com/read/28108660/from-benchmarking-hits-clip-peak-detection-programs-to-a-new-method-for-identification-of-mirna-binding-sites-from-ago2-clip-data
#8
Silvia Bottini, Nedra Hamouda-Tekaya, Bogdan Tanasa, Laure-Emmanuelle Zaragosi, Valerie Grandjean, Emanuela Repetto, Michele Trabucchi
Experimental evidence indicates that about 60% of miRNA-binding activity does not follow the canonical rule about the seed matching between miRNA and target mRNAs, but rather a non-canonical miRNA targeting activity outside the seed or with a seed-like motifs. Here, we propose a new unbiased method to identify canonical and non-canonical miRNA-binding sites from peaks identified by Ago2 Cross-Linked ImmunoPrecipitation associated to high-throughput sequencing (CLIP-seq). Since the quality of peaks is of pivotal importance for the final output of the proposed method, we provide a comprehensive benchmarking of four peak detection programs, namely CIMS, PIPE-CLIP, Piranha and Pyicoclip, on four publicly available Ago2-HITS-CLIP datasets and one unpublished in-house Ago2-dataset in stem cells...
January 20, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28108659/yamat-seq-an-efficient-method-for-high-throughput-sequencing-of-mature-transfer-rnas
#9
Megumi Shigematsu, Shozo Honda, Phillipe Loher, Aristeidis G Telonis, Isidore Rigoutsos, Yohei Kirino
Besides translation, transfer RNAs (tRNAs) play many non-canonical roles in various biological pathways and exhibit highly variable expression profiles. To unravel the emerging complexities of tRNA biology and molecular mechanisms underlying them, an efficient tRNA sequencing method is required. However, the rigid structure of tRNA has been presenting a challenge to the development of such methods. We report the development of Y-shaped Adapter-ligated MAture TRNA sequencing (YAMAT-seq), an efficient and convenient method for high-throughput sequencing of mature tRNAs...
January 20, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28108491/transcriptome-analysis-identifies-multifaceted-regulatory-mechanisms-dictating-a-genetic-switch-from-neuronal-network-establishment-to-maintenance-during-postnatal-prefrontal-cortex-development
#10
Yvet Kroeze, Martin Oti, Ellen van Beusekom, Roel H M Cooijmans, Hans van Bokhoven, Sharon M Kolk, Judith R Homberg, Huiqing Zhou
The prefrontal cortex (PFC) is one of the latest brain regions to mature, which allows the acquisition of complex cognitive abilities through experience. To unravel the underlying gene expression changes during postnatal development, we performed RNA-sequencing (RNA-seq) in the rat medial PFC (mPFC) at five developmental time points from infancy to adulthood, and analyzed the differential expression of protein-coding genes, long intergenic noncoding RNAs (lincRNAs), and alternative exons. We showed that most expression changes occur in infancy, and that the number of differentially expressed genes reduces toward adulthood...
January 19, 2017: Cerebral Cortex
https://www.readbyqxmd.com/read/28108448/arnapipe-a-balanced-efficient-and-distributed-pipeline-for-processing-rna-seq-data-in-high-performance-computing-environments
#11
Arnald Alonso, Brittany N Lasseigne, Kelly Williams, Josh Nielsen, Ryne C Ramaker, Andrew A Hardigan, Bobbi Johnston, Brian S Roberts, Sara J Cooper, Sara Marsal, Richard M Myers
The wide range of RNA-seq applications and their high computational needs require the development of pipelines orchestrating the entire workflow and optimizing usage of available computational resources. We present aRNApipe, a project-oriented pipeline for processing of RNA-seq data in high performance cluster environments. aRNApipe is highly modular and can be easily migrated to any high performance computing (HPC) environment. The current applications included in aRNApipe combine the essential RNA-seq primary analyses, including quality control metrics, transcript alignment, count generation, transcript fusion identification, alternative splicing, and sequence variant calling...
January 19, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28108447/mirmine-a-database-of-human-mirna-expression-profiles
#12
Bharat Panwar, Gilbert S Omenn, Yuanfang Guan
MOTIVATION: MicroRNAs (miRNAs) are small non-coding RNAs that are involved in post-transcriptional regulation of gene expression. In this high-throughput sequencing era, a tremendous amount of RNA-seq data is accumulating, and full utilization of publicly available miRNA data is an important challenge. These data are useful to determine expression values for each miRNA, but quantification pipelines are in a primitive stage and still evolving; there are many factors that affect expression values significantly...
January 19, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28108340/rna-seq-transcriptome-analysis-of-the-olive-flounder-paralichthys-olivaceus-kidney-response-to-vaccination-with-heat-inactivated-viral-hemorrhagic-septicemia-virus
#13
Jee Youn Hwang, Mun Gyeoung Kwon, Sung-Hee Jung, Myoung Ae Park, Dong-Wook Kim, Wang Sik Cho, Jeong Woo Park, Maeng-Hyun Son
Viral hemorrhagic septicemia (VHS) is a highly contagious disease of cultured flounder caused by VHS virus (VHSV). To develop effective VHSV vaccines, it is essential to understand the molecular mechanisms underlying the host's protective response against VHSV. The purpose of this study is to clarify which genes are involved in the protective response of olive flounder after VHSV vaccination. We first injected olive flounder intraperitoneally with 10(7) TCID50 heat-inactivated VHSV vaccine and evaluated the vaccine efficacy at 20 °C...
January 17, 2017: Fish & Shellfish Immunology
https://www.readbyqxmd.com/read/28107812/tissue-resolved-gene-structure-refined-equine-transcriptome
#14
T A Mansour, E Y Scott, C J Finno, R R Bellone, M J Mienaltowski, M C Penedo, P J Ross, S J Valberg, J D Murray, C T Brown
BACKGROUND: Transcriptome interpretation relies on a good-quality reference transcriptome for accurate quantification of gene expression as well as functional analysis of genetic variants. The current annotation of the horse genome lacks the specificity and sensitivity necessary to assess gene expression especially at the isoform level, and suffers from insufficient annotation of untranslated regions (UTR) usage. We built an annotation pipeline for horse and used it to integrate 1.9 billion reads from multiple RNA-seq data sets into a new refined transcriptome...
January 20, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28107438/first-insights-into-the-subterranean-crustacean-bathynellacea-transcriptome-transcriptionally-reduced-opsin-repertoire-and-evidence-of-conserved-homeostasis-regulatory-mechanisms
#15
Bo-Mi Kim, Seunghyun Kang, Do-Hwan Ahn, Jin-Hyoung Kim, Inhye Ahn, Chi-Woo Lee, Joo-Lae Cho, Gi-Sik Min, Hyun Park
Bathynellacea (Crustacea, Syncarida, Parabathynellidae) are subterranean aquatic crustaceans that typically inhabit freshwater interstitial spaces (e.g., groundwater) and are occasionally found in caves and even hot springs. In this study, we sequenced the whole transcriptome of Allobathynella bangokensis using RNA-seq. De novo sequence assembly produced 74,866 contigs including 28,934 BLAST hits. Overall, the gene sequences were most similar to those of the waterflea Daphnia pulex. In the A. bangokensis transcriptome, no opsin or related sequences were identified, and no contig aligned to the crustacean visual opsins and non-visual opsins (i...
2017: PloS One
https://www.readbyqxmd.com/read/28106722/using-network-extracted-ontologies-to-identify-novel-genes-with-roles-in-appressorium-development-in-the-rice-blast-fungus-magnaporthe-oryzae
#16
Ryan M Ames
Magnaporthe oryzae is the causal agent of rice blast disease, the most important infection of rice worldwide. Half the world's population depends on rice for its primary caloric intake and, as such, rice blast poses a serious threat to food security. The stages of M. oryzae infection are well defined, with the formation of an appressorium, a cell type that allows penetration of the plant cuticle, particularly well studied. However, many of the key pathways and genes involved in this disease stage are yet to be identified...
January 17, 2017: Microorganisms
https://www.readbyqxmd.com/read/28106276/crispr-cas9-mediated-deletion-of-c1eis-inhibits-chicken-embryonic-stem-cell-differentiation-into-male-germ-cells-gallus-gallus
#17
Qisheng Zuo, Kai Jin, Yingjie Wang, Jiuzhou Song, Yani Zhang, Bichun Li
We previously found that C1EIS is preferentially expressed in Chicken spermatogonial stem cells (SSCs) by RNA sequencing (RNA-seq), so our current study focused on C1EIS's role in Chicken embryonic stem cells (ESCs) differentiation into male germ cells. We constructed a CRISPR/Cas9 vector targeting C1EIS. T7 endonuclease I (T7EI) digestion method and sequencing of TA cloning were used to detect the knock-out efficiency of the Single guide RNA (sgRNA) after the cas9/gRNA vector transfected into D fibroblasts 1(DF-1), ESCs and Chicken embryos...
January 20, 2017: Journal of Cellular Biochemistry
https://www.readbyqxmd.com/read/28105957/identification-of-nuclear-genes-controlling-chlorophyll-synthesis-in%C3%A2-barley-by-rna-seq
#18
Nickolay A Shmakov, Gennadiy V Vasiliev, Natalya V Shatskaya, Alexey V Doroshkov, Elena I Gordeeva, Dmitry A Afonnikov, Elena K Khlestkina
BACKGROUND: Albinism in plants is characterized by lack of chlorophyll and results in photosynthesis impairment, abnormal plant development and premature death. These abnormalities are frequently encountered in interspecific crosses and tissue culture experiments. Analysis of albino mutant phenotypes with full or partial chlorophyll deficiency can shed light on genetic determinants and molecular mechanisms of albinism. Here we report analysis of RNA-seq transcription profiling of barley (Hordeum vulgare L...
November 16, 2016: BMC Plant Biology
https://www.readbyqxmd.com/read/28105941/the-loss-of-photosynthetic-pathways-in-the-plastid-and-nuclear-genomes-of-the-non-photosynthetic-mycoheterotrophic-eudicot-monotropa-hypopitys
#19
Nikolai V Ravin, Eugeny V Gruzdev, Alexey V Beletsky, Alexander M Mazur, Egor B Prokhortchouk, Mikhail A Filyushin, Elena Z Kochieva, Vitaly V Kadnikov, Andrey V Mardanov, Konstantin G Skryabin
BACKGROUND: Chloroplasts of most plants are responsible for photosynthesis and contain a conserved set of about 110 genes that encode components of housekeeping gene expression machinery and photosynthesis-related functions. Heterotrophic plants obtaining nutrients from other organisms and their plastid genomes represent model systems in which to study the effects of relaxed selective pressure on photosynthetic function. The most evident is a reduction in the size and gene content of the plastome, which correlates with the loss of genes encoding photosynthetic machinery which become unnecessary...
November 16, 2016: BMC Plant Biology
https://www.readbyqxmd.com/read/28105940/integrated-single-cell-data-analysis-reveals-cell-specific-networks-and-novel-coactivation-markers
#20
Shila Ghazanfar, Adam J Bisogni, John T Ormerod, David M Lin, Jean Y H Yang
BACKGROUND: Large scale single cell transcriptome profiling has exploded in recent years and has enabled unprecedented insight into the behavior of individual cells. Identifying genes with high levels of expression using data from single cell RNA sequencing can be useful to characterize very active genes and cells in which this occurs. In particular single cell RNA-Seq allows for cell-specific characterization of high gene expression, as well as gene coexpression. RESULTS: We offer a versatile modeling framework to identify transcriptional states as well as structures of coactivation for different neuronal cell types across multiple datasets...
December 5, 2016: BMC Systems Biology
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