• Through de novo transcriptome assembly with the RNA-seq reads from whole organ samples of C. virgata at the germination stage (2 days after germination, DAG), early young development stage (8 DAG), young development stage (17 DAG), and adult development stage (28 DAG), we identified 21,589 unified transcripts (contigs) and found that 19,346 and 18,156 protein-coding transcripts were homologous to those in rice and Arabidopsis , respectively. (frontiersin.org)
  • De novo transcriptome assembly is the de novo sequence assembly method of creating a transcriptome without the aid of a reference genome. (wikipedia.org)
  • De novo transcriptome assembly is often the preferred method to studying non-model organisms, since it is cheaper and easier than building a genome, and reference-based methods are not possible without an existing genome. (wikipedia.org)
  • De Novo Transcriptome Assembly and Analyses of Gene Expression during Photomorphogenesis in Diploid Wheat Triticum monococcum. (oregonstate.edu)
  • Overall, this study provides a comprehensive transcriptome atlas, and SSRs, contributing to building essential genomic resources to support basic research, genome annotation, functional genomics, and molecular breeding of Chia. (oregonstate.edu)
  • These analyses include gene prediction, automated genomic annotation and genome comparison/alignment. (uni-hamburg.de)
  • We can help researchers identify SNPs, indels, gene copy numbers, and genomic rearrangements from the various types of DNA-sequencing and microarray data and provide tailored downstream analysis of variants and mutations. (nottingham.ac.uk)
  • Julie Poulain is a molecular biologist working in the field of marine environmental genomics at t he Laboratory for the Genomic Analysis of Eukaryotes (LAGE) within Genoscope's UMR 8030 Genomics Metabolics Unit. (cea.fr)
  • However, Rubus breeding is a long and slow process hampered by limited genomic and molecular resources. (pacb.com)
  • Genomic resources such as a complete genome sequencing and transcriptome will be of exceptional value to improve research and breeding of this high value crop. (pacb.com)
  • In order to develop genetic and genomic resources for such a study, we constructed genome-wide transcriptomes of two Triticum monococcum subspecies, the wild winter wheat T. monococcum ssp. (oregonstate.edu)
  • With the ongoing developments of high throughput sequencing machines and advancement of modern bioinformatics tools at unprecedented pace, the target goal of sequencing individual genomes of living organism at a cost of $1,000 each is seemed to be realistically feasible in the near future. (springer.com)
  • During this period, tremendous success has been achieved in the fields of decoding of human genome, technological advancement of new era of human genome applications, toward personalized genomes and discovery of rare variants, leveraging genome sequencing to impact on cancer researches and mammalian evolution and population structure. (springer.com)
  • Although these programs have been generally successful in assembling genomes, transcriptome assembly presents some unique challenges. (wikipedia.org)
  • Developments in sequencing technologies and the sequencing of an ever-increasing number of genomes have revolutionised studies of biodiversity and organismal evolution. (lu.se)
  • This accumulation of data has been paralleled by the creation of numerous public biological databases through which the scientific community can mine the sequences and annotations of genomes, transcriptomes, and proteomes of multiple species. (lu.se)
  • This is the first book on the genome of Salvia miltiorrhiza, summarizing the research advances in the molecular mapping, whole genome sequencing, chloroplast and mitochondria genomes, epigenetics, transcriptomics and functional genomics of this emerging model plant with great economic and medicinal value. (stanford.edu)
  • Our revolutionary sequencing technologies combine the completeness of long reads with the accuracy of short reads to provide the most comprehensive view of genomes, transcriptomes, and epigenomes. (pacb.com)
  • Despite decades of speculation, the processes underlying the expansive genomes of ferns are unclear, largely due to the absence of a sequenced homosporous fern genome. (nsf.gov)
  • The ongoing annotation of these genomes should spark a new wave of interest in the DED pathosystem, as it should lead to the formal identification of genes modulating parasitic fitness. (sisef.it)
  • When comparing the transcriptomes across developmental stages, we found an over-representation of genes involved in growth regulation in the early development stage in C. virgata . (frontiersin.org)
  • To estimate genes related to Pb response and the molecular mechanism associated with Pb tolerance and accumulation, we analyzed the transcriptome of tall fescue in response to Pb treatment. (biomedcentral.com)
  • The assembled transcriptome is estimated to have the complete sequence information for ~86% of the genes found in the Chia genome. (oregonstate.edu)
  • The objective of this research is to identify genes associated to desiccation-rehydration cycle in the transcriptome of H. cruentum to better understand the genetic dynamics behind its desiccation tolerance mechanism. (frontiersin.org)
  • Genome Sequencing of the Phytoseiid Predatory Mite Metaseiulus occidentalis Reveals Completely Atomized Hox Genes and Superdynamic Intron Evolution. (bcm.edu)
  • Aided by transcriptome data, genome annotation cataloged 18,338 protein-coding genes and identified large numbers of Helitron transposable elements. (bcm.edu)
  • Its genes exhibit elevated molecular evolution, with strikingly high numbers of intron gains and losses, in stark contrast to the deer tick Ixodes scapularis Uniquely among examined arthropods, this predatory mite's Hox genes are completely atomized, dispersed across the genome, and it encodes five copies of the normally single-copy RNA processing Dicer-2 gene. (bcm.edu)
  • The recovered transcriptomes were of such good quality that it was possible to identify muscle- and skin-specific protein coding RNAs, and led to the annotation of missing ribosomal RNA and microRNA genes, the later following MirGeneDB recommendations. (phys.org)
  • This is the first time that we have had a glimpse into the existence of thylacine-specific regulatory genes, such as microRNAs, that got extinct more than one century ago," says Marc R. Friedländer, Associate Professor at the Department of Molecular Biosciences, The Wenner-Gren Institute at Stockholm University and SciLifeLab. (phys.org)
  • Genetic and molecular analyses have led to the identification, cloning and characterization of a few genes that contribute to parasitic fitness in the pathogens. (sisef.it)
  • Quantitative PCR and high-throughput methods, such as expressed sequence tag analysis, have been used for measuring gene expression and identifying subsets of elm genes that are differentially expressed in the presence of O. novo-ulmi . (sisef.it)
  • We conducted whole-genome sequencing and epidemiologic analysis of all KPC- Kp isolates in France in 2018 and found that new successful high-risk clones of ST147, ST307, ST231, and ST383 are now the main drivers of bla KPC genes. (cdc.gov)
  • This is achieved through mechanistic studies of functionally important epigenetic "driver" genes and molecular pathways altered by specific cancer risk agents and by the application of cutting-edge epigenomics in conjunction with unique biospecimens from population-based cohorts (Figure 1). (who.int)
  • La determinación de un patrón de genes expresados al nivel de la TRANSCRIPCIÓN GENÉTICA bajo circunstancias específicas o en una célula específica. (bvsalud.org)
  • Jean-Marc Aury works at Genoscope's Scientific Information Technology Laboratory and heads a bioinformatics and sequencing R&D team focused primarily on the processing of next generation sequencing data. (cea.fr)
  • A strong understanding of molecular biology, statistics, and bioinformatics techniques is therefore essential along with excellent communication skills and an enthusiasm for scientific data analysis. (biostars.org)
  • Conclusions: In this study, we integrated two high-throughput sequencing techniques, mass spectrometry analysis, and comprehensive bioinformatics approach in order to arrive at the first comprehensive description of monogenean transcriptome and secretome. (muni.cz)
  • EGE also develops epigenomic methodologies, profiling strategies, and bioinformatics tools, applicable to population-based cohorts and molecular epidemiology studies coordinated by IARC researchers and external collaborators. (who.int)
  • Using experimental infections reproducing the natural route of infection and combining thorough molecular analyses of oyster families with contrasted susceptibilities, we demonstrate that the disease is caused by multiple infection with an initial and necessary step of infection of oyster haemocytes by the Ostreid herpesvirus OsHV-1 µVar. (nature.com)
  • Differential gene expression analyses revealed 22% more light up-regulated and 35% more light down-regulated transcripts in the G3116 transcriptome compared to DV92. (oregonstate.edu)
  • Recently, the enhanced sequencing, assembly and annotation of the P. vivax P01 reference genome opens new avenues for molecular biology and evolutionary studies, including transcriptomic aiming to grasp the molecular mechanisms underlying several aspects of P. vivax pathogenesis that are still lacking. (fapesp.br)
  • C. livia is broadly studied in ecology, genetics, physiology, behavior, and evolutionary biology, and has recently emerged as a model for understanding the molecular basis of anatomical diversity, the magnetic sense, and other key aspects of avian biology. (nih.gov)
  • In genetics and genomics research, gene expression refers to the process by which information encoded in a gene's DNA sequence is converted into functional proteins or RNA molecules. (pharmiweb.com)
  • Greatly increased scaffold lengths in the updated reference assembly, along with an updated annotation set, provide improved tools for evolutionary and functional genetic studies of the pigeon, and for comparative avian genomics in general. (nih.gov)
  • Entrez is NCBI's primary text search and retrieval system that integrates the PubMed database of biomedical literature with 38 other literature and molecular databases including DNA and protein sequence, structure, gene, genome, genetic variation and gene expression. (nih.gov)
  • For the future direction, we need the in-depth genome sequence information and analysis for most of the mammals, including human to fully understand genome variation of economic traits, genetic susceptibility to diseases, and pharmacogenomics of drug response. (springer.com)
  • In addition, we identified 2,411 simple sequence repeats (SSRs) as potential genetic markers from the transcripts. (oregonstate.edu)
  • Genome assembly, annotation and variant analysis - Our team are proficient in dealing with whole genome, whole-exome and targeted sequencing methods that allow for the study of genetic variants or mutations. (nottingham.ac.uk)
  • To accelerate the pummelo breeding program, it is essential to obtain extensive genetic information and develop relative molecular markers. (citrusgenomedb.org)
  • Our study would provide the molecular basis for genetic diversity analysis, genetic map construction and red leaf molecular marker development of E.ulmoides . (nefu.edu.cn)
  • A primary focus is the use of molecular genetic techniques in conservation, including the identification of whale and dolphin products available in commercial markets. (stanford.edu)
  • During the last decades, the development of ever more powerful genetic, molecular and omic approaches has provided plant pathologists with a wide array of experimental tools for elucidating the intricacies of plant-pathogen interactions and proposing new control strategies. (sisef.it)
  • Molecular and omic approaches, however, represent technological advances that should allow rapid developments in the genetic analysis of elms and bark beetle vectors of the disease. (sisef.it)
  • Each of the following platforms utilizes a different type of technology to sequence millions of short reads: 454 Sequencing, Illumina, and SOLiD. (wikipedia.org)
  • The cDNA sequence reads are assembled into transcripts via a short read transcript assembly program. (wikipedia.org)
  • We used ~355 million high-quality reads of total ~394 million raw reads from transcriptome sequencing to generate reference transcriptome assembly and the tissue-specific transcript assemblies. (oregonstate.edu)
  • Using a hybrid sequence assembly approach including data from both long and short sequence reads, we present the first assembly of the Rubus idaeus genome (Joan J. variety). (pacb.com)
  • The DV92 and G3116 mRNA sequence reads aligned against the reference barley genome led to the identification of 500,000 single nucleotide polymorphism (SNP) and 22,000 simple sequence repeat (SSR) sites. (oregonstate.edu)
  • Uing PacBio Iso-Seq technology, we generated high quality full-length transcriptome sequencing reads using four sample types from rhesus macaque: lymph node tissue, peripheral blood mononuclear cells (PBMC), whole blood, and rectal tissue. (nhprtr.org)
  • This includes trimming adapter sequences, filtering low-quality reads, and aligning the reads to a reference genome or transcriptome. (pharmiweb.com)
  • The next step involves mapping the processed reads to a reference genome or transcriptome. (pharmiweb.com)
  • To analyze the regulatory mechanism involved in the high growth potential of C. virgata , we performed RNA-seq-based transcriptome analysis and illustrated a comprehensive gene expression map of the species. (frontiersin.org)
  • The tall fescue assembled transcriptome provided substantial molecular resources for further genomics analysis of turfgrass in response to heavy metal stress. (biomedcentral.com)
  • Furthermore, I used the experimental and data analysis framework to analyze specific molecular features of the three AML subgroups. (uni-heidelberg.de)
  • In summary, this thesis provides novel insights into the tumorigenesis process in AML by using a systematic and functional analysis approach of the transcriptome and open chromatin in single cells for three major genetically defined AML subgroups. (uni-heidelberg.de)
  • genome informatics focuses on the development and application of algorithms and software for analysis of large sets of data, e.g. sequence sets and transcriptome data. (uni-hamburg.de)
  • This study conducted a comparative analysis of the T. wilfordii transcriptome derived from its root and leaf tissues. (techscience.com)
  • We are here to serve you with all sequencing and data analysis requirement for molecular biology. (noeticsbiotech.co.in)
  • Here, we examined the transcriptome of the SCN and whole brain (WB) of mice using meta-analysis of publicly deposited data across a range of microarray platforms and RNA-Seq data. (ox.ac.uk)
  • The SNP and SSR sites identified in our analysis provide additional resources for the development of molecular markers. (oregonstate.edu)
  • Analysis of Red Leaf Color SSR Molecular Markers by Transcriptome Sequencing of Eucommia ulmoides [J]. Bulletin of Botanical Research, 2017, 37(6): 897-906. (nefu.edu.cn)
  • Until recently, however, functional analysis of the DED fungi was hampered by the lack of protocols for efficient gene knockout and by the unavailability of a full genome sequence. (sisef.it)
  • By subjecting DEGs to gene ontology enrichment analysis, pathway analysis, or functional annotation, we gain insights into the biological processes, molecular functions, and pathways associated with the observed gene expression changes. (pharmiweb.com)
  • Whole-genome sequencing (WGS) analysis has suggested that ST258 and ST512 KPC- Kp spread out in Europe from 2 KPC-endemic countries: Greece (ST258) and Italy (ST512) ( 6 , 9 - 11 ). (cdc.gov)
  • To contribute to the hazard identification of low molecular weight (LMW) respiratory allergens, respiratory allergy induced by trimellitic anhydride (TMA) was characterized by whole genome analysis of lung tissue and blood proteomics in Brown Norway rats. (cdc.gov)
  • This study provided new insights for the investigation of the molecular basis of Pb tolerance and accumulation in tall fescue as well as other related turf grass species. (biomedcentral.com)
  • Tall fescue is also a hexaploid outcrossing species with a large genome size [ 8 ], and up to now its genome has not been sequenced. (biomedcentral.com)
  • Our expertise in dealing with both shotgun and high throughput sequencing data can empower researchers with accurate gene prediction and precise species categorisation. (nottingham.ac.uk)
  • The concept was to develop a NHP reference transcriptome resource consisting of deep sequencing complete transcriptomes (RNA-seq) from multiple NHP species. (nhprtr.org)
  • This resulted in the reconstruction of skin and skeletal muscle transcriptomes from an extinct species for the first time. (phys.org)
  • Understanding the molecular basis of insecticide resistance in this species is crucial to design effective resistance management strategies. (cdc.gov)
  • The search for putative molecular markers among 57,212 unigenes identified 10,276 simple sequence repeats (SSRs) and 64,720 single nucleotide polymorphisms (SNPs). (citrusgenomedb.org)
  • Having this goal, we have successfully (i) isolated RNA from a panel of P. vivax field isolates with scarce parasitemia enriched in (cyto-)adhesion phenotypes from the Amazon malaria endemic region, (ii) complete the generation of transcriptomic libraries and (iii) sequenced them using the Illumina® platform. (fapesp.br)
  • Here, we obtained a 12-Gb transcriptome dataset of pummelo through a mixture of RNA from seven tissues using Illumina pair-end sequencing, assembled into 57,212 unigenes with an average length of 1010 bp. (citrusgenomedb.org)
  • When available each record links to detailed diagrams and annotations for individual pathways on the Web sites of the source databases. (nih.gov)
  • Unraveling the underlying molecular pathways enhances our comprehension of stress responses and enables the development of strategies to mitigate their impact. (pharmiweb.com)
  • Molecular paThwayS criTical for cancer developMenT and progreSSion, ThuS enhancing The evidence baSe direcTly relevanT To STudieS of cancer cauSaTion and prevenTion. (who.int)
  • The high-throughput - next generation sequencing (HT-NGS) technologies are currently the hottest topic in the field of human and animals genomics researches, which can produce over 100 times more data compared to the most sophisticated capillary sequencers based on the Sanger method. (springer.com)
  • The completion of the first human genome drafts (Yamey 2000 ) was just a start of the modern DNA sequencing era which resulted in further invention, improved development toward new advanced strategies of high-throughput DNA sequencing, so called the " high-throughput next generation sequencing " (HT-NGS). (springer.com)
  • however, these developed in 2010s high-throughput sequencing (also called next-generation sequencing) technologies are both cost- and labor- effective, and the range of organisms studied via these methods is expanding. (wikipedia.org)
  • Once RNA is extracted and purified from cells, it is sent to a high-throughput sequencing facility, where it is first reverse transcribed to create a cDNA library. (wikipedia.org)
  • Scasa, an isoform-level quantification method for high-throughput single-cell RNA sequencing by exploiting the concepts of transcription clusters and isoform paralogs. (ne.jp)
  • Maša Ivin, Ph.D., Scientific Writer at Lexogen, and Yvonne Goepel Ph.D., Product Manager at Lexogen, remarked that "The high-throughput nature of RNA-seq allows for rapid profiling and deep exploration of the transcriptome. (seqanswers.com)
  • Bacterial and fungal functions were estimated using functional annotation of prokaryotic taxa (FAPROTAX) and fungi functional guild (FUNGuild), respectively. (bvsalud.org)
  • Functional annotation of a full-length mouse cDNA collection. (jax.org)
  • Conserved Domains is a database of protein domains represented by sequence alignments and profiles for protein domains conserved in molecular evolution. (nih.gov)
  • Here, we present a compilation of DNA and protein databases, as well as bioinformatic tools for phylogenetic reconstruction and a wide range of studies on molecular evolution. (lu.se)
  • During the last decade, next generation sequencing has revolutionized our awareness in basic parasite molecular biology, its ecology and epidemiology knowledge. (fapesp.br)
  • However, studies on P. vivax biology and pathogenesis about the molecular mechanisms involved in the P. vivax cytoadhesion capacity are scarce, because of the lack of a reliable in vitro P. vivax long term culture. (fapesp.br)
  • This new dataset will be a valuable resource for molecular biology studies of pummelo and provides reliable information regarding SNP and SSR marker development, thus expediting the breeding program of pummelo. (citrusgenomedb.org)
  • By comparing gene expression patterns during embryogenesis or tissue differentiation, we unravel the molecular events that shape organisms, advancing our understanding of developmental biology. (pharmiweb.com)
  • Exploration of E. nipponicum transcriptome-related nucleotide sequences and translated and secreted proteins offer a better understanding of molecular biology and biochemistry of these, often neglected, organisms. (muni.cz)
  • The main tool used in transcriptomics is total RNA sequencing, which is a powerful tool for analyzing gene expression changes in response to various environmental stresses [ 27 ]. (hindawi.com)
  • Sequencing methods that analyze the transcriptome (scRNA-seq) and epigenome (scATAC-seq) are ideally suited to resolve tumor cell heterogeneity as well as non-malignant cell types in the microenvironment. (uni-heidelberg.de)
  • This hands on course will give you the experience and provide the tools that are needed to analyze next generation sequencing data. (lu.se)
  • This cDNA can then be fragmented into various lengths depending on the platform used for sequencing. (wikipedia.org)
  • Moreover, our transcriptome map demonstrated the expression profiles of orthologs involved in the biosynthesis of these phytohormones and their signaling networks. (frontiersin.org)
  • Here we report an update to the C. livia genome reference assembly and gene annotation dataset. (nih.gov)
  • Principal Findings The de novo transcriptome assemblies of DV92 and G3116 represent 120,911 and 117,969 transcripts, respectively. (oregonstate.edu)
  • Conclusions De novo transcriptome assemblies of two accessions of the diploid wheat T. monococcum provide new empirical transcriptome references for improving Triticeae genome annotations, and insights into transcriptional programming during photomorphogenesis. (oregonstate.edu)
  • The transcriptomes of these organisms can thus reveal novel proteins and their isoforms that are implicated in such unique biological phenomena. (wikipedia.org)
  • The annotation and classification results showed that a total of 39,584 unigenes had similar hits to the known proteins of four public databases, and 31,501 were classified into 55 Gene Ontology (GO) functional sub-categories. (citrusgenomedb.org)
  • First, I characterized changes in the transcriptome and classified developmental stages of leukemic cells carrying MLL-EDC4 fusions along the hematopoietic stem cell to the myeloid trajectory compared to other MLL fusions. (uni-heidelberg.de)
  • Though genome alignment is a robust way of characterizing transcript sequences, this method is disadvantaged by its inability to account for incidents of structural alterations of mRNA transcripts, such as alternative splicing. (wikipedia.org)
  • We provide a protocol for information extraction from biological databases and simple phylogenetic reconstruction using probabilistic and distance methods, facilitating the study of biodiversity and evolution at the molecular level for the broad scientific community. (lu.se)
  • In Hamburg, such methods are developed for virtual screening, design of molecular libraries and visualisation of molecular data for drug design. (uni-hamburg.de)
  • The data comes from three types of RNA library preparation methods: non-directional mRNA-sequencing (RNA), non-directional mRNA-sequencing and Uracil-DNA Glycosolase (UDG), and total RNA (TOT).The RNASeq data was described in Pipes et al, 2013 . (nhprtr.org)
  • ClinVar provides standardized nomenclature for variants and phenotypes, a review status for variants, and links to related NCBI literature and molecular databases. (nih.gov)
  • Third, transcriptome assembly is more challenging because transcript variants from the same gene can share exons and are difficult to resolve unambiguously. (wikipedia.org)
  • Our experience in working with RNA-sequencing or expression microarray data can enable researchers to pinpoint the molecular mechanisms that create associations between genotypes and phenotypes. (nottingham.ac.uk)
  • In conclusion, the proteome and transcriptome correlation results from this study indicate that ion transport plays a critical role in the adaptation of S. paramamosain to sudden reduction in salinity. (hindawi.com)
  • Tissue specific small RNA sequence data is now available for rhesus macaque here . (nhprtr.org)
  • However, reconstructing a functional living Tasmanian tiger not only requires a comprehensive knowledge of its genome (DNA) but also of tissue-specific gene expression dynamics and how gene regulation worked, which are only attainable by studying its transcriptome (RNA). (phys.org)
  • By unraveling the molecular mechanisms underpinning drug response, we can optimize treatment strategies, expedite drug discovery, and develop personalized therapies tailored to individual patients. (pharmiweb.com)
  • Of the 20 SNP primers, 14 primers, including 54 potential SNPs, yielded target amplifications, and 46 loci were verified via Sanger sequencing. (citrusgenomedb.org)
  • Unlike genome sequence coverage levels - which can vary randomly as a result of repeat content in non-coding intron regions of DNA - transcriptome sequence coverage levels can be directly indicative of gene expression levels. (wikipedia.org)
  • BioSample contains descriptions of biological source materials used in studies that have data in other NCBI molecular databases such as Assembly, Nucleotide and SRA. (nih.gov)
  • First, genome sequencing depth is usually the same across a genome, but the depth of transcripts can vary. (wikipedia.org)
  • In addition, unlike genome sequencing, transcriptome sequencing can be strand-specific, due to the possibility of both sense and antisense transcripts. (wikipedia.org)
  • About 65,587 of 82,663 transcripts were translated into 99,307 peptides, and we were successful in assigning InterPro annotations to 45,209 peptides and gene ontology (GO) terms to 32,638 peptides. (oregonstate.edu)
  • I could demonstrate that leukemic cells could be successfully distinguished from the microenvironment based on marker gene annotation from the human cell atlas and ploidy inference. (uni-heidelberg.de)
  • The researchers behind this study have sequenced, for the first time, the transcriptome of the skin and skeletal muscle tissues from a 130-year-old desiccated Tasmanian tiger specimen preserved at room temperature in the Swedish Museum of Natural History in Stockholm. (phys.org)
  • This pioneering study opens up new exciting opportunities and implications for exploring the vast collections of specimens and tissues stored at museums across the globe, where RNA molecules might await to be uncovered and sequenced. (phys.org)
  • 3 Research Institute of Molecular Pathology, Vienna, Austria. (nih.gov)
  • The worldwide spread of KPC has been linked to the dissemination of a main clone of K. pneumoniae (sequence type [ST] 258) and a single-locus variant (ST512) ( 6 ). (cdc.gov)