Genome and transcriptomePlanarian Smed454 Transcriptome BrowserNovo assemblyAnalysesGenesGene expressionSpeciesProteomeAnalysisAssemblersGenomesTumorMicrobesExonTrinityApproachesDataDraftReadsNucleiAssemblySequencingEvolutionAtlasGeneticProtocolComprehensiveTranscriptsPlantsStudyShotgunHumanIncludes
Genome and transcriptome4
- PG2 integrates genome and transcriptome sequencing to incorporate protein variants containing amino acid substitutions, insertions, and deletions, as well as non-canonical reading frames, exons, and other variants caused by genomic and transcriptomic variation. (biorxiv.org)
- Whole genome and transcriptome sequencing of the LLS fungus were obtained. (biomedcentral.com)
- Here we present the first reference genome and transcriptome of C. personatum to support studies in phylogenetics, genetic diversity, pathogenicity, and metabolites of this peanut pathogen. (biomedcentral.com)
- Reconstructing the genome and transcriptome for a new or extant species are essential steps in expanding our understanding of the organisms active RNA landscape and gene regulatory dynamics, as well as for developing therapeutic targets to fight disease. (tamu.edu)
Planarian Smed454 Transcriptome Browser1
- Planarian Smed454 Transcriptome Browser: 333 bp from F6AJIXP02FPWO6:1. (ub.edu)
Novo assembly4
- De novo assembly and analysis of the transcriptome of Ocimum americanum var. (biomedcentral.com)
- For an organism that lacks a high-quality reference genome, the de novo assembly of its transcriptome is a useful method for researchers to find the transcripts or genes responsive to various treatments and to better understand the expression patterns of the candidate genes. (biomedcentral.com)
- This de novo assembly of a red clover transcriptome from leaf material of droughted and non-droughted plants provides a rich source for gene identification, single nucleotide polymorphisms (SNP) and short sequence repeats (SSR). (biomedcentral.com)
- We will discuss our growing body of work on large-scale de novo assembly, reference free methods for investigating community coverage, and diversity estimation for shotgun sequencing data. (iscb.org)
Analyses2
- On the basis of whole-transcriptome analyses, we identify many genes that are expressed in a sex- or life stage-specific manner and characterize the transcriptional landscape of a morphological region with unique biological adaptations, namely, bacillary band and stichosome, found only in whipworms and related parasites. (nature.com)
- In age-stratified analyses, primary series vaccine coverage was very high among the elderly. (cdc.gov)
Genes4
- . pilosum and a de novo assembled transcriptome, which can be used to characterize genes related to diverse biological processes. (biomedcentral.com)
- Besides demonstrating that the probe selection method can be used to study the ovine transcriptome, the benefits of this approach are that it can greatly increase the number of annotated and novel genes that can be studied beyond those currently possible using ovine- or bovine-specific microarrays. (cambridge.org)
- Anonymous Reviewer ( 2020 ) Peer Review #2 of 'Comprehensive transcriptome analysis of reference genes for fruit development of Euscaphis konishii (v0.4)' . (peerj.com)
- It includes over 1,800 genes and 100 pathways and provides a 20-fold increase in RNA coverage resulting in a high-resolution spatial view of cancer biology. (pharmiweb.com)
Gene expression4
- To bridge such gap, we integrated the largest cervical cancer GWAS ( N = 9,347) with gene expression measured in six human tissues to perform a multi-tissue transcriptome-wide association study (TWAS). (jcancer.org)
- This week, Last maintained that Affy is committed to offering the "best, cutting-edge gene-expression tools available," and said that the GeneChip Human Transcriptome and Splice Junction array "is the next generation of these tools, offering an even better view of the transcriptome. (genomeweb.com)
- Recent studies indicated that digital gene expression profiling based on short sequence tags has superior performance as compared to other transcriptome analysis platforms including microarrays. (biomedcentral.com)
- This includes whole transcriptome gene expression for almost 30 different species, Exon microarrays to analyze splicing variants and gene expression microarrays with comprehensive content, including full LNCipedia databases to provide full coverage of the transcriptome in a single experiment. (agilent.com)
Species6
- Here we report a novel approach to characterizing viral AS using whole transcriptome dataset from host species. (nature.com)
- This is the first study to assess the cold-responsive transcriptome in an Ocimum species. (biomedcentral.com)
- These differences largely result from limited knowledge regarding the optimized sequencing depth and assembler for transcriptome assembly of structurally complex plant species genomes. (biomedcentral.com)
- CPTRA is a powerful software package for next generation sequencing-based transcriptome profiling in species with limited genome information. (biomedcentral.com)
- According to our case study, the strategy can greatly broaden the application of the next generation sequencing for transcriptome analysis in species without reference genome sequence. (biomedcentral.com)
- Considering the read length, 454 sequencing has some advantages for transcriptome analysis, since the longer reads allow for better assembly of the sequences, which is particularly important for species without reference genome information. (biomedcentral.com)
Proteome2
- Features such as the transcriptome, methylome, proteome, histone post-translational modifications and the microbiome all influence the host response to various diseases and cancers. (rsc.org)
- The characterization of the transcriptome and proteome of Plasmodium falciparum has been a tremendous resource for the understanding of the molecular physiology of this parasite. (datadryad.org)
Analysis8
- Detailed analysis of the splicing junctions showed clusters of AS events occurred in two regions of the virus genome, demonstrating that transcriptome analysis could gain valuable insights into viral splicing. (nature.com)
- Therefore, a well-assembled, accurate, and comprehensive transcriptome is a prerequisite for the subsequent analysis. (biomedcentral.com)
- The combination of transcriptome data acquisition methods requires cross-platform transcriptome data analysis platforms, including a new software package for data processing. (biomedcentral.com)
- In this paper, we will focus on a software package providing the enabling tools for cross-platform transcriptome analysis. (biomedcentral.com)
- Genome sequence and spore germination-associated transcriptome analysis will contribute to the understanding of the molecular mechanism of pathogenicity and spore germination of C. cassiicola . (biomedcentral.com)
- The authors say that this is the first prospective, pediatric study to assess the feasibility and utility of incorporating multiple, comprehensive sequencing technologies (whole-exome and transcriptome analysis) in cancer care. (g2intelligence.com)
- Thirty-six percent of patients exhibited a driving gene fusion, which indicates a potential role of including RNA sequencing (transcriptome sequencing), in addition to whole-exome analysis, in the work-up of individuals with cancer," write the authors led by Rajen Mody, M.B.B.S., from the University of Michigan, Ann Arbor. (g2intelligence.com)
- To identify clinical and tumor molecular biomarkers associated with exceptional clinical response or resistance, we conducted an integrated clinical, exome, and transcriptome analysis of 41 primary tumors from LT ( n = 20) and ST ( n = 21) HGSOC patients. (biomedcentral.com)
Assemblers3
- We employed different amounts of RNA-sequencing data, ranging from 4 to 84 Gb, to assemble the tea plant transcriptome using five well-known and representative transcript assemblers. (biomedcentral.com)
- The present study compares the performance of five representative transcript assemblers and investigates the key factors that affect the assembly quality of the transcriptome of the tea plants. (biomedcentral.com)
- The Trinity software for RNA-seq, in comparison with other de novo transcriptome assemblers, was reported to recover more full-length transcripts over a broad range of expression levels, with a sensitivity similar to methods that rely on genome alignments. (wikipedia.org)
Genomes1
- For environmental communities, many fewer reference genomes or transcriptomes are typically available than for human-associated microbes, and the substantial diversity of many communities means that terabases of sequencing may be needed to recover a significant fraction of the community metagenome. (iscb.org)
Tumor2
- Recent multi-omics studies have revealed the heterogeneity and complexity of tumor features such as their genetic mutations, transcriptome, proteins, and signaling pathways. (rsc.org)
- more than 150-fold average coverage) and transcriptome (tumor RNA) sequencing. (g2intelligence.com)
Microbes1
- One of the latest metatranscriptomics techniques is stable isotope probing (SIP), which has been used to retrieve specific targeted transcriptomes of aerobic microbes in lake sediment. (wikipedia.org)
Exon1
- 2020). Remarkably, the Spider 2Kv1 overlaps noticeably with the exon information in the transcriptomes, opening a door for incorporating transcriptomic information into UCE studies of spiders (Hedin et al. (researchgate.net)
Trinity1
- What is the fate of low coverage region during Trinity assembly of transcriptome data? (biostars.org)
Approaches2
- Data is being published to demonstrate that as a practical matter for large-scale clinical studies, array-based approaches are a perfect complement to the discovery of transcriptome elements. (genomeweb.com)
- Next-generation sequencing techniques enable several novel transcriptome profiling approaches. (biomedcentral.com)
Data4
- C ross- P latform TR anscriptome A nalysis, to analyze transcriptome profiling data from separate methods. (biomedcentral.com)
- The data indicated that the potential pathogens identified in the blood samples were associated with translocation from the gut, suggesting the presence of bacteremia, which transcriptome data suggested may induce or aggravate the acute-phase response observed during EVD. (asm.org)
- Higher coverage of the genome is not as important as the quality of the input RNA-Seq data. (tamu.edu)
- I'm just thinking out loud about how to incorporate high throughput transcriptome sequencing data into BASE. (lu.se)
Draft1
- The advancement of sequencing technologies has paved the way to generate high-quality draft transcriptomes. (tamu.edu)
Reads3
- A total of 115,022,842 high quality, clean reads were obtained from four libraries (two replicates of control samples and two replicates of chilling-treated samples) and were used to perform de novo transcriptome assembly. (biomedcentral.com)
- RSEM starts with a reference transcriptome or assembly along with RNA-Seq reads generated from the sample and calculates normalized transcript abundance (meaning the number of RNA-Seq reads cor-responding to each reference transcriptome or assembly). (wikipedia.org)
- Ribosome footprint read coverage plots (normalized by millions of reads sequenced). (datadryad.org)
Nuclei4
- The genome and preliminary single-nuclei transcriptome of Lemna minuta reveals mechanisms of invasiveness. (jcvi.org)
- Here we present a chromosome-resolved genome for the highly invasive Lesser Duckweed (Lemna minuta) and generate a preliminary cell atlas leveraging low cell coverage single-nuclei sequencing. (jcvi.org)
- Leveraging SMARTseq2 single-nuclei sequencing, which provided higher gene coverage yet lower cell count, we profiled 269 nuclei covering 36.9% (8,457) of the L. minuta transcriptome. (jcvi.org)
- We developed a combinatorial indexing strategy to profile the transcriptomes of large numbers of single cells or nuclei (Single cell Combinatorial Indexing RNA-seq or sci-RNA-seq). (nih.gov)
Assembly3
- This study will be of significance in helping the tea research community obtain better sequencing and assembly of tea plant transcriptomes under conditions of interest and may thus help to answer major biological questions currently facing the tea industry. (biomedcentral.com)
- What are the most influencing factors in reconstructing a reliable transcriptome assembly? (tamu.edu)
- We carried out an extensive survey of variety of elements that are important in transcriptome assembly. (tamu.edu)
Sequencing5
- As increasing number of next-generation sequencing (NGS) datasets are being produced from various-omics initiatives, transcriptome sequencing of flora and fauna for a specific developmental stage/condition gains its popularity in biological research. (nature.com)
- Our xGen RNA sequencing offerings cover a wide range of diverse inputs while maintaining predictable outputs, efficiencies, and coverage metrics. (idtdna.com)
- 1, The author carried out the three stages of fruit ripening transcriptome sequencing, and made a detailed description in materials and methods, but did not mention in the results. (peerj.com)
- Second, a global view of the transcriptome of C. cassiicola spores during germination was evaluated using RNA sequencing (RNA-Seq). (biomedcentral.com)
- The information in this article contains billing, coding or other guidelines that complement the Local Coverage Determination (LCD) for MolDX: Next Generation Sequencing for Solid Tumors L38045. (cms.gov)
Evolution1
- Two insect transcriptomes ( Acheta domesticus and Planococcus citri ) generated in the 1,000 Insect Transcriptome Evolution (1KITE) project were used as a proof of concept using the new pipeline. (nature.com)
Atlas1
- For instance, Cancer Transcriptome Atlas by Nanostring is the first commercial GeoMx product that is enabled by readout using NGS. (pharmiweb.com)
Genetic1
- In the last decade, many studies have generated the transcriptomes of tea plants at different developmental stages or under abiotic and/or biotic stresses to investigate the genetic basis of secondary metabolites that determine tea quality. (biomedcentral.com)
Protocol1
- QIAseq Stranded RNA Library Kits use a unique protocol, which does not require actinomycin D to retain strand specificity or dUTP to ensure stranded library construction, thereby ensuring highly sensitive detection of low-expression RNA molecules with increased complexity and transcript coverage. (qiagen.com)
Comprehensive1
- The resultant libraries represent uniform and comprehensive genome coverage. (idtdna.com)
Transcripts1
- However, these results exhibited large differences, particularly in the total number of reconstructed transcripts and the quality of the assembled transcriptomes. (biomedcentral.com)
Plants1
- . pilosum and compared the transcriptomes of plants grown under normal and low temperatures. (biomedcentral.com)
Study1
- Inequities in COVID-19 vaccine and booster coverage across Massachusetts ZIP codes after the emergence of Omicron: A population-based cross-sectional study. (cdc.gov)
Shotgun1
- We applied sci-RNA-seq to profile nearly 50,000 cells from C. elegans at the L2 stage, effectively ~56-fold "shotgun cellular coverage" of its somatic cell composition. (nih.gov)
Human1
- The company last week launched its GeneChip Human Transcriptome and Splice Junction Array, a 6.9-million-feature chip designed with researchers from Stanford University. (genomeweb.com)
Includes1
- https://en.wikipedia.org/wiki/Wikipedia:WikiProject_Computational_Biology/ISMB_2014 - this includes the course materials and an outline as well as some suggestions on how you could prepare for the hands-on part of the tutorial (AKA homework). (iscb.org)