• This package implements some convenience methods for readily generating such truncated annotations and their corresponding sequences. (bioconductor.org)
  • Consequently, by analyzing the entire collection of RNA sequences in a cell (the transcriptome) researchers can determine when and where each gene is turned on or off in the cells and tissues of an organism. (genome.gov)
  • Sequences were gathered or generated for 53 nematode species from ESTs, gene predictions from full genome assemblies and transcripts from RNA-Seq experiments. (bl.uk)
  • 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)
  • Efforts to sequence the transcriptome of the commercial highbush blueberry (Vaccinium corymbosum L.) and use the sequences to identify genes associated with cold acclimation and fruit development and develop SSR markers for mapping studies are presented here. (usda.gov)
  • Transcriptome sequences were generated from blueberry fruit at different stages of development, flower buds at different stages of cold acclimation, and leaves by next-generation Roche 454 sequencing. (usda.gov)
  • Here, we use transcriptome data from 15 newly-sequenced species in combination with 26 publicly available genomes and transcriptomes to assess phylogenetic relationships among major cnidarian lineages. (plos.org)
  • Analysis of the blue coral transcriptome revealed enrichment of genes involved in stress response, including heat-shock proteins and antioxidants, as well as genes participating in signal transduction and stimulus response. (nature.com)
  • Analyses that focus on quantification of isoform usage from such data can be aided by using truncated versions of transcriptome annotations, both at the alignment or pseudo-alignment stage, as well as in downstream analysis. (bioconductor.org)
  • Results In the present study, we performed a systematic transcriptome analysis based on the deep RNA sequencing of ten asthmatic children before and after desensitization treatment. (researchsquare.com)
  • Cell Ranger is a set of analysis pipelines that processes Chromium single-cell 3′ RNA-Seq output to align reads, generate gene-cell matrices, and perform clustering and gene-expression analysis. (genengnews.com)
  • PALO ALTO, Calif.--( BUSINESS WIRE )--Curio Bioscience today announced an expansion of its Curio Seeker product line with a larger format to deliver a more complete view of large biological structures, including human tissue samples, providing one hundred times more data compared to other whole transcriptome spatial analysis solutions. (businesswire.com)
  • Curio Seeker is a whole transcriptome analysis reagent kit solution that provides the ability to generate molecular images of tissue sections by capturing and mapping the spatial location of RNA molecules using next-generation sequencers. (businesswire.com)
  • De novo assembly and analysis of the transcriptome of Ocimum americanum var. (biomedcentral.com)
  • Development of new signatures, using full transcriptome analysis and building large real-world evidence databases, are pivotal to answer clinically relevant questions that often remain unresolved in smaller trials. (agendia.com)
  • Looking to fill this gap, researchers from the Chinese Academy of Agricultural Sciences conducted a de novo transcriptome assembly and gene-expression analysis of the alimentary canals of S. avenae before and after feeding on wheat plants, they wrote in BMC Genomics . (genomeweb.com)
  • ResolveOME generates single-cell multiomics datasets by combining whole genome or exome analysis with whole transcriptome analysis within each individual cell. (genengnews.com)
  • 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)
  • Therefore, a well-assembled, accurate, and comprehensive transcriptome is a prerequisite for the subsequent analysis. (biomedcentral.com)
  • Transcriptome analysis has been used in autism spectrum disorder (ASD) to unravel common pathogenic pathways based on the assumption that distinct rare genetic variants or epigenetic modifications affect common biological pathways. (biomedcentral.com)
  • Transcriptome analysis reveals overlap in fusion genes in a phase I clinical cohort of TNBC and HGSOC patients treated with buparlisib and olaparib. (broadinstitute.org)
  • The mechanisms underlying the response and recovery of A. paniculata to Mn toxicity were further investigated using transcriptome analysis. (rhhz.net)
  • Serena Scollen, project coordinator on the FAIRplus project and head of human genomics and translational data at ELIXIR at its headquarters in Hinxton, UK, noted that data generated by IMI-funded projects is often stored in "isolated silos," with inconsistent annotation or in incompatible formats. (genomeweb.com)
  • In 2021, our sustainability efforts sent more than 80 percent of waste from the Genomics Platform to either a recycling facility or to an incineration plant that generates electricity. (broadinstitute.org)
  • A large amount of data is being generated in the post genomic era through research in genomics, proteomics, and structural biology. (lu.se)
  • 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)
  • A total of 330 significantly differential genes were identified through large-scale transcriptome sequencing, among which 103 genes were upregulated and 227 genes were downregulated. (mdpi.com)
  • In addition, transcriptomes may enable researchers to generate a comprehensive, genome-wide picture of what genes are active in which cells. (genome.gov)
  • . pilosum and a de novo assembled transcriptome, which can be used to characterize genes related to diverse biological processes. (biomedcentral.com)
  • A comparison of the transcriptomes of alimentary canals of pre- and post- feeding grain aphids indicated that 5,490 unigenes were differentially expressed, among which diverse genes and/or pathways were identified and annotated. (genomeweb.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)
  • The CBF-mediated transcriptional cascade, a well-known cold tolerance pathway, was reconstructed using our de novo assembled transcriptome. (biomedcentral.com)
  • L1s generate hundreds of developmentally regulated and cell type-specific transcripts, many that are co-opted as chimeric transcripts or regulatory RNAs. (lu.se)
  • These contigs were uploaded to the NCBI Transcriptome Assembly Shotgun Sequence Database, accession numbers JV077153-JV134524. (stanford.edu)
  • 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)
  • 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)
  • 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)
  • 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)
  • 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)
  • The accurate assembly of a transcript is largely determined by the sequencing depth, which leads to the question of how much data should be generated in an RNA-seq experiment to obtain robust results. (biomedcentral.com)
  • In this study, we established RAINBOW-seq and profiled the transcriptome of Escherichia coli biofilm communities with high spatial resolution and high gene coverage. (nature.com)
  • Fig. 2: Spatial transcriptome of E. coli biofilm. (nature.com)
  • The spatial transcriptomic data generated by Curio Seeker enable researchers to better understand cellular functions in the context of their native environment, providing additional biological insight that are not available from single-cell RNA sequencing approaches. (businesswire.com)
  • A highly useful tool to unlock the real potential of this new approach is the new Curio Seeker 10x10 kit, which allows us to use our existing sequencer to generate more unbiased, high-resolution spatial transcriptomics data across larger tissue sections than we could have achieved any other way," said Iwijn De Vlaminck, associate professor of biomedical engineering at Cornell University. (businesswire.com)
  • We are extremely excited about the data being generated from the Curio Seeker kit, and we are already gaining compelling new insights into the spatial relationships between cells and cell neighborhoods in our model system. (businesswire.com)
  • It brings high resolution, whole transcriptome, spatial biology further into the scale of human biology, expanding a researcher's ability to see larger regions of interest in a tissue sample," said Fei Chen. (businesswire.com)
  • Description: RNA profiling data sets generated by the Mouse ENCODE project. (nih.gov)
  • Transcriptome data were analyzed by comparing Ly6C high vs. Ly6C low in control mice, Ly6C high vs. Ly6C low in Cbs -/- mice, Cbs -/- Ly6C high vs. control Ly6C high MC and Cbs -/- Ly6C low vs. control Ly6C low MC by using intensive bioinformatic strategies. (frontiersin.org)
  • Using the GemCode approach, Dr. Hindson and colleagues collected transcriptome data from about 250,000 cells across 29 samples. (genengnews.com)
  • Another challenge is the need to examine the vast amount of data that is generated by such high-throughput, large-scale technologies. (genengnews.com)
  • The transcriptome data revealed differences in ion channel expression among the eight subtypes. (iasp-pain.org)
  • The number of data points that Curio Seeker 10x10 kit delivers is significantly greater than what was generated with the original Slide-seq technique. (businesswire.com)
  • This generates very large amounts of data that can be analysed using deep learning methods. (l3s.de)
  • BioSkryb's ResolveDNA ® and ResolveOME ™ technologies will be used to facilitate characterization of genome editing on a cell-by-cell basis, to help define genome editing and reporting standards, generate benchmark data, and improve the understanding of on-and off-target effects. (genengnews.com)
  • The FAIRplus project evolved out of the perceived failure of large-scale European projects to make the most use of the data generated. (genomeweb.com)
  • Though the IMI, which has a total budget of €5.3 billion, has supported over 100 projects to date, organizers felt the large amounts of data generated in these projects has not been fully utilized. (genomeweb.com)
  • 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)
  • 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)
  • The transcriptome profiling generated 30,427 unigenes with an average length of 664 base pairs, according to the paper. (genomeweb.com)
  • Many alternatively spliced transcript were present in out transcriptome. (stanford.edu)
  • Various mRNA sequencing library preparation methods generate sequencing reads specifically from the transcript ends. (bioconductor.org)
  • New methods are being developed to compare publicly available tissue transcriptomes to the ones generated from organoids as well as their individual single-cell transcriptomes. (mpg.de)
  • By collecting and comparing transcriptomes of different types of cells, researchers can gain a deeper understanding of what constitutes a specific cell type, how that type of cell normally functions, and how changes in the normal level of gene activity may reflect or contribute to disease. (genome.gov)
  • Affymetrix Mouse Gene 1.0 ST Array profiles were generated from AC samples derived from CBA and STR/Ort mice at 3 different ages, corresponding to the stages prior to, at, and late after the natural onset of OA in the STR/Ort mice. (bepress.com)
  • a shared-registry and research platform infrastructure to generate hypotheses for targeted Investigator-Initiated Studies (IIS). (agendia.com)
  • However, these results exhibited large differences, particularly in the total number of reconstructed transcripts and the quality of the assembled transcriptomes. (biomedcentral.com)
  • To better understand the molecular mechanisms underlying its biology and ecology, we generated a reference transcriptome for H. coerulea using next-generation sequencing. (nature.com)
  • To explore the underlying molecular events that are associated with the progression of PGD, we sampled Atlantic salmon from three different marine production sites in Scotland and examined the gill tissue at three different levels of organization: gross morphology with the use of PGD scores (macroscopic examination), whole transcriptome (gene expression by RNA-seq) and histopathology (microscopic examination). (frontiersin.org)
  • Through global transcriptome profiling, we attempted to discover the molecular signature linked with both OA vulnerability and progression. (bepress.com)
  • PacBio sequencing generates much longer reads compared to second-generation sequencing technologies, with a trade-off of lower throughput, higher error rate and more cost per base. (pacb.com)
  • 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)
  • We assembled the transcriptome of a clonal population of adult, aposymbiotic (dinoflagellate-free) Aiptasia pallida from ~208 million reads, yielding 58,018 contigs. (stanford.edu)
  • Pacific Biosciences (PacBio) has provided open access to the transcriptome of MCF-7, a breast cancer cell line that has provided significant therapeutic advancement in breast cancer research since the 1970s. (pacb.com)
  • The Human Cell Atlas relies, to a great extent, on the use of transcriptome sequencing to profile the gene expression of individual cells. (genengnews.com)
  • A transcriptome is a collection of all the gene readouts present in a cell. (genome.gov)
  • These gene readouts are called transcripts, and a transcriptome is a collection of all the gene readouts present in a cell. (genome.gov)
  • etc.) generated from the same biological source such as a cell type or organ during normal versus diseased states. (bvsalud.org)
  • The Rhab- were generated and then assembled to form contigs. (cdc.gov)
  • To unravel recurrent ASD-related neuropathological mechanisms, we took advantage of the En2 -/- mouse model and performed transcriptome profiling on cerebellar and hippocampal adult tissues. (biomedcentral.com)
  • . pilosum and compared the transcriptomes of plants grown under normal and low temperatures. (biomedcentral.com)
  • 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)
  • Using the SURVEYOR nuclease assay 13 , we assessed the ability of each Cas9-sgRNA complex to generate indels in human embryonic kidney (HEK) 293FT cells through the induction of DNA doublestranded breaks (DSBs) and subsequent nonhomologous end joining (NHEJ) DNA damage repair (Online Methods). (cdc.gov)
  • In summary, our results demonstrate that L1-derived transcripts provide a previously undescribed layer of primate- and human-specific transcriptome complexity that contributes to the functional diversification of the human brain. (lu.se)
  • We generated a set of sgRNAs targeting multiple sites within the human EMX1 and PVALB loci with different tracrRNA 3′ truncations ( Fig. 1a ). (cdc.gov)
  • With GemCode, cells are captured in droplets, and the reverse transcription that occurs within each droplet is used to generate barcoded cDNA. (genengnews.com)
  • Comparison of the leukocyte transcriptomes of these two females to the transcriptome of all other females identified several misregulated transcripts on gestation D55 and D105 with LOC783838 and PCDH1 being misregulated at both time-points. (researchsquare.com)