• 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)
  • Here, we combine spatial transcriptomics and scRNA-Seq datasets to define the transcriptome of tumor-proximal and tumor-distal cancer-associated fibroblasts (CAFs) and link this to clinical outcome. (elifesciences.org)
  • ResolveOME generates single-cell multiomics datasets by combining whole genome or exome analysis with whole transcriptome analysis within each individual cell. (genengnews.com)
  • The algorithm is designed for FPKM and RPKM normalized RNA-Seq transcriptome datasets. (bioconductor.org)
  • RNA-Seq cancer transcriptome and clinical datasets must be prepared before applying them in SVMDO. (bioconductor.org)
  • The expected designs of input datasets are indicated in Table-1 and Table-2 for transcriptome and clinical datasets respectively. (bioconductor.org)
  • To provide experience about the GUI usage, a test section involving dummy example using SummarizedExperiment objects of transcriptome (small form) and clinical datasets is also included. (bioconductor.org)
  • Among the five representative assemblers, the Bridger package shows the best performance in both assembly completeness and accuracy as evaluated by the BUSCO datasets and genome alignment. (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)
  • Free yourself to discover more with a complete view of genomes, epigenomes, and transcriptomes on the Revio system. (dksh.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)
  • The Personalized OncoGenomics (POG) program at BC Cancer performs whole genome and transcriptome analysis (WGTA) to identify specific alterations in an individual's cancer tha. (researchgate.net)
  • In this study, we evaluate the impact of whole genome and transcriptome analysis (WGTA) on predictive molecular profiling and histologic diagnosis in a cohort of advanced malignancies. (researchgate.net)
  • Whole-genome and transcriptome (WGS and RNA-seq, respectively) sequencing can discover novel clinically relevant fusions. (researchgate.net)
  • 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)
  • QIAseq UPX 3' Transcriptome Kits enable high-throughput gene expression analysis from cell lysates and isolated total RNA. (qiagen.com)
  • The availability of next-generation sequencing technology has circumvented this barrier for non-model organisms by enabling transcriptome assembly from high-throughput RNA sequencing (RNA-seq) data [ 9 , 10 ]. (biomedcentral.com)
  • With the increasing application of high-throughput sequencing, transcriptome analysis has become an effective method for identifying novel stable reference genes. (biomedcentral.com)
  • With the increasing application of high-throughput sequencing, RNA-seq has provided a new strategy for identifying new highly stable reference genes from transcriptome data. (biomedcentral.com)
  • The Long-read Sequencing - Revio System adds affordability, high throughput, and ease of use to a foundation of long reads, exceptional accuracy, and direct methylation detection. (dksh.com)
  • MUSCLE: multiple sequence alignment with high accuracy and high throughput. (cdc.gov)
  • 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)
  • Analyze 3' RNA-seq data with ease using the GeneGlobe-integrated RNA-seq Analysis Portal - an intuitive, web-based data analysis solution created for biologists and included with QIAseq UPX 3' Transcriptome Kits. (qiagen.com)
  • Transcriptome analysis is beneficial for obtaining information about all RNAs present and can provide valuable insight into the genetic mechanisms that are tissue specific. (wikipedia.org)
  • Transcriptome analysis has proven to be beneficial in identifying disease processes as well as regulatory elements in disease progressions, has aided drug development through identification of disease processes, offers insight into therapeutic strategies, and has improved identification of genes that are able to respond to both biotic and abiotic environmental factors as well as how environmental conditions play a role in gene expression. (wikipedia.org)
  • Gene expression signature of human neuropathic pain identified through transcriptome analysis. (iasp-pain.org)
  • This study aimed to identify genes associated with neuropathic pain through transcriptome analysis in order to gain a better understanding of the mechanisms underlying this chronic, difficult-to-treat pain. (iasp-pain.org)
  • We conducted transcriptome analysis using a training datasetof 202 individuals, including patients with neuropathic pain and healthy controls. (iasp-pain.org)
  • Receiver operating characteristic (ROC) curve analysis demonstrated that this signature had a high level of accuracy in differentiating between neuropathic pain patients and healthy controls, with an area under the curve (AUC) of 0.83 (95% CI 0.65-1). (iasp-pain.org)
  • Our work constitutes the first application of the newly published diploid D5 Gossypium raimondii sequence in the study of tetraploid AD1 upland cotton RNA-seq transcriptome analysis. (usda.gov)
  • 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)
  • If there is not any requirement for survival analysis , preparation of clinical dataset and involvement of id column in the transcriptome dataset are optional. (bioconductor.org)
  • Therefore, a well-assembled, accurate, and comprehensive transcriptome is a prerequisite for the subsequent analysis. (biomedcentral.com)
  • AtRTD3 is a major improvement over existing transcriptomes as demonstrated by analysis of an Arabidopsis cold response RNA-seq time-series. (dundee.ac.uk)
  • Total RNA extracted from second- (MZ-2) and third-generation merozoites (MZ-3) of Eimeria necatrix was subjected to transcriptome analysis using RNA sequencing (RNA-seq) followed by qRT-PCR validation. (biomedcentral.com)
  • Using Transcriptome Analysis to Explore Gray Mold Resistance-Related Genes in Onion (Allium cepa L. (celemics.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)
  • The combination of transcriptome data acquisition methods requires cross-platform transcriptome data analysis platforms, including a new software package for data processing. (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)
  • In this paper, we will focus on a software package providing the enabling tools for cross-platform transcriptome analysis. (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)
  • Eight reference based and 12 de novo assembled transcriptomes were produced, for juvenile shoot tissue from both species. (biomedcentral.com)
  • With the exception of completely de novo mass spectrometry identification algorithms which currently lack the requisite accuracy and efficiency for genome-scale studies, all current methods depend on matching observed mass spectra to reference proteome databases. (biorxiv.org)
  • 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)
  • To increase the predictive accuracy, the research team introduced machine learning algorithms that use protein interaction network that can interact with target proteins as well as the transcriptome of individual proteins that are directly related with drug targets. (postech.ac.kr)
  • First, the candidate will evaluate and compare the predictive capacity of transcriptome and single cell images for a task of cell classification into subpopulations. (dim-elicit.fr)
  • Moreover, results from bulk transcriptome sequencing (RNA-seq) and SCT experiments revealed distinct transcriptomic signatures representing cell injury and stress in primary RPTE in contrast to the uncultured, freshly dissociated PT from human kidney. (simonsfoundation.org)
  • 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)
  • 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)
  • Advances in transcriptome sequencing allow for simultaneous interrogation of differentially expressed genes from multiple species originating from a single RNA sample, termed dual or multi-species transcriptomics. (biomedcentral.com)
  • Avidity sequencing achieves high accuracy, with 96.2% and 85.4% of base calls having an average of one error per 1,000 and 10,000 base pairs, respectively. (rna-seqblog.com)
  • However, accuracy is significantly affected by sequencing errors, mRNA degradation, or incomplete cDNA synthesis. (dundee.ac.uk)
  • Ion AmpliSeq transcriptome sequencing yielded expression values for 12,635 genes. (ons.org)
  • CPTRA is a powerful software package for next generation sequencing-based transcriptome profiling in species with limited genome information. (biomedcentral.com)
  • Benchmarking the empirical accuracy of short-read sequencing across the M. tuberculosis genome. (cdc.gov)
  • Shotgun transcriptome sequencing was performed as described ( 1 , 2 ). (cdc.gov)
  • Predicted protein sequences encoded by the assembled transcriptomes were clustered with reference proteomes from 92 other species to identify pathogenesis related gene families in P. patula, P. tecunumanii and other pine species. (biomedcentral.com)
  • The P. tecunumanii transcriptome is the first gene catalogue for the species, representing an important resource for studying resistance to the pitch canker pathogen, F. circinatum . (biomedcentral.com)
  • Direct calculation of delivered dose in the species of interest potentially affects the magnitude of an uncertainty factor needed to address extrapolation of laboratory animal data to equivalent human exposure scenarios, thereby improving the accuracy of human health risk estimates. (cdc.gov)
  • Genetic testing during treatment can improve accuracy of response and outcome prediction compared to other prognostic tests, according to results from a study assessing on-treatment changes in gene expression in patients receiving chemotherapy. (ons.org)
  • Transcriptomes are now able to be routinely developed due to advances in these methods and new technologies such as microarrays and RNA-Seq. (wikipedia.org)
  • To address this, researchers have developed methods to interrogate the transcriptome of multiple organisms from a single sample. (biomedcentral.com)
  • C ross- P latform TR anscriptome A nalysis, to analyze transcriptome profiling data from separate methods. (biomedcentral.com)
  • Latest basecalling algorithms from Oxford Nanopore's Research & Development teams show consistent improvement to raw, consensus and variant calling accuracies, with latest tools and methods reaching modal raw read accuracy of over 97% (and further improvements being actively worked on). (nanoporetech.com)
  • Partitioning RNAs by length improves transcriptome reconstruction from short-read RNA-seq data. (cdc.gov)
  • Entering high-quality learning data that can reflect a person's drug response as much as possible is the starting point for improving the accuracy of the prediction. (postech.ac.kr)
  • In light of this, a research team led by Professor Sanguk Kim in the Department of Life Sciences at POSTECH is drawing attention by successfully increasing the accuracy of anti-cancer drug response predictions by using data closest to a real person's response. (postech.ac.kr)
  • In this study, we identified candidate reference genes based on transcriptome data covering embryos and larvae of early development, normal adult tissues, and the hindgut under sulfide stress using the coefficient of variation (CV) method in the echiuran Urechis unicinctus , resulting in 6834 (15.82%), 7110 (16.85%) and 13880 (35.87%) candidate reference genes, respectively. (biomedcentral.com)
  • The log 2 (TPM) of the transcriptome data was significantly negatively correlated with the Ct values of RT-qPCR (Ct = − 0.5405 log 2 (TPM) + 34.51), which made it possible to estimate the Ct value before RT-qPCR using transcriptome data. (biomedcentral.com)
  • Our study is the first to select reference genes for RT-qPCR from transcriptome data in Echiura and provides important information for future gene expression studies in U. unicinctus . (biomedcentral.com)
  • The transcriptome profiling data and hallmark gene sets in the Molecular Signatures Database was used to explore the cancer hallmarks most relevant to the prognosis of HNSCC patients. (biomedcentral.com)
  • By simultaneously modeling signal variation across cells and conditions in both omics data types, MAGICAL achieved high accuracy on circuit inference. (simonsfoundation.org)
  • For each individual cell, the relationship between the two types of available data (image and transcriptome) will be studied along three axes. (dim-elicit.fr)
  • Finally, he will develop a deep-learning approach to evaluate with what accuracy it is possible to predict the visual phenotype of a cell from transcriptomic data and vice versa. (dim-elicit.fr)
  • The research team discovered new network-based biomarkers by analyzing the clinical results of more than 700 patients with three different cancers (melanoma, gastric cancer , and bladder cancer) and the transcriptome data of the patients' cancer tissues. (medicalxpress.com)
  • A transcriptome is the sum of all RNA transcripts that are present in a given cell, tissue, or organ within an organism. (wikipedia.org)
  • A total of 1,530 transcripts were differentially expressed between well-watered and water-deficit stressed root tissues, in patterns confirming the accuracy of this technique for future studies in cotton genomics. (usda.gov)
  • However, these results exhibited large differences, particularly in the total number of reconstructed transcripts and the quality of the assembled transcriptomes. (biomedcentral.com)
  • The transcriptome assemblies showed that 44,000-53,000 transcripts were expressed in the roots, leaves or flowers. (biomedcentral.com)
  • Transcriptome-wide association study (TWAS) is a genetic methodology that can be used to compare the genetic components of gene expression and the genetic components of a trait to determine if an association is present between the two components. (wikipedia.org)
  • 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)
  • 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)
  • EvidentialGene pipeline redundancy reduction, expression filtering, protein clustering and taxonomic filtering produced a 50 Mb shoot transcriptome consisting of 28,621 contigs for P. tecunumanii and a 72 Mb shoot transcriptome consisting of 52,735 contigs for P. patula . (biomedcentral.com)
  • It induces learning the transcriptome production of a protein that is functionally close to the target protein. (postech.ac.kr)
  • However, the current predictions were based on genetic information of cancer cells, limiting their accuracy. (postech.ac.kr)
  • This is why the genetic characteristics and transcriptome information of cancer cells are analyzed in order to predict the efficacy of anti-cancer drugs. (postech.ac.kr)
  • We performed a first-of-kind evaluation of two transcriptome-based precision cancer medicine methodologies to predict tumor sensitivity to a comprehensive repertoire of clinically relevant oncology drugs, whose mechanism of action we experimentally assessed in cognate cell lines. (cdc.gov)
  • Researchers identified AAGAB as an on-treatment marker of response, which was associated with a testing accuracy of 100% and a validation accuracy of 78% in the I-SPY 1 trial-a series of trials assessing neoadjuvant treatment of locally advanced breast cancer. (ons.org)
  • Subsequently we validated the accuracy of the trained algorithms in a preclinical rodent model of Parkinson's disease and demonstrated the robustness of the algorithms on tissue obtained from mice, as well as from images provided by three collaborating laboratories. (lu.se)
  • 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)
  • QIAseq UPX 3' Transcriptome Kits are intended for molecular biology applications. (qiagen.com)
  • The QIAseq UPX 3' Transcriptome Kit presents a unique advantage where each cell is tagged with a unique ID (up to 384 different IDs) and each RNA molecule is tagged with a Unique Molecular Index (UMI) during reverse transcription. (qiagen.com)
  • In their investigation, Halloran and his colleagues found that molecular readings correlated with heart function, improved accuracy, and improved prediction of future failure. (medscape.com)
  • Because increased diagnostic accuracy can eliminate confusion between transplant rejection and organ injury, treatment can be more precise and the administration of unnecessary immunosuppression drugs can be prevented, he said. (medscape.com)
  • Subjects underwent personalized omics profiling quarterly for up to 8 years using traditional clinical measures and emerging biomarkers including genome, immunome, transcriptome, proteome, metabolome, microbiome and wearable monitoring. (cdc.gov)
  • 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)
  • Selecting suitable reference genes is extremely important for the accuracy of RT-qPCR results. (biomedcentral.com)
  • Therefore, two or more reference genes are desirable to improve the reliability and accuracy of the RT-qPCR results. (biomedcentral.com)
  • With Celemics' proprietary technologies for assay development and optimization, we offer complete and robust NGS solutions for transcriptome, fusion, and isoform analyses for various sample types and conditions. (celemics.com)
  • The team developed this machine learning technique through algorithms that learn the transcriptome *2 information from artificial organoids derived from actual patients instead of animal models. (postech.ac.kr)
  • The authors demonstrate the effectiveness of the method to reverse several age-related changes including remodeling of the transcriptome. (elifesciences.org)
  • Ensemble methodology in constructing a feature selection method has been mainly preferred for its better accuracy in classification processes [2]. (bioconductor.org)
  • Measurement of the transcriptomes of single cells has been feasible for only a few years, but it has become an extremely popular assay. (nature.com)
  • Under these circumstances, the research team led by Professor Sanguk Kim (Department of Life Sciences) at POSTECH is gaining attention as they have improved the accuracy of predicting patient response to immune checkpoint inhibitors (ICIs) by using network-based machine learning. (medicalxpress.com)