Transcriptome and genome. Medical search. Frequent questions

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)
The study went further by examining the normal and tumor RNA for whole transcriptome sequencing, which can reveal the possible defects in how proteins are synthesized. (tgen.org)
Here we report a novel approach to characterizing viral AS using whole transcriptome dataset from host species. (nature.com)
Because accomplishing this with RNA-seq comes with such high costs and data complexity, we believe the time is right to focus our expertise on the type of analysi?s tools that interrogate the whole transcriptome with better reproducibility and coverage than the equivalent amount of sequencing. (genomeweb.com)

Then, we will comprehensively characterise pathways that mediate impacts of these genes on both the human macrophage and the intracellular Mtb bacilli using dual transcriptome analyses and high-throughput microscopy assays. (europa.eu)
We conducted comprehensive integrative molecular analyses of the complete set of tumors in The Cancer Genome Atlas (TCGA), consisting of approximately 10,000 specimens and representing 33 types of cancer. (nih.gov)
Based on Pan-Cancer Analysis of Whole Genomes data analyses, NOTCH2 mutations affect expression levels particularly in the presence of CTNNB1 missense mutations. (e-crt.org)
To facilitate mammalian genome engineering applications, we provide a web-based software tool to guide the selection and validation of target sequences as well as off-target analyses. (cdc.gov)

We report here the whole-genome sequences of the human-infective Trichuris trichiura and the mouse laboratory model Trichuris muris . (nature.com)
Here we present high-quality genome sequences for T. trichiura and T. muris , the first duo of a major human STH and its mouse counterpart. (nature.com)
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)
First, we reported the draft genome sequences of the cucumber-sampled C. cassiicola isolate HGCC with high virulence. (biomedcentral.com)
Thus, the N. sylvestris and N. tomentosiformis genome sequences are expected to have high identity to the S-genome and T-genome of N. tabacum , respectively. (biomedcentral.com)
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)
Outside BASE, align the new sequences to genome or transcript sequences and calculate "intensities" for each gene on the "array design" and dump into a tab delimited raw data file. (lu.se)

Canada's Michael Smith Genome Sciences Centre (GSC) at BC Cancer is an international leader in genomics, proteomics and bioinformatics for precision medicine. (bcgsc.ca)

We produced a 75.2-Mb high-quality draft genome assembly from a clinically isolated adult male T. trichiura using Illumina technology. (nature.com)
A draft genome will also allow for a more robust phylogenetic analysis of this species, and perhaps settle its systematic placement, which has changed in recent years. (biomedcentral.com)
Draft genomes of N. sylvestris and N. tomentosiformis were assembled to 82.9% and 71.6% of their expected size respectively, with N50 sizes of about 80 kb. (biomedcentral.com)

Genome annotation resulted in 10,703 putative genes. (biomedcentral.com)
BUSCO analysis of the genome and annotation resulted in 91.1% and 89.5% completeness, respectively. (biomedcentral.com)
The paper describes the genome sequence, gene annotation, and transcriptional profiling of the microalga Nannochloropsis gaditana B-31. (elisacorteggiani.com)
As the sequencing and gene annotation projects of entire genomes of many species are headed towards completion (see, e.g. [13] ), massive mapping efforts in biology are now focused on how the genes interact. (lu.se)

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)

Oncotarget published " Actionability evaluation of biliary tract cancer by genome transcriptome analysis and Asian cancer knowledgebase " which reported that it is necessary to investigate actionable genes and candidate drugs using a sophisticated knowledgebase and characterize BTCs immunologically for evaluating the actionability of molecular and immune therapies. (oncotarget.com)
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)
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)
Here we report the first genome-wide analysis of these two Nicotiana species. (biomedcentral.com)
However, genome-wide transcriptomic analysis using RNA sequencing revealed that ESC-derived tenocytes' transcriptomic profile more closely resembled fetal tenocytes as opposed to adult tenocytes. (cam.ac.uk)
Genome sequencing and transcriptome analysis of Trichoderma reesei QM9978 strain reveals a distal chromosome translocation to be responsible for loss of vib1 expression and loss of cellulase induction. (france-genomique.org)
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)
Sequencing, assembly and comparative analysis of four spruce giga-genomes completed as part of the SpruceUp project, which aims to enhance the genomic knowledge and accelerate spruce breeding programs across the nation. (bcgsc.ca)
Recent advances in nucleic acid sequencing now permit rapid and genome-scale analysis of genetic variation and transcription, enabling population-scale studies of human biology, disease, and diverse organisms. (biorxiv.org)
To validate the genetic interaction with expression level in desmoid-tumor condition, we utilized large-scale whole-genome sequencing and transcriptome datasets from the Pan-Cancer Analysis of Whole Genomes project. (e-crt.org)
Comprehensive genome and transcriptome analysis of T schoenleinii showed candidate pathogenic genes. (medscape.com)
Analysis of the genome and transcriptome of Cryptococcus neoformans var. (bvsalud.org)
Advances in molecular biology and genome analysis now also allow for detailed descriptions of DNA-binding transcription factors and transcriptional regulatory networks. (medscape.com)
Transcriptome analysis revealed that estrogen deprivation leads to a global downregulation in gene expression, and more specifically of a gene involved in DNA demethylation ( TET2 ). (who.int)

A total of 233,542,110 reads of the genome were de novo assembled resulting in 1061 scaffolds, and estimated genome size 27,597,787 bp. (biomedcentral.com)
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)

To advance understanding of its biology and facilitate commercial development, we present a C. zofingiensis chromosome-level nuclear genome, organelle genomes, and transcriptome from diverse growth conditions. (researcher-app.com)
The assembly includes 13,057 protein-coding genes in a 62.5-Mbp nuclear genome. (biomedcentral.com)

Screens of the whole human genome can identify novel genes involved in the immune responses to Mtb infection and susceptibility to TB. (europa.eu)
Here, we will for the first time use the groundbreaking CRISPR technology to screen the human genome in macrophages infected with Mtb and discover genes that are critically involved in host-pathogen interactions. (europa.eu)
The human genome is made up of DNA (deoxyribonucleic acid), a long, winding molecule that contains the instructions needed to build and maintain cells. (genome.gov)

In parallel, multiple technologies and manual finishing were used to produce an 85-Mb reference genome assembly from the more readily available mouse parasite species T. muris (Online Methods and Supplementary Note ). (nature.com)
Our goal in this work is to provide a reference genome for research on this pathogen. (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)

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)
Chromosome scale genome assembly and transcriptome profiling of Nannochloropsis gaditana in nitrogen depletion. (elisacorteggiani.com)
T Cell Transcriptome in Chromosome 22q11.2 Deletion Syndrome. (cdc.gov)

The study, Advanced Never Smoker Adenocarcinoma of the Lung: Report of paired normal and tumor whole genome and transcriptome sequencing, will be presented at the conference today, July 6. (tgen.org)
The study used Whole Genome Sequencing (WGS), also called Next-Generation Sequencing (NGS), to look at all 3 billion chemical bases of the patient's normal, as well as the patient's tumor, DNA. (tgen.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)
Whole genome and transcriptome sequencing of the LLS fungus were obtained. (biomedcentral.com)
The assembly, derived from a combination of short- and long-read sequencing in conjunction with optical mapping, revealed a compact genome of ∼58 Mbp distributed over 19 chromosomes containing 15,274 predicted protein-coding genes. (researcher-app.com)
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)
Second, a global view of the transcriptome of C. cassiicola spores during germination was evaluated using RNA sequencing (RNA-Seq). (biomedcentral.com)
Implementation of Whole-Genome and Transcriptome Sequencing Into Clinical Cancer Care. (ox.ac.uk)
PURPOSE: The combination of whole-genome and transcriptome sequencing (WGTS) is expected to transform diagnosis and treatment for patients with cancer. (ox.ac.uk)
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)
What are whole exome sequencing and whole genome sequencing? (medlineplus.gov)
Harnessing cutting-edge genome sequencing and analytical techniques. (bcgsc.ca)
By developing and deploying cutting-edge genome sequencing, computational and analytical technology, we are creating novel strategies to prevent and diagnose cancers and other diseases, uncovering new therapeutic targets and helping the world realize the social and economic benefits of genome science. (bcgsc.ca)
Through the Personalized OncoGenomics (POG) program , the GSC deploys whole genome and transcriptome sequencing to inform therapeutic and management strategies for late-stage cancer patients in real time. (bcgsc.ca)
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)
Therefore, an antibiotic-sensitive isolate PA30 and a multi-resistant isolate PA49 originating from waste waters were compared via whole genome and transcriptome Illumina sequencing after exposure to municipal waste water and tap water. (kit.edu)
We identified somatic mutations in coding and noncoding regions via whole-genome sequencing. (e-crt.org)
New sequencing technology provides thorough characterization of the genome and transcriptome. (lu.se)
I'm just thinking out loud about how to incorporate high throughput transcriptome sequencing data into BASE. (lu.se)

In this study, the researchers combined a novel in vitro protocol adapted for studying estrogen deprivation and re-stimulation with the latest epigenomics and bioinformatics tools, which enabled a genome-wide interrogation of the epigenome and transcriptome changes. (who.int)

N. sylvestris and N. tomentosiformis are diploid species with an estimated 1C genome size of about 2,650 Mb. (biomedcentral.com)

The genome and preliminary single-nuclei transcriptome of Lemna minuta reveals mechanisms of invasiveness. (jcvi.org)
Co-expression pan-network reveals genes involved in complex traits within maize pan-genome. (usda.gov)

Regarding the clinical annotations of cancer genome variants, several knowledge bases integrating massive amounts of genomic and clinical information data from articles and clinical trials have been developed to identify actionable genes and candidate drugs. (oncotarget.com)

Mass spectrometry-based proteomics now enables genome-scale measurements of proteomes from diverse cells, tissues, and organisms. (biorxiv.org)
With an aim to demonstrate LO effects on the body, we have recently established an animal model investigating the influence of orally administered LO in rat tissues, genome-wide. (elsevierpure.com)

The genome has uniform gene density over chromosomes, low repetitive sequence content (∼6%), and a high fraction of protein-coding sequence (∼39%) with relatively long coding exons and few coding introns. (researcher-app.com)
Although conspecific, HGCC exhibited distinct genome sequence differences from a rubber tree-sampled isolate (CCP) and a human-sampled isolate (UM591). (biomedcentral.com)

Here, we established a pan-genome shared across the following plant pathogens: Burkholderia glumae, Ralstonia solanacearum, and Xanthomonas oryzae pv. (figshare.com)
GPHPD was screened for CDC/ATSDR-authored publications about human genomics, including articles that assessed non-human genomes (e.g., pathogens, vectors). (cdc.gov)

The Streptococcus pyogenes Cas9 (SpCas9) nuclease can be efficiently targeted to genomic loci by means of singleguide RNAs (sgRNAs) to enable genome editing 1 - 10 . (cdc.gov)

The transcriptome assemblies showed that 44,000-53,000 transcripts were expressed in the roots, leaves or flowers. (biomedcentral.com)

Together, these genomes and associated functional data elucidate key aspects of the molecular host-parasite interactions that define chronic whipworm infection. (nature.com)
The availability of these two important whipworm genomes and the integration of parasite and host data presented here will underpin future efforts to control these parasites and exploit their immunological interplay for human benefit. (nature.com)
In this regard, genome-scale metabolic models (GSMMs) have emerged as powerful tools to integrate multiple layers of data to build cancer-specific models and identify putative metabolic vulnerabilities. (kent.ac.uk)
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)
To improve our understanding of these mechanisms, we conducted a weighted single-step genome-wide association study (WssGWAS) and then integrated the results with large-scale transcriptome data for five wool traits and one growth trait in Merino sheep: mean fibre diameter (MFD), coefficient of variation of the fibre diameter (CVFD), crimp number (CN), mean staple length (MSL), greasy fleece weight (GFW), and live weight (LW). (sruc.ac.uk)

The publication also reports the set up of a genome resource available online at www.nannochloropsis.org with multiple tools for information retrieval. (elisacorteggiani.com)

This study represents the first genome-wide association study (GWAS) to identify risk loci for EA/TEF. (lu.se)
We used a European case-control sample comprising 764 EA/TEF patients and 5,778 controls and observed genome-wide significant associations at three loci. (lu.se)

Here, we use genome-scale metabolic modelling to reconstruct a GSMM of the THP1 AML cell line and two derivative cell lines, one with acquired resistance to AraC and the second with acquired resistance to DOX. (kent.ac.uk)

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)
The gene expression inventory of rat blood transcriptome under LO, a first report, has been deposited into the Gene Expression Omnibus (GEO): GSE67499. (elsevierpure.com)

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)
The reference genomes of N. sylvestris and N. tomentosiformis represent a significant contribution to the SOL100 initiative because, as members of the Nicotiana genus of Solanaceae, they strengthen the value of the already existing resources by providing additional comparative information, thereby helping to improve our understanding of plant metabolism and evolution. (biomedcentral.com)

Using mutagenesis, we uncovered a relationship between bacterial virulence and functions highly conserved and shared in the studied genomes of the bacterial phytopathogens, including flagellar biosynthesis protein, C4-dicarboxylate ABC transporter, 2-methylisocitrate lyase, and protocatechuate 3,4-dioxygenase (PCD). (figshare.com)

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)

Genome-based transcriptome assembly is performed when working with a model system with well-annotated genome and transcriptome, such as human, mouse, Drosophila melanogaster or Caenorhabditis elegans. (deepseeq.com)

The L. minuta genome and preliminary cell map provide a paradigm to decipher developmental genes and pathways for an entire plant. (jcvi.org)

These gene readouts are called transcripts, and a transcriptome is a collection of all the gene readouts present in a cell. (genome.gov)

We next carried out an esophageal/tracheal transcriptome profiling in rat embryos at four selected embryonic time points. (lu.se)

The authors discuss using transcriptome profiles for comprehensive referencing as an alternative to costly genome referencing. (sagescience.com)
Comprehensive transcriptome information will provide a useful resource for gene discovery and facilitate a deeper understanding of the diversity of the regulatory systems that have evolved in C. virgata while adapting to severe environmental conditions. (frontiersin.org)
In addition, transcriptomes may enable researchers to generate a comprehensive, genome-wide picture of what genes are active in which cells. (genome.gov)

The high-quality genome and transcriptome provide insight into the green algal lineage and carotenoid production. (researcher-app.com)

By characterizing the transcriptome patterns and pathways for these symptoms, our goal is to shed light on the biological mechanisms underlying this comorbidity, which can help prevent the exacerbation of physical symptoms by intervening at the level of etiological pathway. (cdc.gov)

Previously, we successfully used genome-wide association studies to identify human genes associated with susceptibility to TB. (europa.eu)

Anatomy17

Organisms29

Diseases3

Chemicals and Drugs40

Analytical, Diagnostic and Therapeutic Techniques and Equipment30

Phenomena and Processes142

Disciplines and Occupations5

Technology, Industry, Agriculture5

Information Science14

Health Care3

Whole-transcriptome4

Analyses4

Sequences7

Canada's Michael Smith Genome Sciences Centre1

Draft3

Annotation4

Proteome1

Analysis14

Novo2

Nuclear genome2

Human genome3

Reference genome3

Chromosome3

Sequencing19

Deprivation1

Species1

Reveals2

Variants1

Tissues2

Sequence2

Pathogens2

RNAs1

Assemblies1

Data5

Nannochloropsis1

Loci2

Metabolic1

Gene expression2

Evolution2

Protein1

Genes involved1

Assembly1

Developmental1

Transcripts1

Embryonic1

Comprehensive3

Provide1

Patterns1

Identify1