*  Evolutionary insights from de novo transcriptome assembly and SNP discovery in California white oaks | BMC Genomics | Full Text
Further indications of transcriptome quality and purity appear below.. Repeats and transposons. Only 4.4 % of the transcriptome ... Additional file 1: Transcriptome size and coverage per contig. (a) Total transcriptome size in base pairs (red) and number of ... Our transcriptome assembly is of high quality and purity. First, almost all 100-mers in almost all transcriptome contigs are ... We used our transcriptome-wide SNPs to estimate the ratio of nonsynonymous to synonymous substitution rates (d N/d S) as ...
  https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-015-1761-4
*  TransRate: reference-free quality assessment of de novo transcriptome assemblies. - Oxford Neuroscience
Using only the sequenced reads and the assembly as input, we show that multiple common artifacts of de novo transcriptome ... Applying the method to a data set of 155 published de novo transcriptome assemblies, we deconstruct the contribution that ... of the variance in the quality of published de novo transcriptome assemblies. Because TransRate is reference-free, it is ... assembly method, read length, read quantity, and read quality make to the accuracy of de novo transcriptome assemblies and ...
  https://www.neuroscience.ox.ac.uk/publications/628076
*  EMBL Course - Whole Transcriptome Data Analysis
The course participants will use open-source software. R-coding skills and deep knowledge of statistics are not necessary for attendance because most analyses will be performed with docker4seq package, which was developed to facilitate the use of computing demanding applications in the field of NGS data analysis. Docker4seq package uses docker containers that embed demanding computing tasks (e.g. short reads mapping) into isolated containers. This approach provides multiple advantages ...
  https://www.embl.de/training/events/2017/DAT17-02/introduction/index.html
*  CoRegNet: Reconstruction and integrated analysis of Co-Regulatory Networks
object and a matrix of gene expression, whether it is the data used for the inference or another one (cell lines transcriptomes ... This new dataset of transcriptional influence can be used as a condensed view of the whole transcriptome dataset. Data mining ... transcriptome, epigenetic marks, binding sites, …) to learn a global network. Briefly, for each dataset, the method assigns one ...
  http://www.bioconductor.org/packages/release/bioc/vignettes/CoRegNet/inst/doc/CoRegNet.html
*  Hypoxia Modifies the Transcriptome of Primary Human Monocytes: Modulation of Novel Immune-Related Genes and Identification Of...
The hypoxic transcriptome was also characterized by the modulation of a cluster of genes coding for cytokines/chemokines and/or ... Hypoxia Modifies the Transcriptome of Primary Human Monocytes: Modulation of Novel Immune-Related Genes and Identification Of ... The hypoxic transcriptome was characterized by the modulation of a significant cluster of genes with immunological relevance. ... Hypoxia Modifies the Transcriptome of Primary Human Monocytes: Modulation of Novel Immune-Related Genes and Identification Of ...
  http://www.jimmunol.org/content/177/3/1941?ijkey=af87c72f3cb6191afe34bc3f179a2354ed4dae8b&keytype2=tf_ipsecsha
*  Comparison of Muscle Transcriptome between Pigs with Divergent Meat Quality Phenotypes Identifies Genes Related to Muscle...
Comparison of Muscle Transcriptome between Pigs with Divergent Meat Quality Phenotypes Identifies Genes Related to Muscle ... Therefore, a muscle transcriptome analysis was undertaken to compare gene expression profiles between two highly contrasted pig ... Comparison of Muscle Transcriptome between Pigs with Divergent Meat Quality Phenotypes Identifies Genes Related to Muscle ... Comparison of Muscle Transcriptome between Pigs with Divergent Meat Quality Phenotypes Identifies Genes Related to Muscle ...
  http://libros.duhnnae.com/2017/jun7/14981228680-Comparison-of-Muscle-Transcriptome-between-Pigs-with-Divergent-Meat-Quality-Phenotypes-Identifies-Genes-Related-to-Muscle-Metabolism-and-Structure.php
*  Transcriptome Sequencing (RNA-Seq) | SpringerLink
Transcriptome sequencing (RNA-Seq) is a recently developed... ... The transcriptome is the entire assembly of RNA transcripts in ... Transcriptome sequencing to detect gene fusions in cancer. Nature. 2009;458(7234):97-101.PubMedPubMedCentralGoogle Scholar ... Studying bacterial transcriptomes using RNA-seq. Curr Opin Microbiol. 2010;13(5):619-24.PubMedPubMedCentralGoogle Scholar ... Chromosomal instability and transcriptome dynamics in cancer. Cancer Metastasis Rev. 2013;32(3-4):391-402.PubMedGoogle Scholar ...
  https://link.springer.com/chapter/10.1007/978-1-4939-0727-4_3
*  Transcriptome-wide profiling and expression ana...
Transcriptome analysis shows similarity of expression patterns for all plants exposed to nanoparticles and a low impact on gene ... De novo Transcriptome Sequencing and Development of Abscission Zone-Specific Microarray as a New Molecular Tool for Analysis of ... We performed whole transcriptome analyses of chickpea genotypes to investigate the molecular basis of drought and salinity ... In the grapevine transcriptome, during the initial stages of leaf development 1Avs2A showed single transcript was down- ...
  https://www.scoop.it/t/plant-genomics/p/4013279010/2013/12/26/transcriptome-wide-profiling-and-expression-analysis-of-transcription-factor-families-in-a-liverwort-marchantia-polymorpha
*  Glycome and Transcriptome Regulation of Vasculogenesis | Circulation
Glycome and Transcriptome Regulation of Vasculogenesis. Rania Harfouche, Dirk M. Hentschel, Stephanie Piecewicz, Sudipta Basu, ... Glycome and Transcriptome Regulation of Vasculogenesis. Rania Harfouche, Dirk M. Hentschel, Stephanie Piecewicz, Sudipta Basu, ... Glycome and Transcriptome Regulation of Vasculogenesis. Rania Harfouche, Dirk M. Hentschel, Stephanie Piecewicz, Sudipta Basu, ... Endothelial cells preparing to die by apoptosis initiate a program of transcriptome and glycome regulation. FASEB J. 2004; 18: ...
  http://circ.ahajournals.org/content/120/19/1883
*  Brain Transcriptome | 9780128011058 | VitalSource
Buy or Rent Brain Transcriptome as an eTextbook and get instant access. With VitalSource, you can save up to 80% compared to ... Brain Transcriptome Edition by Hitzemann, Robert and Publisher Academic Press. Save up to 80% by choosing the eTextbook option ...
  https://www.vitalsource.com/products/brain-transcriptome-hitzemann-robert-v9780128011058
*  Gene Expression & Transcriptome Analysis & Profiling Solutions
... solutions for high-quality gene expression and transcriptome analysis and profiling studies. ... Whole-Transcriptome Analysis with Sequencing. Capture the broad effects of gene expression changes using whole-transcriptome ... Comprehensive Transcriptome and Gene Expression Analysis. Transcriptome analysis experiments can characterize transcriptional ... AmpliSeq for Illumina Transcriptome Human Gene Expression Panel. Targeted research panel that measures expression levels of , ...
  https://www.illumina.com/techniques/popular-applications/gene-expression-transcriptome-analysis.html
*  Transcriptome Microarray Technology and Methods of Using the Same - Nucleotide - NCBI
Transcriptome Microarray Technology and Methods of Using the Same Transcriptome Microarray Technology and Methods of Using the ...
  https://www.ncbi.nlm.nih.gov/nucleotide/285372414
*  A Transcriptome Post-Scaffolding Method for Assembling High Quality Contigs
In this work, we developed transcriptome post-scaffolding (TransPS) to scaffold preassembled transcriptome from any desired ... nonredundant de novo transcriptomes. TransPS shows promising results on the test transcriptome datasets, where redundancy is ... A Transcriptome Post-Scaffolding Method for Assembling High Quality Contigs. Mingming Liu,1 Zach N. Adelman,2 Kevin M. Myles,2 ... Widely used transcriptome assembly tools include Cufflinks [2] for reference based assembly and Trinity [3] and Oases [4] for ...
  https://www.hindawi.com/journals/cbj/2014/961823/
*  Transcriptome Profiling Using Single-Molecule Direct RNA Sequencing | SpringerLink
RNA sequencing Single-molecule sequencing Transcriptome profiling Polyadenylation site mapping Springer Nature is developing a ... Ozsolak F., Milos P.M. (2011) Transcriptome Profiling Using Single-Molecule Direct RNA Sequencing. In: Kwon Y., Ricke S. (eds) ... Mortazavi, A., Williams, B. A., McCue, K., Schaeffer, L., and Wold, B. (2008) Mapping and quantifying mammalian transcriptomes ... Methods for in-depth characterization of transcriptomes and quantification of transcript levels have emerged as valuable tools ...
  https://link.springer.com/protocol/10.1007%2F978-1-61779-089-8_4
*  Arabidopsis Transcriptome Genomic Express Database
Arabidopsis Transcriptome Functional Genomics Database. gebd Arabidopsis Genome Browser. iSect Tools, iView Tools and Gene ... Reference to cite for transcriptome tiling array data and SSP ORF clones. [Transcriptome] Kayoko Yamada, Jun Lim, Joseph M. ... Genome-Wide High-Resolution Mapping of Exosome Substrates Reveals Hidden Features in the Arabidopsis Transcriptome Cell, Vol ...
  http://signal.salk.edu/cgi-bin/atta?GENE=At1g01110
*  AtTOME: Arabidopsis Transcriptome iSect Tools
AtTOME: Arabidopsis (indica) Functional Genomics Database. Arabidopsis Genome Express Browser. iSect Tools, iView Tools and Gene Expression Atlas, gAtlas Tool. Collection of Arabidopsis T-DNA/Ds, Arabidopsis cDNA, EST, MPSS, SAGE, miRNA, sRNA, Arabidopsis Tiling Array and Gene Expression Data. Created and developed by Huaming Chen
  http://signal.salk.edu/cgi-bin/atta?JOB=APPENDIX&QUERY=GeneAtlas
*  Improved chemistry for single-cell transcriptome analysis
... SMART-Seq v4 Ultra Low Input RNA Kit for the Fluidigm C1 System. * ... In single-cell transcriptome studies, it is critical to obtain high-quality cDNA libraries from individual cells that represent ... To achieve this, we improved upon our existing commercially available mRNA-seq chemistry for single-cell transcriptome studies ...
  http://www.clontech.com/US/Products/cDNA_Synthesis_and_Library_Construction/NGS_Learning_Resources/Technical_Notes/SMART-Seq-v4-for-Fluidigm-C1?sitex=10020:22372:US&PEBCL1=xscoExaBPkBv1Zr7Q9xdeAdRhZ&PEBCL1_pses=ZGC9D8BB32885D3E4FE05DB25013F37FCC330B0BCFA61FCF564B3E0B73ABB914023D0109EFB46C062EAFAEAF972FF729CFA0D9B482A5D0C560
*  Transcriptome - Wikipedia
Transcriptomes may also be used to infer phylogenetic relationships among individuals. The transcriptome can be seen as a ... The transcriptome is the set of all RNA molecules in one cell or a population of cells. It is sometimes used to refer to all ... Analysis of the transcriptomes of human oocytes and embryos is used to understand the molecular mechanisms and signaling ... RNA-seq is emerging (2013) as the method of choice for measuring transcriptomes of organisms, though the older technique of DNA ...
  https://en.wikipedia.org/wiki/Transcriptome
*  Transcriptome instability - Wikipedia
... a phenomenon referred to as transcriptome instability. Transcriptome instability correlates significantly with reduced ... Transcriptome instability is a genome-wide, pre-mRNA splicing-related characteristic of certain cancers. In general, pre-mRNA ... "A Global View of Cancer-Specific Transcript Variants by Subtractive Transcriptome-Wide Analysis". PLoS ONE. 4 (3): e4732. doi: ... Sveen, A; Ågesen, TH; Nesbakken, A; Rognum, TO; Lothe, RA; Skotheim, RI (2011). "Transcriptome instability in colorectal cancer ...
  https://en.wikipedia.org/wiki/Transcriptome_instability
*  Digital transcriptome subtraction - Wikipedia
Digital transcriptome subtraction (DTS) is a bioinformatics method to detect the presence of novel pathogen transcripts through ... Feng H, Taylor JL, Benos PV, Newton R, Waddell K, Lucas SB, Chang Y, Moore PS (August 2007). "Human Transcriptome Subtraction ... Must have a highly reliable, complete reference transcriptome for the organism being studied. Lack of foreign sequence ... "New Pathogen Discovery: Digital Transcriptome Subtraction". Retrieved 1 March 2012. Cox-Foster DL, Conlan S, Holmes EC, ...
  https://en.wikipedia.org/wiki/Digital_transcriptome_subtraction
*  De novo transcriptome assembly - Wikipedia
De novo transcriptome assembly is the de novo sequence assembly method of creating a transcriptome without the aid of a ... 2011). "Reptilian transcriptome v1.0, a glimpse in the brain transcriptome of five divergent Sauropsida lineages and the ... Transcriptome Transcriptomics Human-transcriptome database for alternative splicing (H-DBAS) UniGene Full-parasites Exome ... SeqMan NGen, part of DNASTAR's software pipeline, includes a de novo transcriptome assembler for small or large transcriptome ...
  https://en.wikipedia.org/wiki/De_novo_transcriptome_assembly
*  Transcriptome in vivo analysis tag - Wikipedia
The transcriptome is a set of all RNA, including rRNA, mRNA, tRNA, and non-coding RNA. Specifically mRNA transcripts can be ... A transcriptome in vivo analysis tag (TIVA tag) is a multifunctional, photoactivatable mRNA-capture molecule designed for ... February 2014). "Transcriptome in vivo analysis (TIVA) of spatially defined single cells in live tissue". Nat. Methods. 11 (2 ... Transcriptome profiling is determining the composition of transcripts and their relative expression levels in a given reference ...
  https://en.wikipedia.org/wiki/Transcriptome_in_vivo_analysis_tag