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Showing 1 to 20 of 188 for “"Transcriptomes"”.
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Normal cell signals in human cancer transcriptomes
… reference to neuroblastoma single-cell and bulk transcriptomes in chapter 3. This comparison reveals sympathoblasts as the normal correlate of neuroblastoma cancer cells, and allows identification of transcripts present in both neuroblastoma and fetal adrenal medulla, but not adult tissues, …
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NANOPORE SEQUENCING AS A NEW TOOL TO EXPLORE COMPLEX TRANSCRIPTOMES
Long-read sequencing marked a revolution in the field of transcriptomics by helping to resolve isoform structure, unannotated splicing variants, complex loci and repetitive regions and proposing as a method for RNA modifications detection. This versatility permits its application to different …
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In Situ Perturb-Seq of Transcriptomes and RNA Neural Recordings
In this work, we explore the intersection of in situ sequencing, neural recording, and CRISPR screens. An intracellular technology is outlined for encoding neural activity in the form of RNA, theoretically enabling single-cell resolution recording of whole-brain activity. This neural recording …
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Molecular Analysis of Breast Cancer Transcriptomes, Genomes, and Circulating Tumor DNA
Breast cancer is a very heterogeneous disease in terms of clinical characteristics, genetic aberrations and prognosis. In Paper I, we focused on the CD44 molecule that often is aberrantly expressed in breast cancer and is widely used as a marker for cancer stem cells. Several isoforms of the CD44 …
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The Contribution of Retrotransposons to the Transcriptomes of Murine Somatic Cells
… of retrotransposons and retrocopies to the transcriptomes of adult mouse somatic cells, using purified naive B and T lymphocytes. First, I describe the transcriptomes generated using high-quality total RNA-seq data. Second, I quantify and characterise the retrotransposon content of these …
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Comparative Analysis of Alternative Splicing in Homo sapiens, Mus musculus and Rattus norvegicus Transcriptomes
<p>Analyzing transcriptomes in the context of all available genome and transcript sequence data has the potential to reveal biologically meaningful insight into functional properties of genes and complexity of genomes. Alternative splicing is one of the major mechanisms contributing to the …
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The effect of overfeeding and obesity on canine adipose tissue and skeletal muscle transcriptomes
Overweight dogs have a reduced life expectancy and increased risk of chronic disease. During obesity development, adipose tissue undergoes major expansion and remodeling, but the biological processes involved are not well understood. The objective of study 1 was to analyze global gene expression …
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Conservation and synteny of long non-coding RNAs invertebrate genomes and their identification in novel transcriptomes
… which can effectively identify IncRNAs in entire transcriptomes. The pipeline is able to accurately annotate the coding genes while predicting a conservative estimate of the IncRNA population. It allowed me to show, for the first time, the presence of lncRNA transcription in a diverse range of …
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A Comparative Study of Medicago truncatula Transcriptomes as They Relate to Saponin Defenses Against Insect Pests
<p>Triterpene saponins are a class of defensive plant-derived compounds, which have a</p> <p>variety of functions including antimicrobial, insecticidal, and nematicidal activities. This</p> <p>research assessed the performance of the beet armyworm, Spodoptera exigua, following ad</p> <p>libero …
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Exploration of the transcriptomes and functional contributions of Listeria monocytogenes plasmids during food production-associated stress conditions
Listeria monocytogenes is the causative agent of the foodborne disease listeriosis, which is often fatal in susceptible individuals. The persistence of L. monocytogenes in the food production environment (FPE), defined as the repeated isolation of the same strain over several months, leads to the …
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Comparing Differentiated Rod And Cone Transcriptomes Reveals Rax As A Controller Of A Defined Cone Gene Regulatory Program
… on sorted populations, rods and cone specific transcriptomes by RNA sequencing (RNA- seq) using Illumina Hiseq 1500 (n=3). Moreover, after overexpression of human Retina And Anterior Neural Fold Homeobox (RAX), using subretinal injection of AAV2/8 hGNAT1-hRAX2aeGFP at a dose of 5 x …
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Statistical Analysis of Gene Expression Profile: Transcription Network Inference and Sample Classification
The copious information generated from transcriptomes gives us an opportunity to learn biological processes as integrated systems; however, due to numerous sources of variation, high dimensions of data structure, various levels of data quality, and different formats of the inputs, dissecting and …
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Comprehensive single-cell transcriptional profiling of the regenerative planarian Schmidtea mediterranea
… RNA sequencing have made it possible to generate transcriptomes easily and affordably for tens of thousands of single cells, raising the possibility that transcriptomes could be generated for all cell types and cell states in a complete animal. Planarians are freshwater flatworms renowned for …
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Algorithms And Tools For Computational Analysis Of Human Transcriptome Using Rna-Seq
… to better characterize and understand transcriptomes, in particular useful for the detection of splicing variants between healthy and diseased human transcriptomes.</p> <p> We have developed two novel algorithms and tools and a computational workflow to interrogate human transcriptomes …
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Alternative Splicing Expands Spatiotemporal Expression Complexity of Arthropod N -Cadherin
… from dynamic spatiotemporal regulation of transcriptomes. Both gene duplication and alternative splicing have been proposed as a means to expand transcriptomes. Although gene duplication expands genomics, the small number of protein-coding genes in metazoan genomes is insufficient to …
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Microbial metatranscriptomics : towards understanding microbial gene expression and regulation in natural habitats
… metatranscriptomics, for profiling community transcriptomes on spatial and temporal scales. Several findings and relevant hypotheses have emerged from this work. I show that transcripts of house-keeping genes necessary for the maintenance of basic cellular machinery are abundant and readily …
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Understanding the evolution of the apical organ in the early branching metazoan, Nematostella vectensis
… system. Through generating tissue-specific transcriptomes and integrating this data with an existing single-cell RNA sequencing dataset, this research identified a distinct neuronal signature and at least six cell types comprising the apical domain of N. vectensis, uncovering the molecular …
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Cell Fate Specification and the Regulation of RNA-dependent DNA Methylation in the Arabidopsis Root Meristem
… resolution whole genome DNA methylomes, mRNA transcriptomes, and smallRNA transcriptomes for six different populations of cell types in the Arabidopsis root meristem. We were able to discover that the columella is hypermethylated in the CHH context within transposable elements. This …
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Recoding and reassignment in protists
… of the poly-A tail. In addition I analysed the transcriptomes of over 200 diverse protist species for the protein ornithine decarboxylase antizyme, a key negative regulator of cellular polyamine synthesis. The synthesis of this protein usually requires a +1 ribosomal frameshift at the end of the …
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MATERNAL DETERMINANTS OF OOCYTE AND EMBRYO QUALITY
… microarray analysis was performed, comparing the transcriptomes of rhesus monkey MII oocytes of different qualities, high quality VVM oocytes and poor quality IVM oocytes. A small set of 59 Oocyte quality plays a critical role in establishment of pregnancies, embryo development, implantation and …
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