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Teses / dissertações sobre o tema "Spatial transcriptomic"

Autor: Grafiati

Publicado: 21 de setembro de 2024

Última modificação: 26 de julho de 2025

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1

Castorena, Rodriguez Jimena. "Application of a spatial transcriptomic approach to assess medullar endothelial cells in vascular niches, chronic inflammation and fibrosis in myeloproliferative neoplasm patients." Electronic Thesis or Diss., université Paris-Saclay, 2025. http://www.theses.fr/2025UPASL022.

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Les néoplasmes myéloprolifératifs (NMP) sont des maladies rares du sang qui perturbent la production des cellules sanguines, augmentent le risque de complications vasculaires, dont l’evolution peut être une fibrose de la moelle osseuse (MO) dans un contexte inflammatoire. Notre étude porte sur les cellules endothéliales de la MO (CEMO) et leur implication dans ces maladies. Nous avons utilisé, pour la première fois sur des biopsies osseuses de patients, une approche de biologie spatiale innovante pour étudier les CEMO dans leur contexte architectural. Nous avons mis en évidence que les CEMO su

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2

Larsson, Ludvig. "Optimization of UMI counting strategies for Spatial Transcriptomics." Thesis, KTH, Skolan för kemi, bioteknologi och hälsa (CBH), 2018. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-233838.

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Spatial Transcriptomics (ST) is a microarray-based RNA sequencing technology that allows for genome-wide transcriptome profiling of tissue sections with spatialresolution, which was published in Science by Ståhl and Salmén et al in 2016. Polyadenylated transcripts are captured on a microarray surface through hybridizationwith a barcoded DNA oligo that carries the information necessary to infer spatialposition and transcript uniqueness from the output sequencing reads. The ST protocolutilizes Unique Molecular Identifiers (UMIs) to remove PCR duplicates and obtain reliable estimates of gene coun

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3

Van, Leen Eric. "On the morphogenesis of the D. melanogaster pupa : a study on gene patterning and tissue folding." Electronic Thesis or Diss., Sorbonne université, 2020. http://www.theses.fr/2020SORUS387.

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Au cours du développement, la coordination des comportements cellulaires est essentielle à la formation d’organes complexes et fonctionnels. L’analyse de ces processus cellulaire est essentielle pour comprendre comment les tissues se forment au cours du développement. Pour ce faire, il est tout d’abord primordial d’identifier les gènes dont l’expression est corrélée avec chacun de ces processus cellulaires. Avec pour modèle la formation de l’épithélium dorsal (le notum) de la pupe de drosophile, mon travail de thèse a visé à identifier les mécanismes moléculaires qui gouvernent la régulation s

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4

Peiffer, Jason, Shail Kaushik, Hajime Sakai, et al. "A spatial dissection of the Arabidopsis floral transcriptome by MPSS." BioMed Central, 2008. http://hdl.handle.net/10150/610079.

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BACKGROUND:We have further characterized floral organ-localized gene expression in the inflorescence of Arabidopsis thaliana by comparison of massively parallel signature sequencing (MPSS) data. Six libraries of RNA sequence tags from immature inflorescence tissues were constructed and matched to their respective loci in the annotated Arabidopsis genome. These signature libraries survey the floral transcriptome of wild-type tissue as well as the floral homeotic mutants, apetala1, apetala3, agamous, a superman/apetala1 double mutant, and differentiated ovules dissected from the gynoecia of wild

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5

Jestin, Martin. "Modifications du microenvironnement stromal après irradiation localisée du côlon : identification de voies moléculaires pour optimiser le processus de régénération épithéliale." Electronic Thesis or Diss., Sorbonne université, 2024. https://accesdistant.sorbonne-universite.fr/login?url=https://theses-intra.sorbonne-universite.fr/2024SORUS165.pdf.

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Les cancers pelviens ont une prévalence élevée et sont principalement traités par radiothérapie. Si elle permet un contrôle de la tumeur, la radiothérapie peut également provoquer des lésions aux tissus sains environnants, entrainant des complications invalidantes définies comme une maladie à part entière, la «Pelvic Radiation Disease» ou PRD. Aujourd'hui, il n'existe pas de traitement curatif pour cette pathologie fibrosante. Ce projet vise à étudier le microenvironnement du côlon après irradiation afin d'identifier, à terme, des cibles thérapeutiques pour la prise en charge des séquelles col

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6

Currás, alonso Sandra. "Lung responses to radiation injury at the single cell level." Electronic Thesis or Diss., Université Paris sciences et lettres, 2021. http://www.theses.fr/2021UPSLS060.

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La radiothérapie constitue une option thérapeutique majeure pour le traitement du cancer du poumon. Néanmoins, la radiothérapie induit chez environ 5 à 20 % des patients traités des toxicités pulmonaires irréversibles précoces et tardives, telles que la pneumonite aiguë ou la fibrose pulmonaire induite par la radiothérapie (FPRI). La FPRI est caractérisée par une destruction progressive et irréversible de l'architecture alvéolaire avec perturbation des échanges gazeux conduisant à la mort des patients. Bien que l'ordre des événements moléculaires et cellulaires dans la progression vers la FPRI

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7

Lötstedt, Britta. "Towards spatial host-microbiome profiling." Licentiate thesis, KTH, Genteknologi, 2021. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-289384.

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Sequencing technologies and applications have pushed the limits and enabled novel studies of biological mechanisms, evolutionary relationships and communication networks between cells. The technical developments leading to single cell RNA-sequencing have enabled detection of rare cell populations while spatial resolution added insights into larger biological environments, like tissues and organs. Massively parallel sequencing has paved the way for integrated high-throughput analyses including that of studying gene expression, protein expression and mapping of microbial communities. This thesis

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8

Kaewsapsak, Pornchai. "Spatially-resolved transcriptomic mapping in live cells using peroxidase-mediated proximity biotinylation." Thesis, Massachusetts Institute of Technology, 2017. http://hdl.handle.net/1721.1/113972.

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Thesis: Ph. D., Massachusetts Institute of Technology, Department of Chemistry, 2017.<br>Cataloged from PDF version of thesis.<br>Includes bibliographical references.<br>The spatial organization of RNA within cells is crucial for the regulation of a wide range of biological functions, spanning all kingdoms of life. However, a general understanding of RNA localization has been hindered by a lack of simple, high-throughput methods for mapping the transcriptomes of subcellular compartments. Here, we developed two methods, termed APEX-RIP and APEX-Seq. APEX-RIP combines peroxidase-catalyzed, spati

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9

Mignardi, Marco. "In situ Sequencing : Methods for spatially-resolved transcriptome analysis." Doctoral thesis, Stockholms universitet, Institutionen för biokemi och biofysik, 2014. http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-110057.

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It is well known that cells in tissues display a large heterogeneity in gene expression due to differences in cell lineage origin and variation in the local environment at different sites in the tissue, a heterogeneity that is difficult to study by analyzing bulk RNA extracts from tissue. Recently, genome-wide transcriptome analysis technologies have enabled the analysis of this variation with single-cell resolution. In order to link the heterogeneity observed at molecular level with the morphological context of tissues, new methods are needed which achieve an additional level of information,

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10

Vickovic, Sanja. "Transcriptome-wide analysis in cells and tissues." Doctoral thesis, KTH, Genteknologi, 2017. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-199447.

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High-throughput sequencing has greatly influenced the amount of data produced and biological questions asked and answered. Sequencing approaches have also enabled rapid development of related technological fields such as single-cell and spatially resolved expression profiling. The introductory parts of this thesis give an overview of the basic molecular and technological apparatus needed to analyse the transcriptome in cells and tissues. This is succeeded by a summary of present investigations that report recent advancements in RNA profiling. RNA integrity needs to be preserved for accurate ge

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11

Zhang, Yang. "A visualization interface for spatial pathway regulation data." Thesis, KTH, Skolan för kemi, bioteknologi och hälsa (CBH), 2018. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-237741.

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Data visualization is an essential methodology for bioinformatics studies. Spatial Transcriptomics(ST) is a method that aims at measuring the transcriptome of tissue sections while maintaining its spacial information. Finally, the study of biological pathway focuses on a series of biochemical reactions that take place in organisms. As these studies generate a large number of datasets, this thesis attempts to combine the ST’s data with pathwayinformation and visualize it in an intuitive way to assist user comprehension and insight.In this thesis, Python was used for integrating the dataset and

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12

Sugiyama, Michael. "Sex differences in the intestinal transcriptome and spatial patterns of lipid uptake capacity and intestinal lipid-metabolic gene expression." Thesis, McGill University, 2012. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=107881.

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The mammalian small intestine expresses three members of the fatty acid binding protein family; Fabp1, Fabp2, and Fabp6 that differ in their spatial expression pattern and ligand binding preference. In vitro studies using recombinant FABPs suggest an important role in lipid uptake and intestinal lipid metabolism, although the in vivo functions remain unclear. Mice genetically altered to lack Fabp2 exhibit a sex-dimorphic response to high fat diet feeding featuring weight gain and fatty liver in males but not females, suggesting that Fabp2 is involved in a sex-dimorphic intestinal metabolic pro

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13

Parreau, Simon. "Etude du remodelage vasculaire de l’Artérite à Cellules Géantes par caractérisation inflammatoire et lésionnelle spatiale." Electronic Thesis or Diss., Limoges, 2024. http://www.theses.fr/2024LIMO0040.

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Rationnel : L’artérite à cellules géantes (ACG) est une vascularite affectant l’aorte et ses principales branches, caractérisée par un infiltrat inflammatoire et un remodelage vasculaire. Les complications ischémiques de la maladie sont liées à une hyperplasie de l’intima par prolifération de myofibroblastes. Les fibroblastes adventitiels ont été peu étudiés au cours de l’ACG et pourraient participer au phénomène de remodelage vasculaire.Objectifs : Nous émettons l’hypothèse que les fibroblastes adventitiels sont impliqués dans le remodelage vasculaire de l’ACG.Méthodes : Nous avons inclus des

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14

Wahle, Philipp. "Transcriptome dynamics in early Drosophila development at tissue and single-cell resolution." Doctoral thesis, Humboldt-Universität zu Berlin, 2019. http://dx.doi.org/10.18452/19976.

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Das Nervensystem von Drosophila melanogaster entwickelt sich aus dem Neuroectoderm entlang der anterior-posterioren Axe des Embryos. Dieses Gewebe unterteilt sich in drei Expressionsdomänen, die von ventral nach dorsal durch Expression der drei Homöobox-Transkriptionsfaktoren vnd, ind und msh charakterisiert sind. Vnd und Ind wurden als notwendig und ausreichend beschrieben, um die Zellidentitäten ihrer jeweiligen Gewebe zu determinieren. Um zu untersuchen, wie diese Transkriptionsfaktoren agieren, um ihre jeweiligen Zelltypen hervorzubringen, habe ich die genomweiten Genexpressionsmuster dies

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15

Marques, Christine. "Dégénérescence des neurones moteurs cortico-spinaux dans un modèle murin de sclérose latérale amyotrophique : dynamique spatio-temporelle et mécanismes moléculaires." Thesis, Strasbourg, 2017. http://www.theses.fr/2017STRAJ063/document.

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La sclérose latérale amyotrophique (SLA) se définit cliniquement par la dégénérescence combinée des neurones moteurs cortico-spinaux (NMCS) et des motoneurones bulbaires et spinaux (MnB et MnS). Quoique l’idée d’une origine corticale de la SLA soit de plus en plus considérée, la pathologie corticale, la dynamique spatio-temporelle de la dégénérescence des NMCS et les voies moléculaires impliquées restent peu connues. Ce travail de thèse a essentiellement cherché à pallier ce manque. Nous avons montré que chez les souris Sod1G86R, la perte des NMCS, qui semble se produire en l’absence de gliose

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16

Sünkel, Christin. "Analyzing the neural transcriptional landscape in time and space." Doctoral thesis, Humboldt-Universität zu Berlin, 2020. http://dx.doi.org/10.18452/21011.

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Zirkuläre RNAs sind eine Klasse endogener, tierischer RNAs. Obwohl sie hoch abundant sind, ist weder ihre Funktion noch ihre Expression im Nervensystem bekannt. Es wurde ein Katalog zirkulärer RNAs in neuralen Proben erstellt. Es konnten tausende zirkuläre RNAs von Mensch und Maus entdeckt und analysiert werden. Zirkuläre RNAs sind außerordentlich angereichert im Säugetiergehirn, ihre Sequenz ist gut konserviert und sie sind häufig gemeinsam in Mensch und Maus exprimiert. Zirkuläre RNAs waren generell höher exprimiert im Verlauf der neuronalen Differenzierung, sind stark angereichert an Synaps

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17

Mashayamombe, Chipo. "A rat model study of the spatio-temporal effects of progesterone signalling on the transcriptome of uterine tissues during pregnancy and parturition." Thesis, University of Warwick, 2015. http://wrap.warwick.ac.uk/79940/.

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The steroid hormone progesterone is essential for the maintenance of pregnancy in mammalian species, but its role at term and during labour is not fully understood. While the effects of progesterone be either genomic or non-genomic, this thesis focuses on the genomic effects of progesterone, and its withdrawal, on rat uterine tissues. Using laser Capture Microdissection, homogeneous cell populations from the the outer myometrium, inner myometrium, and decidua basalis were isolated from uterine horns obtained from timed-pregnant Sprague Dawley rats that were randomised to receive either progest

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18

Diaz, Herrero Alba. "Characterization of Tumor Immune Microenvironment in Human Diffuse Large B-cell Lymphoma." Electronic Thesis or Diss., université Paris-Saclay, 2024. http://www.theses.fr/2024UPASL057.

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Le lymphome diffus à grandes cellules B (DLBCL) est le sous-type le plus fréquent de lymphome non hodgkinien (NHL), caractérisé par une prolifération anormale de cellules B matures. C'est une maladie agressive pour laquelle les stratégies thérapeutiques actuelles sont insuffisantes. Le microenvironnement tumoral (TME) est un réseau dynamique de cellules, molécules et des autres éléments qui entourent une tumeur. Ceux-ci tiennent un rôle prépondérant dans le développement du cancer, la réponse au traitement et la survie des patients. Étudier le TME chez les patients atteints de DLBCL est essent

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19

"Multiplexed Single-cell Spatial Proteomics and Transcriptomics." Doctoral diss., 2018. http://hdl.handle.net/2286/R.I.51771.

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abstract: Single-cell proteomics and transcriptomics analysis are crucial to gain insights of healthy physiology and disease pathogenesis. The comprehensive profiling of biomolecules in individual cells of a heterogeneous system can provide deep insights into many important biological questions, such as the distinct cellular compositions or regulation of inter- and intracellular signaling pathways of healthy and diseased tissues. With multidimensional molecular imaging of many different biomarkers in patient biopsies, diseases can be accurately diagnosed to guide the selection of the ideal tr

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20

Eng, Chee Huat (Linus). "Plus Ultra: Genome-Wide Spatial Transcriptomics with RNA seqFISH+." Thesis, 2021. https://thesis.library.caltech.edu/14204/1/CheeHuat%28Linus%29Eng_thesis.pdf.

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<p>Visualizing single cells and their organization in intact tissue is crucial to understanding their governing biological function. Even though single cell RNA sequencing has provided many insights into the heterogeneity and gene expression profiles across many tissue types, the dissociation process which loses the spatial information is hindering our deeper understanding of how these transcriptional distinct cell types are organized and interacting in their native tissue environment.</p> <p>The thesis begins by giving a background on how single cell RNA sequencing has transformed biology

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