Global ETD Search
Search theses and dissertations gathered from participating repositories worldwide. Every result links back to the library that holds it. No account is needed.
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Showing 1 to 20 of 25 for “"snRNA-seq"”.
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Selective Neuronal Vulnerability in Neocortices from Patients with C9ORF72-related Neurodegeneration
… . M1 tissue was processed for single nuclei RNA-sequencing (snRNA-seq) and 10X Visium spatial transcriptomics (Chapter 2). I first investigated cortical neuron vulnerability using snRNA-seq (Chapter 3). Upper motor neurons (herein called L5 ETs: layer 5 extratelencephalic-projecting excitatory …
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Exploring the gene regulatory dynamics of the maturing human brain
… a nuclei isolation protocol. Single nuclei RNA-seq (snRNA-seq) libraries were generated using the 10x Genomics Platform. snRNA-seq datasets were then sequenced and analysed using bioinformatics tools, including Cell Ranger and Seurat. The major cell types in the pediatric brain were identified, …
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Towards a complete human cell atlas: a single-nucleus RNA sequencing study of the paediatric and adult human brain
… cell atlas comprising of 6 single nucleus RNA sequencing (snRNA-seq) datasets generated from antemortem human brain tissue samples obtained during elective surgeries to treat epilepsy. To complement these, we included 6 snRNA-seq datasets from adult brain tissue. The 12 samples are all of …
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Integrating Bulk and Single-Cell Transcriptomics to Investigate Intratumor Heterogeneity
… with single-cell/nucleus (sc/sn) RNA-seq data has emerged as a powerful approach to dissect both cellular composition and cell-type-specific expression patterns, yet the technological discrepancy across sequencing platforms limits accuracy.</p> <p>To systematically evaluate the impact …
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Dopamine-dependent Transcriptional Dynamics in Striatal Physiology and Cocaine Reward
… optogenetic, and single-nucleus RNA-sequencing (snRNA-seq) approaches in a rodent model system to define the acute physiological and transcriptional responses of NAc medium spiny neurons (MSNs) following acute cocaine experience. Acute cocaine exposure produced rapid but prolonged …
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The development and use of cutting edge next generation sequencing methodologies to study RNA viruses
With new next generation sequencing technologies and methodologies being published often, our ability to sequence viruses and host transcriptomes (in response to viral infection) has expanded – driving virology forward. Here we show the development and use of novel methodologies to study RNA …
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Profiling the dynamics of the active transcriptome in the juvenile and adult brain using spatial transcriptomics
… studies have used single-cell/single nucleus RNA-sequencing (sc/snRNA-seq) to provide vital information on gene expression at a cell-specific level. These studies, which focused on either the pre-natal or adult brain, lacked comprehensive information about the spatial dynamics of cell …
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Cells that Kill: The Chemosensory Cell Types of Aedes aegypti Mosquitoes
… and the maxillary palp, for single nucleus RNA-sequencing (snRNA-seq). Performing careful analysis, we found that mosquitoes co-express multiple chemosensory receptor genes within individual OSNs. In the maxillary palp, nearly all the OSNs co-expressed multiple chemo receptor subunits from at …
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A computational approach to understanding maternal influences on the development of ruminant neonates
… of this cellular transfer may have long-term consequences, including increased neonatal morbidity and mortality due to impaired immune competence against infectious diseases. Despite these critical functional roles, common colostrum management practices in livestock production systems, such as …
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Correlation-based Linking of Epigenomic Regions to Target Genes in Bulk and Single Cell Epigenomic Data
Single-cell sequencing has catalyzed a significant shift in biological modeling and hypothesis generation. In this study, we present advanced algorithms that utilize multiple modalities for peak-gene linking via correlation-based mechanisms. This approach provides a robust framework for bias …
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Inference of single cell profiles from histology stains with the Single-Cell omics from Histology Analysis Framework (SCHAF)
… profiling methods, such as single-cell RNA-seq (scRNA-seq), and histology imaging data, such as Hematoxylin-and-Eosin (H&E) stains. While single-cell profiles provide rich molecular information, they can be challenging to collect routinely and do not have spatial resolution. Conversely, …
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Using single nucleus RNA-seq to determine the effect of immunosuppression on the transcriptional activity of resident CNS cells in a mouse model of CNS-TB
… so atsingle cell resolution. Single nucleus RNA Sequencing (snRNA-seq) was used to determine the effect of immunosuppression on the transcriptional activity of resident CNS cells in a mouse model of CNS-TB. The model consisted of two mouse genotypes, namely Wildtype and TNF knockout (TNF-/- ). …
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The Role of the Circadian Clock in the Paraventricular Nucleus of the Hypothalamus in Diurnal Energy Balance
… BMAL1 chromatin immunoprecipitation followed by sequencing and single nuclei RNA sequencing (snRNA-seq), we analyzed the genomic and transcriptional regulation by BMAL1 across time and in PVN cell types. Our study reveals not only rhythmic binding at specific loci by BMAL1, but that loss of BMAL1 …
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MULTI-OMIC LINEAGE TRACING PREDICTS THE MOLECULAR DRIVERS OF CANCER STEM CELLS IN TRIPLENEGATIVE BREAST CANCER EVOLUTION.
… and chromatin accessibility profiling (via snRNA-seq and snATAC-seq) and integrates these with phenotypic assays. Applying GALILEO to the intrinsically heterogeneous and highly tumorigenic TNBC cell line SUM159PT, we identified two distinct subpopulations: drug-tolerant cells (DTCs) and …
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Molecular Profiling and Mechanisms of Cerebrovascular Function in Health and Neurodegeneration
… brain tissue samples. Using single-nucleus RNAsequencing (snRNA-seq), we profile cerebrovascular nuclei across 11 subtypes, including endothelial cells, mural cells, and perivascular fibroblasts. We uncover human-specific expression patterns along the arteriovenous axis and determine previously …
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The Molecular Regulation of Wiring Specificity in the Serotonin System Across Key Postnatal Stages
… developmental timepoints. We further integrated snRNA-seq datasets from projection-defined subpopulations targeting five distinct brain regions in adult mice. This comprehensive approach enabled us to establish developmental transcriptomic profiles for projection-defined serotonin neurons, …
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Transcriptional Heterogeneity in ALS: Patients with Retrovirus-mediated Disease and Potential Cell-type Specific Therapeutic Approaches
… To address this hypothesis, a bulk RNA sequencing (RNA-seq) dataset from almost 2,000 ALS and unaffected control samples was leveraged to uncover transcriptionally distinct patient subpopulations. Using non-negative matrix factorization (NMF), an unsupervised clustering algorithm, four …
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Spontaneously Regenerative Corticospinal Neurons in Mice
… tracing methods, tissue clearing, and Smart-seq3 single-nucleus RNA-sequencing (snRNA-seq), we found that ipsilateral CSN axons project to regions of the ventral horn, including directly to motor neurons. Barcode-based Multiplexed Analysis of Projections by Sequencing (MAPseq) of the CST …
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Comprehensive analysis of cellular contribution to delayed skeletal muscle recovery after disuse
Submission published under a 24 month embargo labeled 'U of I Access', the embargo will last until 2025-05-01
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The molecular memory of exercise in skeletal muscle
… resistance-type exercise. The single nucleus RNA-seq (snRNA-seq) data presented in chapter 4 allowed me to investigate the potential of a cell specific memory of exercise following endurance exercise. Utilizing isolated nuclei from the gastrocnemius muscle of mice fed a control diet from the …
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