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Exploring the gene regulatory dynamics of the maturing human brain
The human brain develops gradually overtime where distinct molecular profiles are established in the embryo. These molecular profiles continue to change through aging and in response to environmental factors. The complexity and dynamics of gene expression and regulation at the cell type-specific lev...
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| Format: | Thesis |
| Language: | English |
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Department of Human Biology
2023
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| _version_ | 1867613329682333696 |
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| access_status_str | Open Access |
| author | Fillmore, Stephanie |
| author2 | Hockman, Dorit |
| author_browse | Fillmore, Stephanie Hockman, Dorit |
| author_facet | Hockman, Dorit Fillmore, Stephanie |
| author_sort | Fillmore, Stephanie |
| collection | Thesis |
| description | The human brain develops gradually overtime where distinct molecular profiles are established in the embryo. These molecular profiles continue to change through aging and in response to environmental factors. The complexity and dynamics of gene expression and regulation at the cell type-specific level are still poorly understood, especially during the process of brain maturation. The overall aim of this project was to obtain a better understanding of how the brain cell atlas changes over time by contributing to the current brain cell atlas with pediatric single cell data. Bio-banked pediatric and adult brain tissue samples, obtained during surgery to treat epilepsy, were used to optimise and generate 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, including the genes being expressed by these cell types. In addition, a pilot differential expression analysis study was conducted between snRNA-seq libraries from the temporal and frontal lobes. Furthermore, Assays for Transposase Accessible Chromatin (ATAC-seq) was performed on pediatric and adult tissue and bulk ATAC-seq libraries were successfully generated. A consensus list of putative enhancers and promoters was generated after testing several bioinformatic pipelines. Differential accessibility analysis was performed on the bulk ATAC-seq datasets and the promoters or enhancers that are being dynamically used over the course of brain development, were also identified. Ultimately, with these findings and with the generation of optimised protocols, this study has contributed to our understanding of gene expression and gene regulation of brain maturation. |
| format | Thesis |
| id | oai:open.uct.ac.za:11427/37185 |
| institution | University of Cape Town (South Africa) |
| language | eng |
| last_indexed | 2026-06-10T12:34:25.395Z |
| license_str | Not specified — see source repository |
| provenance_str_mv | Harvested via OAI-PMH from UCTD — University of Cape Town Open Access Repository |
| publishDate | 2023 |
| publishDateRange | 2023 |
| publishDateSort | 2023 |
| publisher | Department of Human Biology |
| publisherStr | Department of Human Biology |
| record_format | dspace |
| source_str | UCTD — University of Cape Town Open Access Repository |
| spelling | oai:open.uct.ac.za:11427/37185 Exploring the gene regulatory dynamics of the maturing human brain Fillmore, Stephanie Hockman, Dorit Medicine The human brain develops gradually overtime where distinct molecular profiles are established in the embryo. These molecular profiles continue to change through aging and in response to environmental factors. The complexity and dynamics of gene expression and regulation at the cell type-specific level are still poorly understood, especially during the process of brain maturation. The overall aim of this project was to obtain a better understanding of how the brain cell atlas changes over time by contributing to the current brain cell atlas with pediatric single cell data. Bio-banked pediatric and adult brain tissue samples, obtained during surgery to treat epilepsy, were used to optimise and generate 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, including the genes being expressed by these cell types. In addition, a pilot differential expression analysis study was conducted between snRNA-seq libraries from the temporal and frontal lobes. Furthermore, Assays for Transposase Accessible Chromatin (ATAC-seq) was performed on pediatric and adult tissue and bulk ATAC-seq libraries were successfully generated. A consensus list of putative enhancers and promoters was generated after testing several bioinformatic pipelines. Differential accessibility analysis was performed on the bulk ATAC-seq datasets and the promoters or enhancers that are being dynamically used over the course of brain development, were also identified. Ultimately, with these findings and with the generation of optimised protocols, this study has contributed to our understanding of gene expression and gene regulation of brain maturation. 2023-03-03T09:59:28Z 2023-03-03T09:59:28Z 2022 2023-02-20T12:45:04Z Master Thesis Masters MSc http://hdl.handle.net/11427/37185 eng application/pdf Department of Human Biology Faculty of Health Sciences |
| spellingShingle | Medicine Fillmore, Stephanie Exploring the gene regulatory dynamics of the maturing human brain |
| thesis_degree_str | Master's |
| title | Exploring the gene regulatory dynamics of the maturing human brain |
| title_full | Exploring the gene regulatory dynamics of the maturing human brain |
| title_fullStr | Exploring the gene regulatory dynamics of the maturing human brain |
| title_full_unstemmed | Exploring the gene regulatory dynamics of the maturing human brain |
| title_short | Exploring the gene regulatory dynamics of the maturing human brain |
| title_sort | exploring the gene regulatory dynamics of the maturing human brain |
| topic | Medicine |
| url | http://hdl.handle.net/11427/37185 |
| work_keys_str_mv | AT fillmorestephanie exploringthegeneregulatorydynamicsofthematuringhumanbrain |