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.
Results
Showing 1 to 20 of 57 for “"ATAC-seq"”.
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Leveraging Single-Cell ATAC-Seq for Genomic Language Models and Multimodal Foundation Models
… Assay for Transposase-Accessible Chromatin using sequencing (scATAC-seq) has emerged as a powerful tool for profiling chromatin accessibility at single-cell resolution. By capturing epigenomic landscapes, scATAC-seq provides critical insights into the regulatory elements that govern gene …
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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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Integrating -Omics For Studying Functional Role Of Ulcerative Colitis Risk Associated Loci.
… types. Method: We assessed chromatin activity (ATAC seq) and transcriptional behavior (RNA seq) of primary cell types extracted from intestinal biopsies and blood from diseased and healthy participant. Next, to pinpoint the mechanistic of how UC associated loci contributes to disease risk, we …
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Aligning heterogenous single cell assay datasets
… on an existing paired single-cell dataset of ATAC-seq and RNA-seq for human A549 cells. We then apply these methods to map the variability between three single-cell datasets-ATAC-seq, RNA-seq, and Hi-C-on pluripotent mouse embryonic stem cells and assess the performance of these methods.
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Transcriptional and Chromatin Disorientation Associated with BRCA2 Inactivation
… cancer remains unclear. In this study, using RNA-seq and ATAC-seq I investigated whether BRCA2 acts as a tumour suppressor via regulating the transcriptional and chromatin organization. Using RNA seq datasets from BRCA2 mutant MCF10A cell lines and TCGA breast cancers, I report that BRCA2 …
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The Role of the Proneural Transcription Factor ASCL1 in Neuroblastoma Cell Division and Differentiation
… ASCL1 is considered a pioneer factor and ATAC-Seq analysis shows that chromatin accessibility is reduced in the ASCL1 knock-out lines, suggesting ASCL1 could be limiting both chromatin accessibility and directly recruiting transcription factors to the chromatin. In addition to these …
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Role of host chromatin remodelling in Mycobacterium leprae-induced Schwann cell fate change
… and dissemination. METHOD: Externally generated ATAC-seq data sets and Sox2 ChIP-seq data on three cell states, control mouse Schwann cells (mSwCs), M. leprae infected cells (ML-mSwCs) and progenitor/stem-cell like cells (pSLCs). Data quality was checked then analysed using PCA, differential peak …
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Molecular mediators of cardiac-specific enhancer activation
… the Assay for Transposase-Accessible Chromatin (ATAC-seq) to map changes in chromatin accessibility and integrated these data with maps of histone modification patterns and gene expression across several stages of embryonic stem cell (ESC) differentiation toward cardiomyocytes (CMs). Based on …
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Probabilistic models to resolve cell identity and tissue architecture
… assay for transposase-accessible chromatin with sequencing (ATAC-seq), DNA accessibility provides a readout of intermediate gene regulation steps at single-cell resolution, with technologies measuring both RNA and ATAC providing the necessary evidence to build mechanistic models of regulation. …
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Spatially-resolved multiomic profiling of the human heart in adulthood and development
… somatic mutations called in both RNA- and ATAC-seq reads and used mutational profiles to infer cell type lineage divergence. Finally, we generated similar data from hearts with Trisomy 21 and use a variety of approaches to draw comparisons with our euploid atlas, finding that formation of …
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Using a novel large-scale epigenetic analysis method to uncover the cis-regulatory potential of individual transposable elements
Transposable elements (TEs) are DNA sequences with the potential to move or replicate and insert themselves at new genomic locations. Over evolutionary time, many sequences derived from TEs have accumulated and account for 50% of the human genome. These mobile elements were initially considered …
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Knowledge-Guided Machine Learning for Single-Cell Regulatory Genomics
… coordinate gene regulation, and single-cell sequencing now enables these programs to be studied at high resolution. However, single-cell RNA-seq and ATAC-seq data are sparse and high-dimensional, making it difficult for existing methods to reliably infer TF activity and gene-regulatory …
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Single Cell Methods to Learn Transcription Factor Interactions and Necessary Noncoding DNA During Zebrafish Somitogenesis
… In this thesis, I will present a method sciPlex ATAC-seq, a multiplexed low cost method for single-cell assay for transposable accessible chromatin. Pairing this method with sciPlex RNA-seq, a similar method for transcriptomic measurement, allowed me to build an integrated single-cell atlas of …
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Chromatin Accessibility Beyond the Peaks
… but respond to changing conditions, and DNA sequence which is invariant across conditions but varies locally around genes. Assays that measure features of chromatin state can help us understand this interplay between sequence and trans factors that ultimately governs transcriptional …
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Decoding Brain Somatic Mosaicism with New Single-Cell Copy Number Analysis Methods
… and disease. While single-cell whole-genome sequencing (scWGS) enables genome-wide profiling at single-cell resolution, existing computational methods struggle to accurately detect non-clonal CNVs, limiting our understanding of genomic mosaicism in the brain. In this thesis, I present two …
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Droplet-Based Microfluidics for High-Throughput Single-Cell Omics Profiling
… techniques to accomplish high-throughput scRNA-seq, scDNA-seq, scATAC-seq, scChIP-seq, as well as scMulti-omics-seq. These advanced technologies have been providing unique and novel insights into both normal differentiation and disease development at single-cell level. In this thesis, we develop …
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Uncovering Functional Alzheimer’s Disease Variants and Their Effector Genes through Single-Cell CRISPRi Screening and 3D Genomics
… by leveraging our genomics datasets comprising ATAC-seq, RNA-seq, and high-resolution promoter-focused Capture C from brain-relevant cell models. We identified 89 candidate causal SNPs and 69 effector genes. Second, we designed a single-cell CRISPRi screen to perturb 74 candidate regulatory …
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Engineering Cell Lines to Investigate the Function of Mammalian SWI/SNF Complexes
… Bioinformatics analyses of tumour sample sequencing studies have shown that members of the mSWI/SNF complexes are mutated in almost 20% of all cases, suggesting many subunits have tumour suppressor functions. The residual complex that remains upon inactivation of a subunit is thought to …
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A CELL CYCLE CLOCK REGULATES THE EPIGENETIC LANDSCAPE OF AML CELLS AND DETERMINES SENSITIVITY TO LSD1 INHIBITION
… focusing on modifications of the epigenome. Our ATAC-seq investigations show that extension of the G1 phase alters chromatin accessibility. The epigenomic remodeling is further characterized by ChIP-seq and mass spectrometry experiments on genomic distribution and quantities of functionally …
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Understanding the Conserved and Species-Specific Functions of FOXP2, a Gene Implicated in Speech and Language Development
… and tested this theory by performing RNA-seq in human differentiating neurons and leveraging publically available developmental expression data from human, macaque, and mouse cortex in order to identify human specific, primate specific, and conserved subplate genes regulated by FOXP2. This …
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