Post-graduate theses
Current Record: 17 of 802
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Identifier |
000460518 |
Title |
Establishment of a multi-omic strategy for the identification of enhancer-gene regulatory networks in model organisms |
Alternative Title |
Εδραίωση πολυ-ωμικών μεθοδολογιών για τον προσδιορισμό ρυθμιστικών δικτύων ενισχυτών-γονιδίων στόχων σε οργανισμούς-μοντέλα |
Author
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Μίτλεττον, Μυρτώ Φ.
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Thesis advisor
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Lavigne, Matthieu
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Reviewer
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Παυλόπουλος, Αναστάσιος
Δελιδάκης, Χρήστος
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Abstract |
Ever since the emergence of Next Generation Sequencing techniques, -omics and multiomics strategies have been offering amazing insights in structural and functional
annotation of genomes and have boosted the development of both research and
therapeutic approaches.
The first goal of this project was the construction and implementation of a pipeline for
the analysis of ATAC-seq (chromatin accessibility) and RNA-seq (gene expression)
data, enabling genome-wide enhancer identification and prediction of putative
enhancer–gene links. The above pipeline was first established to analyze data derived
from wild-type mice (Mus musculus) and mice with a gene knocked-out.
Once established and tested on the mouse dataset, the pipeline was used for the analysis
of a developmental time-course dataset derived from the crustacean model organisms
Parhyale hawaiensis. Parhyale has been put forward as an attractive experimental
model to study tissue and organ morphogenesis during normal development and
regeneration. I analyzed already produced mRNA-seq and Omni-ATAC-seq datasets,
acquired at different stages of Parhyale embryogenesis: S13, S17 and S19.
My analyses identified Differentially Expressed Genes and Differentially Accessible
Regions between these experimental conditions and generated hypotheses about the
composition of enhancer-gene regulatory networks. I then selected three Parhyale
genes for detailed analysis by quantitative RT-PCR and immunofluorescence:
gooseberry (gsb), homothorax (hth) and lola-like (lolal), which were shown to have
correlating expression and accessibility characteristics and implicated in developmental
processes like segmentation, appendage formation and Hox gene regulation,
respectively.
The established pipeline provides great amounts of data available for future research in
mouse and Parhyale, and can be easily adjusted for data analysis of other model
organisms and types of experiments.
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Language |
English |
Subject |
Atac-sequancing analysis |
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Atac-sequancing ανάλυση |
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Correlation analysis |
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Mouse |
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Mus musculus |
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Ngs analysis |
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Ngs pipeline |
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Parhyale hawaiensis |
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Rna-sequencing analysis |
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Rna-sequencing ανάλυση |
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Αλληλουχίσης νέας γενιάς |
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Ανάλυση δεδομένων |
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Παρυαλός |
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Ποντίκι |
Issue date |
2023-11-24 |
Collection
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School/Department--School of Sciences and Engineering--Department of Biology--Post-graduate theses
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Type of Work--Post-graduate theses
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Permanent Link |
https://elocus.lib.uoc.gr//dlib/9/2/4/metadata-dlib-1700655868-951544-12956.tkl
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Views |
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