RNA-Seq for the detection of differential expressed genes under several experimental conditions

Detalhes bibliográficos
Autor(a) principal: Fernandes, Isabel Cristina Moniz
Data de Publicação: 2021
Tipo de documento: Dissertação
Idioma: eng
Título da fonte: Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
Texto Completo: http://hdl.handle.net/10451/54267
Resumo: Tese de mestrado, Bioinformática e Biologia Computacional, 2021, Universidade de Lisboa, Faculdade de Ciências
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spelling RNA-Seq for the detection of differential expressed genes under several experimental conditionsRNA-seqCasuarinaCoffeaLimoniumtranscriptómicaTeses de mestrado - 2021Departamento de InformáticaTese de mestrado, Bioinformática e Biologia Computacional, 2021, Universidade de Lisboa, Faculdade de CiênciasBioinformatics aims to analyze and store complex biological datasets, which, due to the multidisciplinarity of the field, can be essential for finding meaning in biological systems, contributing to the modern life sciences knowledge. Transcriptomics is currently one of the areas if bioinformatics in greater expansion, namely through RNA sequencing (RNA-seq), which is an efficient transcriptome profiling approach. Its main application is the analysis of differentially expressed genes (DEGs), to assign biological meaning to specific tissues, environmental conditions, and other aspects. Reproductive strategies, resistance and stress responses can be evaluated through this technique, leading to a better understanding of the species fitness and survival. This thesis intended to detect and functionally annotate DEGs through the application of RNA seq pipelines. Moreover, since there’s still no gold standard for its best practices, this work mostly aimed to find the best suited tools and methods for each data type, such as length, depth and replicates, according to the research goals. Furthermore, it established a better understanding of the different expression profiles of species from three different genera, namely Casuarina, Coffea and Limonium. In general, the RNA-seq workflow was performed as follows: quality analysis, assembly (for non-model species), alignment, quantification, differential expression, and functional annotation. Since this project was developed as four separated analyses, each step and respective tools were evaluated according to each dataset features. The results of these analyses break the path for further studies and integration with other omics, which can help unravel relevant mechanism and pathways of the studied species. During the work of this thesis, a large set of scripts were developed to speed up and automatize the analysis, using Python and R languages, which have been made publicly available and can be applied by other users that work on similar studies.Paulo, Octávio, 1963-Repositório da Universidade de LisboaFernandes, Isabel Cristina Moniz2023-10-30T01:32:01Z202120212021-01-01T00:00:00Zinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/masterThesisapplication/pdfhttp://hdl.handle.net/10451/54267TID:202933202enginfo:eu-repo/semantics/openAccessreponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãoinstacron:RCAAP2023-11-08T17:00:41Zoai:repositorio.ul.pt:10451/54267Portal AgregadorONGhttps://www.rcaap.pt/oai/openaireopendoar:71602024-03-19T22:05:10.595240Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãofalse
dc.title.none.fl_str_mv RNA-Seq for the detection of differential expressed genes under several experimental conditions
title RNA-Seq for the detection of differential expressed genes under several experimental conditions
spellingShingle RNA-Seq for the detection of differential expressed genes under several experimental conditions
Fernandes, Isabel Cristina Moniz
RNA-seq
Casuarina
Coffea
Limonium
transcriptómica
Teses de mestrado - 2021
Departamento de Informática
title_short RNA-Seq for the detection of differential expressed genes under several experimental conditions
title_full RNA-Seq for the detection of differential expressed genes under several experimental conditions
title_fullStr RNA-Seq for the detection of differential expressed genes under several experimental conditions
title_full_unstemmed RNA-Seq for the detection of differential expressed genes under several experimental conditions
title_sort RNA-Seq for the detection of differential expressed genes under several experimental conditions
author Fernandes, Isabel Cristina Moniz
author_facet Fernandes, Isabel Cristina Moniz
author_role author
dc.contributor.none.fl_str_mv Paulo, Octávio, 1963-
Repositório da Universidade de Lisboa
dc.contributor.author.fl_str_mv Fernandes, Isabel Cristina Moniz
dc.subject.por.fl_str_mv RNA-seq
Casuarina
Coffea
Limonium
transcriptómica
Teses de mestrado - 2021
Departamento de Informática
topic RNA-seq
Casuarina
Coffea
Limonium
transcriptómica
Teses de mestrado - 2021
Departamento de Informática
description Tese de mestrado, Bioinformática e Biologia Computacional, 2021, Universidade de Lisboa, Faculdade de Ciências
publishDate 2021
dc.date.none.fl_str_mv 2021
2021
2021-01-01T00:00:00Z
2023-10-30T01:32:01Z
dc.type.status.fl_str_mv info:eu-repo/semantics/publishedVersion
dc.type.driver.fl_str_mv info:eu-repo/semantics/masterThesis
format masterThesis
status_str publishedVersion
dc.identifier.uri.fl_str_mv http://hdl.handle.net/10451/54267
TID:202933202
url http://hdl.handle.net/10451/54267
identifier_str_mv TID:202933202
dc.language.iso.fl_str_mv eng
language eng
dc.rights.driver.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
dc.source.none.fl_str_mv reponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação
instacron:RCAAP
instname_str Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação
instacron_str RCAAP
institution RCAAP
reponame_str Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
collection Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
repository.name.fl_str_mv Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação
repository.mail.fl_str_mv
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