Optimizing of pre-processing analysis for Illumina RNA-Seq data
in Arabidopsis thaliana

D 2024

Optimizing of pre-processing analysis for Illumina RNA-Seq data in Arabidopsis thaliana

SCHWARZEROVÁ, Jana; Patrícia JANIGOVÁ; Martina DVOŘÁČKOVÁ a Wolfram WECKWERTH

Základní údaje

Originální název

Optimizing of pre-processing analysis for Illumina RNA-Seq data in Arabidopsis thaliana

Autoři

SCHWARZEROVÁ, Jana; Patrícia JANIGOVÁ; Martina DVOŘÁČKOVÁ a Wolfram WECKWERTH

Vydání

2024. vyd. Brno, Proceedings II of the Conference Student EEICT, od s. 142 - 145, 4 s. 2024

Nakladatel

Brno University of Technology

Další údaje

Jazyk

angličtina

Typ výsledku

Stať ve sborníku

Obor

10611 Plant sciences, botany

Stát vydavatele

Česká republika

Utajení

není předmětem státního či obchodního tajemství

Forma vydání

tištěná verze "print"

Označené pro přenos do RIV

Ano

Organizační jednotka

Středoevropský technologický institut

ISSN

DOI

https://doi.org/10.13164/eeict.2024.142

EID Scopus

2-s2.0-85210249350

Klíčová slova anglicky

Arabidopsis thaliana; Gene expression analysis; Quality control; Transcriptomics

Štítky

rivok

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 26. 3. 2026 23:42, Mgr. Eva Dubská

Anotace

V originále

Gene expression analysis through RNA sequencing (RNA-Seq) has revolutionized molecular biology, providing profound insights into the intricate transcriptional landscapes of organisms. Arabidopsis thaliana, a widely studied model plant, serves as a cornerstone for investigating fundamental biological and ecology processes. However, accurate interpretation of RNASeq data hinges on meticulous pre-processing methods to ensure data integrity and trustworthiness, especially in the context of Illumina sequencing. In this research, we present a comprehensive framework for optimizing pre-processing analysis tailored specifically for Arabidopsis thaliana RNA-Seq datasets generated through Illumina sequencing. Our approach encompasses rigorous quality control, precise read alignment, transcript quantification, and normalization procedures crucial for subsequent differential expression analysis. Additionally, we address unique considerations and challenges inherent to Arabidopsis thaliana datasets, providing valuable insights for researchers in the field.

Návaznosti

LM2015043, projekt VaV

Název: Česká infrastruktura pro integrativní strukturní biologii (Akronym: CIISB)

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, Czech Infrastructure for Integrative Structural Biology

LM2015085, projekt VaV

Název: CERIT Scientific Cloud (Akronym: CERIT-SC)

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, CERIT Scientific Cloud

Citovat

SCHWARZEROVÁ, Jana; Patrícia JANIGOVÁ; Martina DVOŘÁČKOVÁ a Wolfram WECKWERTH. Optimizing of pre-processing analysis for Illumina RNA-Seq data in Arabidopsis thaliana. In Novák V. Proceedings II of the Conference Student EEICT. 2024. vyd. Brno: Brno University of Technology, 2024, s. 142 - 145. ISSN 2788-1334. Dostupné z: https://doi.org/10.13164/eeict.2024.142.

@inproceedings{2563178,
   author = {Schwarzerová, Jana and Janigová, Patrícia and Dvořáčková, Martina and Weckwerth, Wolfram},
   address = {Brno},
   booktitle = {Proceedings II of the Conference Student EEICT},
   doi = {https://doi.org/10.13164/eeict.2024.142},
   edition = {2024},
   editor = {Novák V.},
   keywords = {Arabidopsis thaliana; Gene expression analysis; Quality control; Transcriptomics},
   howpublished = {tištěná verze "print"},
   language = {eng},
   location = {Brno},
   pages = {142 - 145},
   publisher = {Brno University of Technology},
   title = {Optimizing of pre-processing analysis for Illumina RNA-Seq data in Arabidopsis thaliana},
   year = {2024}
}

TY  - CONF
ID  - 2563178
AU  - Schwarzerová, Jana - Janigová, Patrícia - Dvořáčková, Martina - Weckwerth, Wolfram
PY  - 2024
TI  - Optimizing of pre-processing analysis for Illumina RNA-Seq data in Arabidopsis thaliana
PB  - Brno University of Technology
CY  - Brno
KW  - Arabidopsis thaliana
KW  - Gene expression analysis
KW  - Quality control
KW  - Transcriptomics
N2  - Gene expression analysis through RNA sequencing (RNA-Seq) has revolutionized molecular biology, providing profound insights into the intricate transcriptional landscapes of organisms. Arabidopsis thaliana, a widely studied model plant, serves as a cornerstone for investigating fundamental biological and ecology processes. However, accurate interpretation of RNASeq data hinges on meticulous pre-processing methods to ensure data integrity and trustworthiness, especially in the context of Illumina sequencing. In this research, we present a comprehensive framework for optimizing pre-processing analysis tailored specifically for Arabidopsis thaliana RNA-Seq datasets generated through Illumina sequencing. Our approach encompasses rigorous quality control, precise read alignment, transcript quantification, and normalization procedures crucial for subsequent differential expression analysis. Additionally, we address unique considerations and challenges inherent to Arabidopsis thaliana datasets, providing valuable insights for researchers in the field.
ER  -

SCHWARZEROVÁ, Jana; Patrícia JANIGOVÁ; Martina DVOŘÁČKOVÁ a Wolfram WECKWERTH. Optimizing of pre-processing analysis for Illumina RNA-Seq data in Arabidopsis thaliana. In Novák V. \textit{Proceedings II of the Conference Student EEICT}. 2024. vyd. Brno: Brno University of Technology, 2024, s.~142 - 145. ISSN~2788-1334. Dostupné z: https://doi.org/10.13164/eeict.2024.142.

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