---
OA_type: closed access
_id: '20870'
abstract:
- lang: eng
  text: RNA sequencing (RNA-seq) methodologies have evolved rapidly, offering powerful
    tools to study gene expression, transcriptome dynamics, and molecular mechanisms
    in various biological contexts. However, the complexity of these approaches poses
    challenges in data interpretation, sensitivity, and applicability. This chapter
    provides a comprehensive overview of RNA-seq methodologies, highlighting their
    advantages, limitations, and applications, particularly in cardiovascular research.
    Bulk RNA sequencing enables high-throughput gene expression profiling but lacks
    the resolution to capture cellular heterogeneity and spatial context. Direct RNA
    sequencing preserves native RNA modifications, offering insights into post-transcriptional
    regulation, though it remains technically challenging. Single-cell RNA sequencing
    (scRNA-seq) and spatial transcriptomics (ST) bridge these gaps by resolving transcriptomic
    complexity at the cellular level and within tissue architecture, providing crucial
    insights into disease mechanisms such as atherosclerosis. By summarizing the strengths
    and limitations of these methodologies, this chapter aims to guide researchers
    in selecting the most suitable transcriptomic approach for their studies, ultimately
    advancing precision medicine and biomarker discovery in cardiovascular disease.
article_processing_charge: No
author:
- first_name: Victoria
  full_name: Stopa, Victoria
  last_name: Stopa
- first_name: Miron
  full_name: Sopić, Miron
  last_name: Sopić
- first_name: Guanliang
  full_name: Li, Guanliang
  last_name: Li
- first_name: Judith
  full_name: Sluimer, Judith
  last_name: Sluimer
- first_name: José
  full_name: Basílio, José
  last_name: Basílio
- first_name: Sander W.
  full_name: van der Laan, Sander W.
  last_name: van der Laan
- first_name: David P.
  full_name: Kreil, David P.
  last_name: Kreil
- first_name: Yvan
  full_name: Devaux, Yvan
  last_name: Devaux
- first_name: Bernhard
  full_name: Hochreiter, Bernhard
  id: e6cab3de-17f6-11ed-9210-c1e42e045e9d
  last_name: Hochreiter
citation:
  ama: 'Stopa V, Sopić M, Li G, et al. Essentials of transcriptomic methods: Navigating
    through RNA sequencing and beyond. In: Devaux Y, Sopic M, eds. <i>Transcriptomics
    in Atherosclerosis</i>. Elsevier; 2025:131-172. doi:<a href="https://doi.org/10.1016/b978-0-443-33064-3.00016-5">10.1016/b978-0-443-33064-3.00016-5</a>'
  apa: 'Stopa, V., Sopić, M., Li, G., Sluimer, J., Basílio, J., van der Laan, S. W.,
    … Hochreiter, B. (2025). Essentials of transcriptomic methods: Navigating through
    RNA sequencing and beyond. In Y. Devaux &#38; M. Sopic (Eds.), <i>Transcriptomics
    in Atherosclerosis</i> (pp. 131–172). Elsevier. <a href="https://doi.org/10.1016/b978-0-443-33064-3.00016-5">https://doi.org/10.1016/b978-0-443-33064-3.00016-5</a>'
  chicago: 'Stopa, Victoria, Miron Sopić, Guanliang Li, Judith Sluimer, José Basílio,
    Sander W. van der Laan, David P. Kreil, Yvan Devaux, and Bernhard Hochreiter.
    “Essentials of Transcriptomic Methods: Navigating through RNA Sequencing and Beyond.”
    In <i>Transcriptomics in Atherosclerosis</i>, edited by Yvan Devaux and Miron
    Sopic, 131–72. Elsevier, 2025. <a href="https://doi.org/10.1016/b978-0-443-33064-3.00016-5">https://doi.org/10.1016/b978-0-443-33064-3.00016-5</a>.'
  ieee: 'V. Stopa <i>et al.</i>, “Essentials of transcriptomic methods: Navigating
    through RNA sequencing and beyond,” in <i>Transcriptomics in Atherosclerosis</i>,
    Y. Devaux and M. Sopic, Eds. Elsevier, 2025, pp. 131–172.'
  ista: 'Stopa V, Sopić M, Li G, Sluimer J, Basílio J, van der Laan SW, Kreil DP,
    Devaux Y, Hochreiter B. 2025.Essentials of transcriptomic methods: Navigating
    through RNA sequencing and beyond. In: Transcriptomics in Atherosclerosis. , 131–172.'
  mla: 'Stopa, Victoria, et al. “Essentials of Transcriptomic Methods: Navigating
    through RNA Sequencing and Beyond.” <i>Transcriptomics in Atherosclerosis</i>,
    edited by Yvan Devaux and Miron Sopic, Elsevier, 2025, pp. 131–72, doi:<a href="https://doi.org/10.1016/b978-0-443-33064-3.00016-5">10.1016/b978-0-443-33064-3.00016-5</a>.'
  short: V. Stopa, M. Sopić, G. Li, J. Sluimer, J. Basílio, S.W. van der Laan, D.P.
    Kreil, Y. Devaux, B. Hochreiter, in:, Y. Devaux, M. Sopic (Eds.), Transcriptomics
    in Atherosclerosis, Elsevier, 2025, pp. 131–172.
date_created: 2025-12-29T12:16:22Z
date_published: 2025-10-24T00:00:00Z
date_updated: 2026-01-05T11:49:54Z
day: '24'
department:
- _id: Bio
doi: 10.1016/b978-0-443-33064-3.00016-5
editor:
- first_name: Yvan
  full_name: Devaux, Yvan
  last_name: Devaux
- first_name: Miron
  full_name: Sopic, Miron
  last_name: Sopic
fulldoi: https://doi.org/10.1016/b978-0-443-33064-3.00016-5
language:
- iso: eng
month: '10'
oa_version: None
page: 131-172
publication: Transcriptomics in Atherosclerosis
publication_identifier:
  isbn:
  - '9780443330643'
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Essentials of transcriptomic methods: Navigating through RNA sequencing and
  beyond'
type: book_chapter
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2025'
...