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Related Concept Videos

RNA Interference01:23

RNA Interference

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RNA interference (RNAi) is a process in which a small non-coding RNA molecule blocks the post-transcriptional expression of a gene by binding to its messenger RNA (mRNA) and preventing the protein from being translated.
This process occurs naturally in cells, often through the activity of genomically-encoded microRNAs. Researchers can take advantage of this mechanism by introducing synthetic RNAs to deactivate specific genes for research or therapeutic purposes. For example, RNAi could be used...
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RNA-seq03:21

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RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
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Ribosomal RNA Synthesis02:53

Ribosomal RNA Synthesis

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Ribosome synthesis is a highly complex and coordinated process involving more than 200 assembly factors. The synthesis and processing of ribosomal components occurs not only in the nucleolus but also in the nucleoplasm and the cytoplasm of eukaryotic cells.
Ribosome biogenesis begins with the synthesis of 5S and 45S pre-rRNAs by distinct RNA polymerases. The primary transcripts are extensively processed and modified before they are bound and folded by ribosomal proteins and assembly factors,...
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siRNA - Small Interfering RNAs02:30

siRNA - Small Interfering RNAs

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Small interfering RNAs, or siRNAs, are short regulatory RNA molecules that can silence genes post-transcriptionally, as well as the transcriptional level in some cases. siRNAs are important for protecting cells against viral infections and silencing transposable genetic elements.
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Nucleic Acids02:43

Nucleic Acids

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Nucleic acids are the most important macromolecules for the continuity of life. They carry the cell's genetic blueprint and carry instructions for its functioning.
DNA and RNA
The two main types of nucleic acids are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). DNA is the genetic material in all living organisms, ranging from single-celled bacteria to multicellular mammals. It is in the nucleus of eukaryotes and in the organelles, chloroplasts, and mitochondria. In prokaryotes,...
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Nucleic acids02:43

Nucleic acids

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Nucleic acids are the most important macromolecules for the continuity of life. They carry the cell's genetic blueprint and carry instructions for its functioning.
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Updated: Mar 20, 2026

MS2-Affinity Purification Coupled with RNA Sequencing in Gram-Positive Bacteria
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SePIA: RNA and small RNA sequence processing, integration, and analysis.

Katherine Icay1, Ping Chen1, Alejandra Cervera1

  • 1Research Programs Unit, Genome-Scale Biology, Medicum and Department of Biochemistry and Developmental Biology, Faculty of Medicine, University of Helsinki, POB 63, Helsinki, 00014 Finland.

Biodata Mining
|May 24, 2016
PubMed
Summary
This summary is machine-generated.

SePIA is a new open-source workflow for standardizing the processing and analysis of RNA and small RNA sequencing data. This computational tool simplifies complex experiments and integrates diverse datasets for comprehensive biological insights.

Keywords:
Breast cancerIntegrationRNASequencingmiRNAtotalRNA

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Large-scale sequencing experiments generate complex data requiring specialized computational tools.
  • Integrating small RNA and complementary RNA data analysis presents significant challenges.
  • A standardized, easy-to-implement computational workflow is needed for efficient RNA sequencing data processing.

Purpose of the Study:

  • To develop a comprehensive computational workflow for processing and analyzing both small RNA and RNA sequencing data.
  • To provide a standardized and integrated approach for complex sequencing projects.
  • To enhance the ease of implementation and analysis of RNA sequencing data.

Main Methods:

  • Development of SePIA (Sequence Processing, Integration, and Analysis) workflow.
  • Integration of over 20 common RNA-seq tools within a workflow engine.
  • Implementation using Docker for portability and ease of execution.
  • Demonstration of utility through case studies with breast cancer datasets.

Main Results:

  • SePIA offers a comprehensive workflow for small RNA and RNA data analysis.
  • The workflow supports individual and integrated analysis of diverse RNA sequencing data types.
  • SePIA is portable, easy to configure, and generates organized HTML reports.
  • The system efficiently manages computational resources for optimal performance.

Conclusions:

  • SePIA provides an open-source solution for standardized RNA and small RNA data processing and analysis.
  • Its modular design allows for robust customization while maintaining workflow integrity.
  • The workflow simplifies complex sequencing experiments and facilitates integrated data interpretation.