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Related Concept Videos

RNA-seq03:21

RNA-seq

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 microarray-based...
Ribosome Profiling02:24

Ribosome Profiling

Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
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DNA Microarrays02:34

DNA Microarrays

Microarrays are high-throughput and relatively inexpensive assays that can be automated to analyze large quantities of data at a time. They are used in genome-wide studies to compare gene or protein expression under two varied conditions, such as healthy and diseased states. Microarrays consist of glass or silica slides on which probe molecules are covalently attached through surface functionalization. Most commonly, the slides are prepared through the chemisorption of silanes to silica...

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Gene Expression Profiling of Infecting Microbes Using a Digital Bar-coding Platform
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Published on: January 13, 2016

Identifying reference genes with stable expression from high throughput sequence data.

Harriet Alexander1, Bethany D Jenkins, Tatiana A Rynearson

  • 1MIT-WHOI Joint Program in Oceanography/Applied Ocean Science and Engineering Cambridge, MA, USA ; Biology Department, Woods Hole Oceanographic Institution Woods Hole, MA, USA.

Frontiers in Microbiology
|November 20, 2012
PubMed
Summary
This summary is machine-generated.

Identifying stable reference genes in diatoms is crucial for accurate gene expression studies. This research identified actin and ubiquitin ligase as potential reference genes in Thalassiosira pseudonana using transcriptome data and a novel analysis method.

Keywords:
RT-qPCRThalassiosira pseudonanadiatomhousekeeping genesphytoplanktonreference generelative gene expressiontranscriptome

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A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq
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A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq

Published on: May 28, 2021

Area of Science:

  • Marine biology
  • Molecular biology
  • Genomics

Background:

  • Accurate gene expression quantification, especially via quantitative reverse transcriptase polymerase chain reaction (RT-qPCR), relies on stably expressed reference genes.
  • Identifying suitable reference genes in non-model organisms like diatoms is challenging, often necessitating reliance on data from distantly related species.

Purpose of the Study:

  • To identify reliable reference genes for gene expression studies in the diatom Thalassiosira pseudonana.
  • To evaluate the efficacy of different analytical methods for reference gene discovery in transcriptomic data.

Main Methods:

  • Analysis of transcriptome datasets from T. pseudonana under various nutrient conditions.
  • Literature-based searches for homologous reference genes.
  • Application of k-means clustering and Analysis of Sequence Counts (ASC) to identify stably expressed genes.

Main Results:

  • ASC analysis identified 179 stably expressed genes, including known stable genes like actin.
  • ASC proved more robust than k-means clustering in identifying stable genes, even without biological replicates.
  • Actin and ubiquitin ligase were highlighted as promising reference genes for T. pseudonana.

Conclusions:

  • The Analysis of Sequence Counts (ASC) method is effective for identifying stable reference genes in diatom transcriptomes.
  • Actin and ubiquitin ligase are proposed as suitable reference genes for Thalassiosira pseudonana and potentially other diatoms.
  • The availability of transcriptome data facilitates the application of ASC for reference gene discovery in diverse phytoplankton species.