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Related Concept Videos

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.
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MicroRNA (miRNA) are short, regulatory RNA transcribed from introns (non-coding regions of a gene) or intergenic regions (stretches of DNA present between genes). Several processing steps are required to form biologically active, mature miRNA. The initial transcript, called primary miRNA (pri-mRNA), base-pairs with itself, forming a stem-loop structure. Within the nucleus, an endonuclease enzyme, called Drosha, shortens the stem-loop structure into hairpin-shaped pre-miRNA. After the pre-miRNA...
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MicroRNA (miRNA) are short, regulatory RNA transcribed from introns—non-coding regions of a gene—or intergenic regions—stretches of DNA present between genes. Several processing steps are required to form biologically active, mature miRNA. The initial transcript, called primary miRNA (pri-mRNA), base-pairs with itself forming a stem-loop structure. Within the nucleus, an endonuclease enzyme, called Drosha, shortens the stem-loop structure into hairpin-shaped pre-miRNA. After the pre-miRNA ends...
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Profiling of Estrogen-regulated MicroRNAs in Breast Cancer Cells
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Profiling of Estrogen-regulated MicroRNAs in Breast Cancer Cells

Published on: February 21, 2014

Expression profiling of microRNAs by deep sequencing.

Chad J Creighton1, Jeffrey G Reid, Preethi H Gunaratne

  • 1Dan L. Duncan Cancer Center Division of Biostatistics, Baylor College of Medicine, Houston, TX 77030, USA. creighto@bcm.edu

Briefings in Bioinformatics
|April 1, 2009
PubMed
Summary
This summary is machine-generated.

Deep sequencing enables comprehensive microRNA profiling, identifying novel microRNAs and their absolute abundance. Integrating this data with gene expression aids in validating microRNA:mRNA interactions.

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Last Updated: Jun 24, 2026

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High Throughput MicroRNA Profiling: Optimized Multiplex qRT-PCR at Nanoliter Scale on the Fluidigm Dynamic ArrayTM IFCs
07:27

High Throughput MicroRNA Profiling: Optimized Multiplex qRT-PCR at Nanoliter Scale on the Fluidigm Dynamic ArrayTM IFCs

Published on: August 3, 2011

Area of Science:

  • Molecular Biology
  • Genomics
  • Bioinformatics

Background:

  • MicroRNAs (miRNAs) are crucial regulators of gene expression, impacting mRNA stability and translation.
  • miRNA profiling experiments using microarrays or deep sequencing have revealed tissue-specific, developmental, and disease-associated expression patterns.
  • Deep sequencing offers high-throughput analysis, generating millions of small RNA reads for comprehensive miRNA profiling.

Purpose of the Study:

  • To discuss tools and methodologies for analyzing microRNA expression data obtained from deep sequencing.
  • To highlight the advantages of deep sequencing for absolute miRNA abundance measurement and novel miRNA discovery.
  • To explain the integration of miRNA and gene expression data for identifying functional miRNA:mRNA pairs.

Main Methods:

  • Utilizing deep sequencing for massively parallel sequencing of small RNA samples.
  • Applying bioinformatics tools for the analysis of large-scale miRNA sequence reads.
  • Integrating miRNA expression profiles with gene expression data for target validation.

Main Results:

  • Deep sequencing provides accurate absolute quantification of miRNA abundance.
  • This technology facilitates the discovery of previously uncharacterized microRNAs.
  • Integration strategies enable the identification of high-confidence miRNA:mRNA functional relationships.

Conclusions:

  • Deep sequencing is a powerful approach for in-depth microRNA profiling and discovery.
  • Computational analysis and data integration are essential for interpreting miRNA expression data.
  • Understanding miRNA function through expression profiling aids in elucidating biological processes and disease mechanisms.