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Large-scale tag/PCR-based gene expression profiling

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Abstract

An intriguing enigma in molecular biology is how genes within a single genome are differentially expressed in different cell types of a multicellular organism, or in response to different developmental or environmental queues in a single cell type. Quantification of transcript levels on a genome-wide scale, often termed transcript profiling, provides a powerful approach to identifying protein-coding and non-coding RNAs functionally relevant to a given biological process. Indeed, transcriptome analysis has been a key area of biological inquiry for decades and successfully produced discoveries in a multitude of processes and disease states, and in an increasingly large number of organisms. The evolution of technologies with increasing levels of informational content, ranging from hybridization-based technologies such as Northern blot analysis and microarrays to tag/polymerase chain reaction (PCR)- and sequence-based technologies including differential display and SAGE, along with the next-generation sequencing, has provided hope for revealing the molecular details of biological systems as they respond to change. This review is an overview of selected high throughput tag/PCR-based methods for genome-wide expression profiling amenable to high-throughput automated operation in any standard laboratory.

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Abbreviations

DD-PCR:

Differential display polymerase chain reaction

RAP-PCR:

RNA fingerprinting by arbitrarily primed-PCR

RC4D:

Restriction fragment length polymorphism-coupled domain directed differential display

ODD:

Ordered differential display

RFDD:

Restriction fragment differential display

PACS:

Preferential amplification of coding sequences

AFLP:

Amplified fragment length polymorphism

iAFLP:

Introduced amplified fragment length polymorphism

IBDD:

Indexing-based differential display

HiCEP:

High coverage expression profiling

dCSTs:

Differentially expressed coding sequence tags

DRSP:

Double restriction site primers

SMB:

Streptavidin magnetic bead

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  1. Department of Cell and Molecular Biology, Faculty of Biological Sciences, Kharazmi University, Tehran, Islamic Republic of Iran

    Saeed Irian

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Irian, S. Large-scale tag/PCR-based gene expression profiling. World J Microbiol Biotechnol 30, 2125–2139 (2014). https://doi.org/10.1007/s11274-014-1641-0

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  • DOI: https://doi.org/10.1007/s11274-014-1641-0

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