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Review of siRNA/shRNA Applications in Cell-Based Microarrays

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Book cover Cell-Based Microarrays

Part of the book series: SpringerBriefs in Cell Biology ((SBCB))

Abstract

This chapter reviews the development and the application of siRNA cell-based microarrays. Starting from reverse transfection as a common ground, siRNA cell-based microarrays quickly evolved into assays of very different formats, and now range from arrays containing chemically synthesized siRNA to viral arrays encoding short hairpin RNA (shRNA), which gives rise to siRNA upon cell transduction. They encompass arrays printed onto microscopic slides as well as arrays in 384-well plates, with microwell chips as a speciality format in between. In order to reflect this variety of technical and biological solutions, representatives of each format are discussed, highlighting the particular features and the steps taken towards optimization of the siRNA/shRNA transfer efficiency. The chapter concludes with a brief discussion of the general limitations of this technology.

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Abbreviations

APS:

Aminopropylsilane

CDK2:

Cyclin-dependent kinase 2

cDNA:

Complementary DNA

dsDNA:

Double-stranded DNA

ECM:

Extracellular matrix

eGFP:

Enhanced green fluorescent protein

GAPDH:

Glyceraldehyde-3-phosphate dehydrogenase

GFP:

Green fluorescent protein

hCAR:

Human coxsackievirus and adenovirus receptor

hMSCs:

Human mesenchymal stem cells

HUVEC:

Human umbilical vein endothelial cells

INCENP:

Inner centromere protein

MAP2:

Microtubule-associated protein 2

mCAT-1:

Murine cationic amino acid receptor 1

MOI:

Multiplicity of infection

MoMuLV:

Moloney’s murine leukemia virus

MSCV:

Murine stem cell virus

mTOR:

Mammalian target of Rapamycin

MVP:

Major vault protein

nts:

Nucleotides

PKR:

Protein kinase R

PLK1:

Polo-like kinase 1

PLL:

Poly-l-lysine

RFP:

Red fluorescent protein

RNAi:

RNA interference

shRNA:

Short hairpin RNA

siRNA:

Small interfering RNA

TUNEL:

Terminal deoxynucleotidyl transferase dUTP nick end labelling

VSV-G:

Vesicular stomatitis virus glycoprotein

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  1. The Natural and Medical Sciences Institute (NMI), University of Tübingen, Reutlingen, Germany

    Frank Weise

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© 2014 Ella Palmer

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Weise, F. (2014). Review of siRNA/shRNA Applications in Cell-Based Microarrays. In: Cell-Based Microarrays. SpringerBriefs in Cell Biology. Springer, New York, NY. https://doi.org/10.1007/978-1-4939-0594-2_2

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