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Table 2 Advantages and disadvantages of different platforms for gene expression profiling

From: Advances in genomics for flatfish aquaculture

Feature

RNA-seq

Microarray

OpenArray®

Dynamic range (order of magnitude)

5

3

7–8

Price

High

Medium

Medium–low

Number of genes

Complete set of RNA families and splicings

Transcriptome. Usually, coding mRNAs and small RNAs

Maximum 56–128 genes per analysis

Probes

Neither design nor previous knowledge of sequences is required

Limitation for number of sequences, design and orientation of probes

Limitation for number of sequences, primers design

Sensitivity

High and low background

Low and high background

Very high and low background

Specificity

Very high

Depends on platform

Very high

Bioinformatics

Under development

Well developed

Very easy

Sample preparation

Complex. Requires specialized skills for cDNA library preparation

Easy

Easy

Time

Weeks

Days

Hours