Table 1 Comparison of traditional and new microarray platforms with sequencing approaches

3′ RNA sequencing

Lexogen QuantSeq

RNA → RT, oligodT priming from 3′ end, random priming towards 3′ end → amplification and barcoding → sequencing

96 samples per 5 days

10 M

500

90

N/A

QiaSeq UPX 3′ Transcriptome

RNA → RT, oligodT priming for cDNA synthesis →template switching for 2nd strand synthesis priming → fragmentation → end repair addition, adapter ligation → PCR to add indices → sequencing

96 samples per 5 days

15 M

10

50

N/A

Specific Targeted Sequencing

BioSpyder TempO-Seq

RNA → annealed 50 bp detector oligos are ligated then amplified and barcoded → sequencing

192 samples per 4 days

12 M

20 μm FFPE Section

160

N/A

Ion Ampliseq Transcriptome

RNA → RT, multiplex PCR → sequence barcoding → emulsion PCR → sequencing of ~ 150 bp targets

96 samples per 5 days

8 M

10

160

100% (108)

Targeted Probes

Nanostring

RNA → hybridisation to fluorescent barcoded probes in solution → immobilised in nCounter cartridge → scan

12 samples per day (800 genes)

N/A

50

250

N/A

Newer Microarray

Affymetrix Clariom S

RNA → cRNA amplification → hybridisation to GeneChip → scan

192 samples per 4 days

N/A

50

100

100% (3)

Traditional Microarray

Affymetrix U133A

192 per day

N/A

50

360

100% (178)

Illumina BeadChip HT-12 v3 / v4

RNA → RT, amplification, biotinylation (NuGEN WT Ovation kit) → hybridisation to 50 bp probes on chip → scan

96 samples per 1.5 days

N/A

1500

195

91% (348)

Full RNA Sequencing

RNA-seq

RNA → fragmentation → RT → barcoded library construction → genome-wide full RNA sequencing

8 samples per 5 days

136 M paired reads

2000

250–500

100% (52)