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Table 2 Cost, Time, and Qualitative Metrics comparison of 3’Pool-seq and TrusSeq, as well as two additional 3′-end sequencing techniques: Plate-Seq and DRUG-seq. (N/A) indicates that values were not readily accessible in the corresponding article. (*) Represents sequencing costs on a HighSeq platform, while others represent costs on a NextSeq platform

From: 3’Pool-seq: an optimized cost-efficient and scalable method of whole-transcriptome gene expression profiling

 

3’Pool-seq

TruSeq

Plate-Seq

DRUG-seq

Library prep cost per sample

$3

$60

$3

$0.2–1

Sequencing cost per sample

$12

$100

$12*

$2–4*

Overall time for library prep

8–12 h

2–3 days

> 2 days

N/A

Hands-on time

2–3 h

6–8 h

N/A

N/A

Samples per Run

96

12–24

96

384–1536

Major

Advantage

No custom equipment or sequencing primers, stringently benchmarked against ERCC and TruSeq.

Best option for detecting low-abundance genes or splice variants.

Oligo-dT Plate-based RNA purification.

Most affordable option, highest throughput, manual alternative is described.

Major Disadvantage

Involves RNA purification step, lowest throughput of three 3′-end techniques described herein.

Most expensive option, low-throughput, technically tedious.

Requires custom liquid dispensing equipment, no detailed benchmarking with ERCC or TruSeq.

Requires custom liquid dispensing equipment, manual protocol not benchmarked.