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Table 3 Library preparation: purification methods

From: Biomarker discovery: quantification of microRNAs and other small non-coding RNAs using next generation sequencing

Method

Specificity

Throughput

Cost ($)

Study size

Novex TBE PAGE gel

High

Low

$$$$$

Small

(manually cutting band; very specific)

(few libraries/day)

 

(2–10 samples)

Pippin Prep Automated gel system

Medium

Low

$$$

Medium

(automated band; less specific)

(4 libraries/run [2 hrs])

 

(10–50 samples)

AMPure XP beads

Low

High

$

Large

(all products >100 nt)

(24 libraries/2 hrs)

 

(50 and up)

  1. Recommendations for small RNA sequencing library purification. Recommendations include: (1) Specificity: based on specificity to a particular small RNA population. (2) Throughput: based on the number of libraries that can be prepared per day and efficiency of processing. This number is relative to the number of people working and instruments available in the lab. (3) Cost: based on price of reagents, hands-on laboratory time, service fees by genome centers. (4) Study Size: based on number of biological or technical replicates