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

BMC Medical Genomics

Table 3 Library preparation: purification methods

Method	Specificity	Throughput	Cost ($)	Study size
Novex TBE PAGE gel	High	Low	$$$$$	Small
Novex TBE PAGE gel	(manually cutting band; very specific)	(few libraries/day)		(2–10 samples)
Pippin Prep Automated gel system	Medium	Low	$$$	Medium
Pippin Prep Automated gel system	(automated band; less specific)	(4 libraries/run [2 hrs])		(10–50 samples)
AMPure XP beads	Low	High	$	Large
AMPure XP beads	(all products >100 nt)	(24 libraries/2 hrs)		(50 and up)

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

ISSN: 1755-8794