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Small RNA Sequencing across Diverse Biofluids Identifies Optimal Methods for exRNA Isolation.

  • Author(s): Srinivasan, Srimeenakshi
  • Yeri, Ashish
  • Cheah, Pike See
  • Chung, Allen
  • Danielson, Kirsty
  • De Hoff, Peter
  • Filant, Justyna
  • Laurent, Clara D
  • Laurent, Lucie D
  • Magee, Rogan
  • Moeller, Courtney
  • Murthy, Venkatesh L
  • Nejad, Parham
  • Paul, Anu
  • Rigoutsos, Isidore
  • Rodosthenous, Rodosthenis
  • Shah, Ravi V
  • Simonson, Bridget
  • To, Cuong
  • Wong, David
  • Yan, Irene K
  • Zhang, Xuan
  • Balaj, Leonora
  • Breakefield, Xandra O
  • Daaboul, George
  • Gandhi, Roopali
  • Lapidus, Jodi
  • Londin, Eric
  • Patel, Tushar
  • Raffai, Robert L
  • Sood, Anil K
  • Alexander, Roger P
  • Das, Saumya
  • Laurent, Louise C
  • et al.
Abstract

Poor reproducibility within and across studies arising from lack of knowledge regarding the performance of extracellular RNA (exRNA) isolation methods has hindered progress in the exRNA field. A systematic comparison of 10 exRNA isolation methods across 5 biofluids revealed marked differences in the complexity and reproducibility of the resulting small RNA-seq profiles. The relative efficiency with which each method accessed different exRNA carrier subclasses was determined by estimating the proportions of extracellular vesicle (EV)-, ribonucleoprotein (RNP)-, and high-density lipoprotein (HDL)-specific miRNA signatures in each profile. An interactive web-based application (miRDaR) was developed to help investigators select the optimal exRNA isolation method for their studies. miRDar provides comparative statistics for all expressed miRNAs or a selected subset of miRNAs in the desired biofluid for each exRNA isolation method and returns a ranked list of exRNA isolation methods prioritized by complexity, expression level, and reproducibility. These results will improve reproducibility and stimulate further progress in exRNA biomarker development.

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