Evidence map›Paper›PMID 30951671›Full record

ArticleCell2019

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

Srimeenakshi Srinivasan, Ashish Yeri, Pike See Cheah, Allen Chung, Kirsty Danielson, Peter De Hoff, Justyna Filant, Clara D Laurent, Lucie D Laurent, Rogan Magee and 24 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Cell, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 195 papers, 2 of them syntheses that pooled it.

0numbers the graph read from it
0cells of the map it votes in
195citing papers in PubMed, 2 pooled it
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

195 citing papers in PubMed, 2 syntheses or guidelines pooled it.

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135 more citing papers are in PubMed but not listed here.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

34 authors.

Srimeenakshi SrinivasanDepartment of Obstetrics, Gynecology, and Reproductive Sciences and Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA, USA.
Ashish YeriCardiovascular Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
Pike See CheahNeurology and Radiology Services and Program in Neuroscience, Harvard Medical School, Massachusetts General Hospital, Boston, MA, USA; Department of Human Anatomy, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Malaysia.
Allen ChungDepartment of Surgery, University of California, San Francisco and VA Medical Center San Francisco, San Francisco, CA 94121, USA.
Kirsty DanielsonCardiovascular Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
Peter De HoffDepartment of Obstetrics, Gynecology, and Reproductive Sciences and Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA, USA.
Justyna FilantDepartment of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
Clara D LaurentDepartment of Obstetrics, Gynecology, and Reproductive Sciences and Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA, USA; Cardiovascular Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
Lucie D LaurentDepartment of Obstetrics, Gynecology, and Reproductive Sciences and Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA, USA.
Rogan MageeComputational Medicine Center, Sidney Kimmel College of Medicine, Thomas Jefferson University, Philadelphia, PA, USA.
Courtney MoellerDepartment of Obstetrics, Gynecology, and Reproductive Sciences and Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA, USA.
Venkatesh L MurthyDepartment of Medicine, Division of Cardiovascular Medicine, Frankel Cardiovascular Center, University of Michigan, Ann Arbor, MI, USA.
Parham NejadDepartment of Neurology, Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
Anu PaulDepartment of Neurology, Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
Isidore RigoutsosComputational Medicine Center, Sidney Kimmel College of Medicine, Thomas Jefferson University, Philadelphia, PA, USA.
Rodosthenis RodosthenousCardiovascular Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
Ravi V ShahCardiovascular Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
Bridget SimonsonCardiovascular Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
Cuong ToDepartment of Obstetrics, Gynecology, and Reproductive Sciences and Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA, USA.
David WongDepartment of Surgery, University of California, San Francisco and VA Medical Center San Francisco, San Francisco, CA 94121, USA.
Irene K YanMayo Clinic Florida, Jacksonville, FL, USA.
Xuan ZhangNeurology and Radiology Services and Program in Neuroscience, Harvard Medical School, Massachusetts General Hospital, Boston, MA, USA.
Leonora BalajNeurology and Radiology Services and Program in Neuroscience, Harvard Medical School, Massachusetts General Hospital, Boston, MA, USA; Department of Neurosurgery, Harvard Medical School, Massachusetts General Hospital, Boston, MA, USA.
Xandra O BreakefieldNeurology and Radiology Services and Program in Neuroscience, Harvard Medical School, Massachusetts General Hospital, Boston, MA, USA.
George DaaboulNanoView Biosciences, Boston, MA, USA.
Roopali GandhiDepartment of Neurology, Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
Jodi LapidusOregon Health Sciences University, Portland, OR, USA.
Eric LondinComputational Medicine Center, Sidney Kimmel College of Medicine, Thomas Jefferson University, Philadelphia, PA, USA.
Tushar PatelMayo Clinic Florida, Jacksonville, FL, USA.
Robert L RaffaiDepartment of Surgery, University of California, San Francisco and VA Medical Center San Francisco, San Francisco, CA 94121, USA.
Anil K SoodDepartment of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; Center for RNA Interference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
Roger P AlexanderPacific Northwest Research Institute, Seattle, WA 98122, USA.
Saumya DasCardiovascular Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
Louise C LaurentDepartment of Obstetrics, Gynecology, and Reproductive Sciences and Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA, USA. Electronic address: llaurent@ucsd.edu.

Funding

The role of microvesicles in giloma virotherapyP01CA069246 · NCI · MASSACHUSETTS GENERAL HOSPITAL · PI BREAKEFIELD, XANDRA OWENS, CHIOCCA, E. ANTONIO · 1996 to 2021
$30.9M
SOC CoreU54DA036134 · NIDA · BAYLOR COLLEGE OF MEDICINE · PI GALAS, DAVID J., GERSTEIN, MARK BENDER · 2013 to 2018
$15.0M
Transfer of microRNA regulators from glioblastoma to brain microenvironment U19CA179563 · NCI · MASSACHUSETTS GENERAL HOSPITAL · PI BREAKEFIELD, XANDRA OWENS, CHAREST, ALAIN · 2013 to 2017
$8.6M
U.T. M. D. Anderson Cancer Center SPORE in Ovarian CancerP50CA217685 · NCI · UNIVERSITY OF TX MD ANDERSON CAN CTR · PI BAST, ROBERT C, SOOD, ANIL K · 2017 to 2021
$7.9M
Transcellular epigenetic regulation by ex-small RNA in C. elegantU19CA179512 · NCI · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI BLELLOCH, ROBERT · 2013 to 2017
$7.4M
The power of extracellular vesicles in glioblastomaR35CA232103 · NCI · MASSACHUSETTS GENERAL HOSPITAL · PI BREAKEFIELD, XANDRA OWENS · 2018 to 2024
$6.9M
Harnessing the power of exosomes for non-coding RNA deliveryR35CA209904 · NCI · UNIVERSITY OF TX MD ANDERSON CAN CTR · PI SOOD, ANIL K · 2017 to 2023
$5.0M
TRAINING IN REPRODUCTIVE SCIENCEST32HD007203 · NICHD · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI PAMELA L MELLON · 1988 to 2026
$4.8M
Reference Profiles of ExRNAs in Normal Human PregnancyU01HL126494 · NHLBI · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI LAURENT, LOUISE CHANG · 2014 to 2018
$3.4M
Plasma miRNA predictors of adverse mechanical and electrical remodeling after MIUH3TR000901 · NCATS · MASSACHUSETTS GENERAL HOSPITAL · PI DAS, SAUMYA, KWONG, RAYMOND Y · 2015 to 2017
$3.2M
Novel extra cellular RNA-based combinatorial RNA inhibition therapyUH3TR000943 · NCATS · UNIVERSITY OF TX MD ANDERSON CAN CTR · PI CALIN, GEORGE A., LOPEZ-BERESTEIN, GABRIEL · 2015 to 2017
$3.2M
Extracellular non-coding RNA biomarkers of hepatocellular cancerUH3TR000884 · NCATS · MAYO CLINIC JACKSONVILLE · PI PATEL, TUSHAR · 2015 to 2017
$3.0M
NCATS NIH HHS UH2 TR000884NCATS NIH HHS UH2 TR000890NCATS NIH HHS UH2 TR000901NCATS NIH HHS UH2 TR000906NCATS NIH HHS UH2 TR000943NCATS NIH HHS UH3 TR000884NCATS NIH HHS UH3 TR000890NCATS NIH HHS UH3 TR000901NCATS NIH HHS UH3 TR000906NCATS NIH HHS UH3 TR000943NCI NIH HHS P01 CA069246NCI NIH HHS P50 CA217685NCI NIH HHS R01 CA217833NCI NIH HHS R35 CA209904NCI NIH HHS R35 CA232103NCI NIH HHS U19 CA179512NCI NIH HHS U19 CA179563NHLBI NIH HHS K23 HL127099NHLBI NIH HHS R01 HL122547NHLBI NIH HHS R01 HL133575NHLBI NIH HHS U01 HL126494NICHD NIH HHS T32 HD007203NIDA NIH HHS U54 DA036134
6 · The paper itself

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.

Indexed as

AdultBody FluidsCell-Free Nucleic AcidsCell LineCirculating MicroRNAExtracellular VesiclesFemaleHealthy VolunteersHumansMaleMicroRNAsReproducibility of ResultsRNASequence Analysis, RNACell-Free Nucleic AcidsCirculating MicroRNAMicroRNAsRNAextracellular RNAextracellular vesicleslipoproteinribonucleoprotein

Identifiers

PMID30951671
PMCPMC6557167

What OpenQuestion holds

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Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.