Table 3.
Comparison of RNA extraction methods used for HTS.
| Paper | Target RNA | Extraction kit/platfo | Type of extraction | DNase | RIN | Best performing extraction method |
|---|---|---|---|---|---|---|
| Aarem et al., 2016 | microRNA (6 generic, 13 specific) | MagMAXTM for Stabilized Blood Tubes RNA Isolation Kit, compatible with TempusTM Blood RNA Tubes manual and semi-manual, Preserved Blood RNA Purification Kit I (for use with Tempus Blood RNA Tubes), TempusTM Spin RNA Isolation Kit,TempusTM 6-Port RNA Isolation Kit | Magnetic bead-based RNA purification system, spin column chromatography | TURBO DNase with MagMAX | 7.88–7.93 average for adult and cord sample | No significant differences |
| Ahmed et al., 2019 | Cetyl trimethylammonium bromide (CTAB) with additional wash steps, potassium acetate, and lithium chloride for precipitation | Organic extraction (CTAB) | 7.3–8.8 | Modified CTAB | ||
| Asai et al., 2015 | tRNA | TRIzolTM Reagent, Qiagen RNeasy Micro Kit, Aurum Total RNA Mini Kit | Organic extraction, Silica Spin Filter Columns, Spin- or vacuum-mediated silica binding | Included in Qiagen and Aurum kits | 3.9–8.9 | Qiagen RNeasy Micro Kit |
| Di et al., 2019† | Highly pathogenic avian influenza (HPAI) H5N1 | 1: MagNA Pure compact RNA isolation-Lysis/Binding buffer (Roche)+ MagNA Pure compact RNA isolation kit [RNA-Tissue-V3-1 protocol (Roche)]. 2: Buffer RLT (QIAgen) containing 1%-mercaptoethanol+ RNeasy mini kit. 3: Buffer AVL (QIAgen) + QIAamp viral RNA mini kit (QIAgen). 4: TRIzol reagent (Invitrogen) + TRIzol/chloroform (Invitrogen). | MagNA Pure Magnetic Glass Particle Technology, Silica Spin Filter Column, Organic extraction | Turbo DNA-free kit (Ambion) | MagNA Pure compact RNA isolation-Lysis/Binding buffer (Roche)+ MagNA Pure compact RNA isolation kit [RNA-Tissue-V3-1 protocol (Roche)]. | |
| Garcia-Nogales et al., 2010* | 16S/23s rRNA | RiboPureTM Bacteria Kit (Ambion), RNeasy Protect Bacteria Mini kit (Qiagen), NucliSENSⓇ miniMAGⓇ (Biomerieux) + mechanical disruption cycle, TRIzolⓇ Max Bacterial (Invitrogen) + mechanical disruption cycle | Organic Extraction +Spin column, Silica-coated magnetic beads (BOOM technology), Organic extraction + mechanical disruption | RNeasy Protect Bacteria Mini kit from QIAGEN | ||
| Guichet et al., 2018 | HIV RNA | NucliSens EasyMag (Biomérieux, Marcy-l'Etoile, France), NucliSens EasyMag + free virus elution method, m2000sp method (Abbott Molecular, IL, USA) | Silica-coated magnetic beads (BOOM technology), Silica-coated magnetic beads (BOOM technology) +FVE | Turbo DNase-free (Ambion by Life Technologies, CA, USA) and HL dsDNase (“Heat and Run” gDNA removal kit, TATAA Biocenter AB, Sweden) | NucliSens EasyMag + free virus elution method | |
| Hedegaard et al., 2014 | QIAsymphony RNA Mini Kit and performed on QiaSymphony robot, Nucleospin FFPE RNA/DNA kit (Machery-Nagel), RecoverAll Total Nucleic Acid Isolation Kit for FFPE (Ambion), purification with: miRNeasy FFPE (QIAGEN), Nucleospin FFPE RNA (Machery-Nagel) and ExpressArt FFPE RNAready (Amp Tec) kits | Silica-coated magnetic beads, silica membrane technology, Spin Column (Glass Fiber Filter) | DNase I and the other was additionally treated with Exonulcease I | miRNeasy FFPE (QIAGEN) and ExpressArt FFPE RNAready (Amp Tec) | ||
| Hjelmsø et al., 2017* | Viral DNA/RNA, MCO RNA | Nucleospin RNA XS, QIAamp Viral RNA Mini Kit, NucliSENSⓇ miniMAGⓇ, or PowerViralⓇ Environmental RNA/DNA Isolation Kit | Spin Column (Glass Fiber Filter), spin column-based RNA purification, Silica-coated magnetic beads (BOOM technology), Silica Spin Filter Columns with chemical lysis | OmniCleave endonuclease (Epicentre, Wisconsin, USA). Further purified by extraction using a 1:1 mixture of chloroform-butanol | Nucleospin RNA XS | |
| Le et al., 2018* | HAV, NoV GI, NoV GII | Nuclisens EasyMag (Biomérieux, Marcy-l'Etoile, France), Trizol (Invitrogen) + Purelink mini RNA kit+CTAB+LiCl precipitation | Silica-coated magnetic beads (BOOM technology), Organic extraction, Organic extraction (CTAB) | Trizol, PureLink RNA Mini Kit, followed by Cetyltrimethylammonium bromide (CTAB) treatment and LiCl precipitation | ||
| Li et al., 2015 | DNA and RNA viruses | QIAamp Viral RNA Mini Kit (Qiagen, Hilden, Germany), Maxwell 16 Viral Total Nucleic Acid Purification Kit (Promega, Madison, WI, USA), and Trizol Reagent (Life Technologies, Grand Island, NY, USA) | Silica Spin Filter Columns, chemical lysis+ Magnetic bead-based RNA purification system, GTPC | Turbo DNase (Ambion, Life Technologies, Grand Island, NY, USA), 3U Baseline-ZERO (Epicentre, Chicago, IL, USA) | QIAamp Viral RNA Mini Kit (Qiagen, Hilden, Germany) | |
| Marston et al., 2013 | Lyssavirus RNA | TRIzol +PEG, RNeasy plus mini kit | Organic extraction, Silica Spin Filter Columns | RNeasy plus mini kit | TRIzol +PEG | |
| Pauly et al., 2019 | HAV, HBV, HCV, HDV, and HEV. | MagNA Pure Compact Nucleic Acid Isolation Kit I, MagNA Pure LC 2.0 Total Nucleic Acid | MagNA Pure Magnetic Glass Particle Technology, magnetic-bead technology | MagNA Pure ure LC 2.0 for ssRNA best | ||
| Isolation Kit, MagNA Pure LC 2.0 Total Nucleic Acid Kit - High Performance, MagNA Pure 96 DNA and | ||||||
| Viral NA Small Volume Kit | ||||||
| Schwochow et al., 2012 | miRNA | RiboPure,RNeasyⓇ, PAXgeneTM, TRIzolⓇ LS,LeukoLOCKTM | Spin column + organic extraction, Silica Spin Filter Columns, organic extraction, Leukocyte Capture Filter+Magnetic Bead | rDNaseI (Ambion) | 4.6–7.7 | LeukoLOCKTM filter system |
| Strubbia et al., 2019a* | norovirus | PEG, PEG +sodium chloride at pH 3, PGM capture+ PEG, NucliSens kit (bioMerieux), Zymo-spin column (RNA Clean & Concentrator, Zymo Research, Irvine, USA) for all | Organic extraction, Silica-coated magnetic beads (BOOM technology), Silica Spin filter column, | Turbo DNAse | PEG samples had longer contigs, no clear optimal extraction process | |
| Strubbia et al., 2019b* | norovirus | PEG, Pyro-PEG, PK-PEG, NucliSens kit (bioMérieux) | PEG+ Silica-coated magnetic beads (BOOM technology), sodium pyrophosphate decahydrate +sonication+PEG+ Silica-coated magnetic beads, Proteinase K lysis +Silica-coated magnetic beads | TURBOTM DNase | Pyro-PEG sewage, PK-PEG shellfish | |
| Sultan et al., 2014 | mRNA | RNeasy preparation method (Qiagen), TRIzol PARIS (Life Technologies) | Silica Spin Filter Columns, Organic extraction | TURBO DNA-freeTM (Life Technologies, #AM1907) | TRIzol | |
| Tavares et al., 2011 | 28s/18s rRNA | TRIzolⓇ Plus RNA Purification System (Invitrogen), E.Z.N.A.TM Total RNA kit II (Omega Bio-Tek), AxyPrep Multisource Total RNA Miniprep, RNeasyⓇ Mini, EasySpin and Illustra RNAspin Mini RNA Isolation | Organic extraction, Silica Spin Filter Columns | TurboTM DNase I (Ambion) | AxyPrep Multisource Total RNA Miniprep kit | |
| Wong et al., 2019 | miRNA | MagnaZol (Bioo Scientific) or miRNeasy (QIAGEN) | Magnetic bead-based RNA purification system, Silica Spin Filter Columns | MagnaZol RNA |
*
Environmental application,
†
Veterinary application.