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The Impact of RNA Extraction Method on Ribosomal-depleted RNA Sequencing (RNA-Seq) Experiments in a Translational Setting

ABSTRACT: Background Ribosome depleted RNA-seq is well suited for understanding coding- and noncoding transcript expression in clinical samples with diverse input RNA quality and mass. Current choices for RNA extraction include phase-separation (e.g., ThermoFisher TRIzol) approaches to column-based (e.g., Norgen Spin Columns) approaches. Each method, however, has been noted to have differing effects on the properties of the extracted nucleic acids, precluding the straightforward bioinformatic comparison of data generated by the two methods. Methods In this study, we present differences in data differing only in total RNA extraction approaches (phase separation vs. column) from clinical samples processed by the same tissue bank and sequencing facility personnel. We use data from seven samples with libraries generated from RNA extracted with both extraction methods to characterize the effect of ‘differentially extracted’ genes (DExGs) on transcriptomic profiles. We then use another set of 148 samples extracted with one or the other method to confirm the differences observed in the 7-sample dataset. Results The large number of samples employed in this study allows us to find significant differences in important quality control parameters as well as many DExGs between the two methods. We identify several biophysical properties which are potential drivers of these differences. Conclusions We show that partial correction of extraction method mediated differences can be achieved but full correction is not possible. These results lay the foundation for principled decision making of RNA extraction methods for use in clinical samples in a translational environment, particularly in light of recent reagent shortages during the COVID-19 pandemic.

ORGANISM(S): Homo sapiens

PROVIDER: GSE158705 | GEO | 2023/09/28

REPOSITORIES: GEO

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Project description:This a model from the article: Critical study of and improvements in chromatographic methods for the analysis of type B trichothecenes. Mateo JJ, Llorens A, Mateo R, Jimenez M. J Chromatogr A 2001 May 18;918(1):99-112 11403460 , Abstract: Various analytical methods used in the analysis of type B trichothecenes (deoxynivalenol, nivalenol, 3- and 15-acetyldeoxynivalenol) in cereals were compared and optimised in this work. These methods use either GC-electron-capture detection (ECD) of trimethylsilyl, trifluoroacetyl and heptafluorobutyryl derivatives or HPLC with UV or photodiode array detection of analytes. A new HPLC procedure using fluorescence detection prior derivatisation with coumarin-3-carbonyl chloride has been also tested. Five extraction solvents and two solid-phase extraction cartridges (silica, Florisil) plus a especial clean-up column (MycoSep 225) were compared in order to obtain the best recovery of the mycotoxins with minimal presence of coextractives in the chromatograms. The chosen extraction solvent was a mixture of acetonitrile-water (84:16, v/v). The MycoSep 225 column was chosen as the best alternative for clean-up of grain samples. For GC-ECD analysis, derivatisation of analytes with heptafluorobutyric anhydride prior the final determination was chosen as the most suitable procedure. HPLC-photodiode array (at 221 nm) analysis was more suitable for determination of type B trichothecenes than HPLC of the fluorescent coumarin-3-carbonyl derivatives. Recoveries obtained in spiked corn, rice and wheat are reported. The utility of the proposed methodology was assayed in cereal cultures of various Fusarium strains. This model was taken from the CellML repository and automatically converted to SBML. The original model was: Mateo JJ, Llorens A, Mateo R, Jimenez M. (2001) - version=1.0 The original CellML model was created by: Catherine Lloyd c.lloyd@auckland.ac.nz The University of Auckland This model originates from BioModels Database: A Database of Annotated Published Models (http://www.ebi.ac.uk/biomodels/). It is copyright (c) 2005-2011 The BioModels.net Team. To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication for more information. In summary, you are entitled to use this encoded model in absolutely any manner you deem suitable, verbatim, or with modification, alone or embedded it in a larger context, redistribute it, commercially or not, in a restricted way or not.. To cite BioModels Database, please use: Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V, Li L, He E, Henry A, Stefan MI, Snoep JL, Hucka M, Le Novère N, Laibe C (2010) BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol., 4:92.

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The Impact of RNA Extraction Method on Ribosomal-depleted RNA Sequencing (RNA-Seq) Experiments in a Translational Setting

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