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Difference between revisions of "Yepez 2018 PLOS One"

From Bioblast
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::::* Interval 3: ET (Uncoupler) - take the maximum
::::* Interval 3: ET (Uncoupler) - take the maximum
::::* Interval 4: Rbl (Rot&Ama) - take the minimum
::::* Interval 4: Rbl (Rot&Ama) - take the minimum


== Cited by ==
== Cited by ==
{{Template:Cited by Iglesias-Gonzalez 2021 MitoFit PT}}
{{Template:Cited by Iglesias-Gonzalez 2021 MitoFit PT}}
== Correction: FAD and S-pathway ==
[[File:Yepez 2018 PLOS One Fig1B.jpg|400px|left|link=Yepez 2018 PLOS One]]
* A commonly found error requires correction. For clarification, see page 48 in [[Gnaiger_2020_BEC_MitoPathways |Gnaiger (2020)]]
{{Labeling
{{Labeling
|area=Instruments;methods
|area=Instruments;methods

Revision as of 14:41, 13 May 2021

Publications in the MiPMap
Yépez VA, Kremer LS, Iuso A, Gusic M, Kopajtich R, Koňaříková E, Nadel A, Wachutka L, Prokisch H, Gagneur J (2018) OCR-Stats: Robust estimation and statistical testing of mitochondrial respiration activities using Seahorse XF Analyzer. PLOS ONE 13:e0199938.

» PMID: 29995917 Open Access

Yepez VA, Kremer LS, Iuso A, Gusic M, Kopajtich R, Konarikova E, Nadel A, Wachutka L, Prokisch H, Gagneur J (2018) PLOS ONE

Abstract: The accurate quantification of cellular and mitochondrial bioenergetic activity is of great interest in medicine and biology. Mitochondrial stress tests performed with Seahorse Bioscience XF Analyzers allow the estimation of different bioenergetic measures by monitoring the oxygen consumption rates (OCR) of living cells in multi-well plates. However, studies of the statistical best practices for determining aggregated OCR measurements and comparisons have been lacking. Therefore, to understand how OCR behaves across different biological samples, wells, and plates, we performed mitochondrial stress tests in 126 96-well plates involving 203 fibroblast cell lines. We show that the noise of OCR is multiplicative, that outlier data points can concern individual measurements or all measurements of a well, and that the inter-plate variation is greater than the intra-plate variation. Based on these insights, we developed a novel statistical method, OCR-Stats, that: i) robustly estimates OCR levels modeling multiplicative noise and automatically identifying outlier data points and outlier wells; and ii) performs statistical testing between samples, taking into account the different magnitudes of the between- and within-plate variations. This led to a significant reduction of the coefficient of variation across plates of basal respiration by 45 % and of maximal respiration by 29 %. Moreover, using positive and negative controls, we show that our statistical test outperforms the existing methods, which suffer from an excess of either false positives (within-plate methods), or false negatives (between-plate methods). Altogether, this study provides statistical good practices to support experimentalists in designing, analyzing, testing, and reporting the results of mitochondrial stress tests using this high throughput platform.

Selected quotes

Extreme differences (default) method to compute bioenergetic measures. - On every plate independently, for each well, in interval 1 take the OCR corresponding to the last measurement, in intervals 2 and 4 take the minimum, and in interval 3 the maximum OCR value [19]. Then, use the corresponding differences to estimate the bioenergetic measures. Report the results per patient as the mean across wells plus standard deviation or standard error, separately for each plate.

Respiratory states

  • Interval 1: ROUTINE - take measurement 3
  • Interval 2: LEAK (Omy) - take the minimum
  • Interval 3: ET (Uncoupler) - take the maximum
  • Interval 4: Rbl (Rot&Ama) - take the minimum

Cited by

  • Iglesias-Gonzalez et al (2021) Proficiency test in mt-respiration: A necessary tool for reliable and reproducible results. MitoFit Preprints 2021 (in prep).


Correction: FAD and S-pathway

Yepez 2018 PLOS One Fig1B.jpg
  • A commonly found error requires correction. For clarification, see page 48 in Gnaiger (2020)


Labels: MiParea: Instruments;methods 



Preparation: Intact cells 


Coupling state: LEAK, ROUTINE, ET 


MitoFit 2021 PT