Quantification noise in single cell experiments

Reiter, Martina; Kirchner, Benedikt; Müller, Helena; Holzhauer, C.; Mann, Wolfgang; Pfaffl, Michael W.

doi:10.1093/nar/gkr1136

Cited by 18 publications

(5 citation statements)

References 26 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The copyright holder for this preprint (which this version posted June 9, 2020. ; https://doi.org/10.1101/2020.06.06.138206 doi: bioRxiv preprint was defined as the point at which there was a 95% replication rate (35 Ct) (Reiter et al, 2011).…”

Section: Single Cell Amplification and Qpcrmentioning

confidence: 99%

Unique Molecular Characteristics of Visceral Afferents Arising from Different Levels of the Neuraxis: Location of Afferent Somata Predicts Function and Stimulus Detection Modalities

Meerschaert

Adelman²,

Friedman

et al. 2020

J. Neurosci.

View full text Add to dashboard Cite

All authors have no conflict of interest. Acknowledgements:The authors acknowledge and thank Mr. Christopher Sullivan for expert technical support and mouse husbandry.Author contributions: KAM, conception and design, acquisition of data, analysis and interpretation of data, drafting and revising the article. PCA and RLF, acquisition of data, analysis and interpretation of data. KMA, HRK and BMD, conception and design, analysis and interpretation of data, drafting and revising the article.

show abstract

Section: Single Cell Amplification and Qpcrmentioning

confidence: 99%

Unique Molecular Characteristics of Visceral Afferents Arising from Different Levels of the Neuraxis: Location of Afferent Somata Predicts Function and Stimulus Detection Modalities

Meerschaert

Adelman²,

Friedman

et al. 2020

J. Neurosci.

View full text Add to dashboard Cite

show abstract

“…In certain scientific experiments, the signal to noise ratio can be extremely low. This is especially the case in some experiments of physics 20,21 , social science 22,23 and biological science [24][25][26] . Thus we also tested our model under noise level of 200% (signal to noise ratio 1:2), 500% (signal to noise ratio 1:5) and 1000% (signal to noise ratio 1:10).…”

Section: Evaluating the Contextual Regression Model On Simulated Datamentioning

confidence: 95%

Contextual Regression: An Accurate and Conveniently Interpretable Nonlinear Model for Mining Discovery from Scientific Data

Liu

Wang

2017

Preprint

View full text Add to dashboard Cite

Machine learning algorithms such as linear regression, SVM and neural network have played an increasingly important role in the process of scientific discovery. However, none of them is both interpretable and accurate on nonlinear datasets. Here we present contextual regression, a method that joins these two desirable properties together using a hybrid architecture of neural network embedding and dot product layer. We demonstrate its high prediction accuracy and sensitivity through the task of predictive feature selection on a simulated dataset and the application of predicting open chromatin sites in the human genome. On the simulated data, our method achieved high fidelity recovery of feature contributions under random noise levels up to ±200%. On the open chromatin dataset, the application of our method not only outperformed the state of the art method in terms of accuracy, but also unveiled two previously unfound open chromatin related histone marks. Our method fills in the gap of accurate and interpretable nonlinear modeling in scientific data mining tasks. IntroductionPredictive models are important tools for data analysis. Linear models, such as linear

show abstract

“…Cycle time (Ct) values were determined via regression. Quantification threshold for PCR 151 was defined as the point at which there was a 95% replication rate (35 Ct) (Reiter et al, 2011). 152…”

Section: Single Cell Amplification and Qpcr 145mentioning

confidence: 99%

Unique molecular characteristics of visceral afferents arising from different levels of the neuraxis: location of afferent somata predicts function and stimulus detection modalities

Meerschaert

Adelman²,

Friedman

et al. 2020

Preprint

View full text Add to dashboard Cite

Visceral organs receive neural innervation from sensory ganglia located adjacent to multiple levels of the brainstem and spinal cord. Here we examined whether molecular profiling could be used to identify functional clusters of colon afferents from thoracolumbar (TL), lumbosacral (LS), and nodose ganglia (NG) in the mouse. Profiling of TL and LS bladder afferents was also done. Visceral afferents were back-labeled using retrograde tracers injected into proximal and distal regions of colon or bladder, followed by single cell RT-qPCR and analysis via an automated hierarchical clustering method. Genes were chosen for assay (32 for bladder; 48 for colon) based on their established role in stimulus detection, regulation of sensitivity/function or neuroimmune interaction. A total of 132 colon afferents (from NG, TL and LS) and 128 bladder afferents (from TL and LS) were analyzed. Retrograde labeling from the colon showed NG and TL afferents innervate proximal and distal regions of the colon whereas 98% of LS afferents only project to distal regions. There were clusters of colon and bladder afferents, defined by mRNA profiling, that localized to either TL or LS ganglia. Mixed TL/LS clustering also was found. In addition, transcriptionally, NG colon afferents were almost completely segregated from colon DRG (TL or LS) neurons. These results indicate that populations of primary visceral afferents are functionally “tuned” to detect and interact with the internal environment and that information from all levels is integrated at higher (CNS) levels, not only for regulation of homeostatic functions, but for conscious visceral sensations including pain.Significance StatementVisceral organs are innervated by sensory neurons whose cell bodies are located in multiple ganglia associated with the brainstem and spinal cord. For the colon, this overlapping innervation is proposed to facilitate visceral sensation and homeostasis, where sensation and pain is mediated by spinal afferents and fear and anxiety (the affective aspects of visceral pain) are the domain of nodose afferents. Transcriptomic analysis performed here reveals that genes implicated in both homeostatic regulation and pain are found in afferents across all ganglia types, suggesting that conscious sensation and homeostatic regulation is the result of convergence, and not segregation, of sensory input.

show abstract

Quantification noise in single cell experiments

Cited by 18 publications

References 26 publications

Unique Molecular Characteristics of Visceral Afferents Arising from Different Levels of the Neuraxis: Location of Afferent Somata Predicts Function and Stimulus Detection Modalities

Unique Molecular Characteristics of Visceral Afferents Arising from Different Levels of the Neuraxis: Location of Afferent Somata Predicts Function and Stimulus Detection Modalities

Contextual Regression: An Accurate and Conveniently Interpretable Nonlinear Model for Mining Discovery from Scientific Data

Unique molecular characteristics of visceral afferents arising from different levels of the neuraxis: location of afferent somata predicts function and stimulus detection modalities

Contact Info

Product

Resources

About