Erratum to: Mutational landscape of mucinous ovarian carcinoma and its neoplastic precursors

Ryland, Georgina L; Hunter, Sally M.; Doyle, Maria A.; Caramia, Franco; Li, Jason; Rowley, Simone M.; Christie, Michael; Allan, Prue E.; Stephens, Andrew N.; Bowtell, David D.L.; Gorringe, Kylie L.

doi:10.1186/s13073-016-0392-y

Cited by 115 publications

(142 citation statements)

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“…It is important to confirm that the chemistry used for library construction is compatible with the sequencing technology. Currently, there are two major outputs for libraries from scRNAseq: full-length transcript or 3′-end counted libraries, which each require different read depths ( Haque et al, 2017 ). Full-length transcript libraries are typically sequenced at a depth of 10 6 reads per cell, but may still yield important biological information at as low as 5 × 10 4 reads per cell ( Pollen et al, 2014 ).…”

Section: Single-cell Library Sequencingmentioning

confidence: 99%

“…For specific applications such as alternative splicing analysis on the single-cell level, much higher sequencing depth up to 15– 25 × 10 6 reads per cell is necessary. On the other hand, 3′-end counting libraries are sequenced at much lower depth of around 10 4 or 10 5 reads per cells ( Haque et al, 2017 ). Reaching the optimal sequencing depth can be an iterative process and may require multiple rounds of optimization.…”

Section: Single-cell Library Sequencingmentioning

confidence: 99%

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Experimental Considerations for Single-Cell RNA Sequencing Approaches

Nguyen

Pervolarakis

Nee

et al. 2018

Front. Cell Dev. Biol.

151

117

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Single-cell transcriptomic technologies have emerged as powerful tools to explore cellular heterogeneity at the resolution of individual cells. Previous scientific knowledge in cell biology is largely limited to data generated by bulk profiling methods, which only provide averaged read-outs that generally mask cellular heterogeneity. This averaged approach is particularly problematic when the biological effect of interest is limited to only a subpopulation of cells such as stem/progenitor cells within a given tissue, or immune cell subsets infiltrating a tumor. Great advances in single-cell RNA sequencing (scRNAseq) enabled scientists to overcome this limitation and allow for in depth interrogation of previously unexplored rare cell types. Due to the high sensitivity of scRNAseq, adequate attention must be put into experimental setup and execution. Careful handling and processing of cells for scRNAseq is critical to preserve the native expression profile that will ensure meaningful analysis and conclusions. Here, we delineate the individual steps of a typical single-cell analysis workflow from tissue procurement, cell preparation, to platform selection and data analysis, and we discuss critical challenges in each of these steps, which will serve as a helpful guide to navigate the complex field of single-cell sequencing.

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Section: Single-cell Library Sequencingmentioning

confidence: 99%

Section: Single-cell Library Sequencingmentioning

confidence: 99%

Experimental Considerations for Single-Cell RNA Sequencing Approaches

Nguyen

Pervolarakis

Nee

et al. 2018

Front. Cell Dev. Biol.

151

117

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“…The proband, currently an 8-year-old male, was part of a whole exome sequencing study by Eldomery et al (2017) . This study revealed that the proband was heterozygous for the SCN1B missense mutation c.308A>T. This mutation results in an amino acid change from a hydrophilic aspartic acid to a hydrophobic valine at position 103 (p.D103V) of the sodium channel auxiliary β subunit.…”

Section: Resultsmentioning

confidence: 99%

“…D103 is probably important to channel function, as it is highly conserved among all sodium channel β subunits, except for β4, and is also conserved among different species ( Figures 1A,B ). Eldomery et al indexed the β1 subunit variant D103V as pathogenic ( Eldomery et al, 2017 ).…”

Section: Resultsmentioning

confidence: 99%

“…We investigated a mutation located in exon 3 of SCN1B [Chr19:35524503 A>T (hg19): NM_001037.4 c.308A>T] identified in a patient with a history of proarrhythmic conditions with progressive atrial standstill, cognitive and motor deficits, and structural brain abnormalities. The patient was part of a sequencing study by Eldomery et al (2017) that proposed a dual diagnosis for this case. As a result, this β1 variant (β1 D103V ) (dbSNP ID: 1057519457) is indexed as pathogenic in the ClinVar database 1 .…”

Section: Introductionmentioning

confidence: 99%

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An SCN1B Variant Affects Both Cardiac-Type (NaV1.5) and Brain-Type (NaV1.1) Sodium Currents and Contributes to Complex Concomitant Brain and Cardiac Disorders

Martinez-Moreno

Selga

Riuró

et al. 2020

Front. Cell Dev. Biol.

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Voltage-gated sodium (Na V ) channels are transmembrane proteins that initiate and propagate neuronal and cardiac action potentials. Na V channel β subunits have been widely studied due to their modulatory role. Mice null for Scn1b , which encodes Na V β1 and β1b subunits, have defects in neuronal development and excitability, spontaneous generalized seizures, cardiac arrhythmias, and early mortality. A mutation in exon 3 of SCN1B , c.308A>T leading to β1_p.D103V and β1b_p.D103V, was previously found in a patient with a history of proarrhythmic conditions with progressive atrial standstill as well as cognitive and motor deficits accompanying structural brain abnormalities. We investigated whether β1 or β1b subunits carrying this mutation affect Na V 1.5 and/or Na V 1.1 currents using a whole cell patch-clamp technique in tsA201 cells. We observed a decrease in sodium current density in cells co-expressing Na V 1.5 or Na V 1.1 and β1 D103V compared to β1 WT . Interestingly, β1b D103V did not affect Na V 1.1 sodium current density but induced a positive shift in the voltage dependence of inactivation and a faster recovery from inactivation compared to β1b WT . The β1b D103V isoform did not affect Na V 1.5 current properties. Although the SCN1B _c.308A>T mutation may not be the sole cause of the patient’s symptoms, we observed a clear loss of function in both cardiac and brain sodium channels. Our results suggest that the mutant β1 and β1b subunits play a fundamental role in the observed electrical dysfunction.

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