<scp>RNA</scp>‐Seq methods for transcriptome analysis

Hrdličková, Radmila; Toloue, Masoud; Tian, Bin

doi:10.1002/wrna.1364

Cited by 529 publications

(380 citation statements)

References 124 publications

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“…To settle this question, integrative RNA‐Seq and TMT‐based proteomic analysis were performed. The transcriptome, which is assessed by RNA‐seq, is widely considered to be the most mature omics technology with a long measure and the greatest depth of coverage . This approach is also advantageous when the protein products of genes are either recalcitrant to proteomic analysis or of low abundance, which can result in their under‐representation in some conditions .…”

Section: Discussionmentioning

confidence: 99%

Notch3 promotes 3T3‐L1 pre‐adipocytes differentiation by up‐regulating the expression of LARS to activate the mTOR pathway

Guo

Tan

Xiong

et al. 2019

J Cellular Molecular Medi

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Adipocytes constitute a major component of the tumour microenvironment. Numerous studies have shown that adipocytes promote aggressiveness and invasion by stimulating cancer cells proliferation and modulating their metabolism. Herein, we reported that Notch3 promotes mouse 3T3‐L1 pre‐adipocytes differentiation by performing the integrative transcriptome and TMT‐based proteomic analyses. The results revealed that aminoacyl‐tRNA_biosynthesis pathway was significantly influenced with Nocth3 change during 3T3‐L1 pre‐adipocytes differentiation, and the expression of LARS in this pathway was positively correlated with Notch3. Published studies have shown that LARS is a sensor of leucine that regulates the mTOR pathway activity, and the latter involves in adipogenesis. We therefore supposed that Notch3 might promote 3T3‐L1 pre‐adipocytes differentiation by up‐regulating LARS expression and activating mTOR pathway. CHIP and luciferase activity assay uncovered that Notch3 could transcriptionally regulate the expression of LARS gene. Oil Red staining identified a positive correlation between Notch3 expression and adipocytic differentiation. The activation of mTOR pathway caused by Notch3 overexpression could be attenuated by knocking down LARS expression. Altogether, our study revealed that Notch3 promotes adipocytic differentiation of 3T3‐L1 pre‐adipocytes cells by up‐regulating LARS expression and activating the mTOR pathway, which might be an emerging target for obesity treatment.

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Section: Discussionmentioning

confidence: 99%

Notch3 promotes 3T3‐L1 pre‐adipocytes differentiation by up‐regulating the expression of LARS to activate the mTOR pathway

Guo

Tan

Xiong

et al. 2019

J Cellular Molecular Medi

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“…Although tRNA detection by nanopore has previously been explored and reported (Henley et al, 2016;Smith, Abu-Shumays, Akeson, & Bernick, 2015), the ONT nanopore sequencer commercialized direct RNA sequencing kits in 2017. Conventional "RNA-seq" with short reads, which is rather inappropriately termed so since the RNA molecules are not directly sequenced (Hrdlickova, Toloue, & Tian, 2017), requires reverse transcription (RT) of the template RNA molecule into complementary DNA (cDNA), which is typically further amplified by PCR. Direct RNA sequencing (again, it is unfortunate that true RNA sequencing has to add the word "direct" to differentiate itself from conventional "RNA-Seq"), on the other hand, directly detects the ribonucleobases passing through the pore without RT or PCR amplification, and this approach is free of possible biases or misamplifications introduced during such steps.…”

Section: Tr Anscrip Tome Analys Is and D Irec T Rna S Equen Cingmentioning

confidence: 99%

Nanopore sequencing: Review of potential applications in functional genomics

2019

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Molecular biology has been led by various measurement technologies, and increased throughput has developed omics analysis. The development of massively parallel sequencing technology has enabled access to fundamental molecular data and revealed genomic and transcriptomic signatures. Nanopore sequencers have driven such evolution to the next stage. Oxford Nanopore Technologies Inc. provides a new type of single molecule sequencer using protein nanopore that realizes direct sequencing without DNA synthesizing or amplification. This nanopore sequencer can sequence an ultra‐long read limited by the input nucleotide length, or can determine DNA/RNA modifications. Recently, many fields such as medicine, epidemiology, ecology, and education have benefited from this technology. In this review, we explain the features and functions of the nanopore sequencer, introduce various situations where it has been used as a critical technology, and expected future applications.

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“…Transcriptomics studies entire sets of RNA transcripts in a particular context. Sample collection is critical; standardized collection tubes (eg PAXgene) can stabilize RNA for transport and storage.…”

Section: Resultsmentioning

confidence: 99%

The national blueprint for pregnancy/birth longitudinal cohorts to study factor VIII immunogenicity: NHLBI State of the Science (SOS) Workshop on factor VIII inhibitors

Johnsen

Brown

2019

Haemophilia

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Introduction Patients with haemophilia can develop inhibitors to exogenous coagulation factors. Some patients are tolerant to factor, while those who develop inhibitors do so early in life. Genetics and environmental factors are known to contribute to inhibitor risk. However, it is not yet possible to predict inhibitor formation or treatment responsiveness in individuals. We hypothesize that factors in the antenatal/neonatal period inform inhibitor risk development. Aim To consider the design of longitudinal studies beginning in the antenatal/neonatal period and the use of new technologies to better understand haemophilia inhibitors. Methods A working group was formed for the NHLBI State of the Science Workshop: Factor VIII Inhibitors: Generating a National Blueprint for Future Research to solicit input from the US haemophilia community and international collaborators to consider design of pregnancy/birth longitudinal cohorts that leverage ‐omics, existing phenotypic data, and in silico modelling to study inhibitors. Results An antenatal/neonatal longitudinal cohort should begin with enrolment of pregnant genetic carriers of haemophilia and span the at‐risk period for inhibitor development in the child. Data and samples from the mother, placenta, neonate and young child can be obtained that are amenable to existing assays, genomics and other ‐omics studies. Data can inform in silico prediction and mathematical models. Conclusion A longitudinal study beginning before birth offers the unique opportunity to study factors that influence inhibitor development prior to exposure. Advances in ‐omics and computational biology can study complex phenotypes in this rare disease. This study could be accomplished through interdisciplinary efforts and patient community engagement.

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RNA‐Seq methods for transcriptome analysis

Cited by 529 publications

References 124 publications

Notch3 promotes 3T3‐L1 pre‐adipocytes differentiation by up‐regulating the expression of LARS to activate the mTOR pathway

Notch3 promotes 3T3‐L1 pre‐adipocytes differentiation by up‐regulating the expression of LARS to activate the mTOR pathway

Nanopore sequencing: Review of potential applications in functional genomics

The national blueprint for pregnancy/birth longitudinal cohorts to study factor VIII immunogenicity: NHLBI State of the Science (SOS) Workshop on factor VIII inhibitors

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