RNA sequencing: the teenage years

Stark, Rory; Grzelak, Marta; Hadfield, James

doi:10.1038/s41576-019-0150-2

Cited by 1,365 publications

(1,125 citation statements)

References 282 publications

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“…expression of phototransduction cascade genes is linked to calcium baseline changes. To pinpoint intrinsic differences between UVcones that might underlie the observed elevation in calcium baseline leading to a light-preference in SZ UV-cones we used a transcriptomics approach (Stark et al, 2019). For this, we dissected entire retinas expressing GFP in all UV-cones and surgically separated the SZ from the remainder of the retina (non-SZ).…”

Section: Differentialmentioning

confidence: 99%

Cellular and molecular mechanisms of photoreceptor tuning for prey capture in larval zebrafish

Yoshimatsu

Schröder

et al. 2019

Preprint

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Correspondence to t. yoshimatsu@sussex.ac.uk and t.baden@sussex.ac.uk In the eye, the function of same-type photoreceptors must be regionally adjusted to process a highly asymmetrical natural visual world. Here we show that UV-cones in the larval zebrafish area temporalis are specifically tuned for UV-bright prey capture in their upper frontal visual field, which uses the signal from a single cone at a time. For this, UV-detection efficiency is regionally boosted 42-fold. Next, in vivo 2-photon imaging, transcriptomics and computational modelling reveal that these cones use an elevated baseline of synaptic calcium to facilitate the encoding of bright objects, which in turn results from expressional tuning of phototransduction genes. Finally, this signal is further accentuated at the level of glutamate release driving retinal networks. These regional differences tally with variations between peripheral and foveal cones in primates and hint at a common mechanistic origin. Together, our results highlight a rich mechanistic toolkit for the tuning of neurons.

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Section: Differentialmentioning

confidence: 99%

Cellular and molecular mechanisms of photoreceptor tuning for prey capture in larval zebrafish

Yoshimatsu

Schröder

et al. 2019

Preprint

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“…For instance, transcriptomic changes on immediate early genes can be observed in a matter of minutes following a stimulus . Third, a wide range of techniques for interrogating the transcriptomic state of a tissue or cell have been developed through the years . These methods can be divided into two main categories: low‐ and high‐throughput.…”

Section: Introductionmentioning

confidence: 99%

“…38 Third, a wide range of techniques for interrogating the transcriptomic state of a tissue or cell have been developed through the years. 39 These methods can be divided into two main categories: low-and high-throughput. To the first group classically belong techniques such as northern blot (NB), in situ hybridization (ISH), or quantitative realtime polymerase chain reaction (qPCR).…”

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confidence: 99%

Sex differences: Transcriptional signatures of stress exposure in male and female brains

Brivio

López

Chen

2020

Genes Brain and Behavior

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More than two‐thirds of patients suffering from stress‐related disorders are women but over two‐thirds of suicide completers are men. These are just some examples of the many sex differences in the prevalence and manifestations of stress‐related disorders, such as major depressive disorder, post‐traumatic stress disorder, and anxiety disorders, which have been extensively documented in clinical research. Nonetheless, the molecular origins of this sex dimorphism are still quite obscure. In response to this lack of knowledge, the NIH recently advocated implementing sex as biological variable in the design of preclinical studies across disciplines. As a result, a newly emerging field within psychiatry is trying to elucidate the molecular causes underlying the clinically described sex dimorphism. Several studies in rodents and humans have already identified many stress‐related genes that are regulated by acute and chronic stress in a sex‐specific fashion. Furthermore, current transcriptomic studies have shown that pathways and networks in male and female individuals are not equally affected by stress exposure. In this review, we give an overview of transcriptional studies designed to understand how sex influences stress‐specific transcriptomic changes in rodent models, as well as human psychiatric patients, highlighting the use of different methodological techniques. Understanding which mechanisms are more affected in males, and which in females, may lead to the identification of sex‐specific mechanisms, their selective contribution to stress susceptibility, and their role in the development of stress‐related psychiatric disorders.

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“…Underlying reads are typically deposited to the Sequence Read Archive [5], currently containing reads for more than 1,5 million samples (https://www.ncbi.nlm.nih.gov/sra/?term=RNA-Seq). One of the most popular applications of RNA-Seq is for Differential Expression Analysis (DEA) where one identifies genes that are expressed at different levels between two classes of samples (e.g., healthy, disease) [6].…”

Section: Introductionmentioning

confidence: 99%

RASflow: An RNA-Seq Analysis Workflow with Snakemake

Zhang

Jonassen

2019

Preprint

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Background: With the cost of DNA sequencing decreasing, increasing amounts of RNA-Seq data are being generated giving novel insight into gene expression and regulation. Prior to analysis of gene expression, the RNA-Seq data has to be processed through a number of steps resulting in a quantification of expression of each gene / transcript in each of the analyzed samples. A number of workflows are available to help researchers perform these steps on their own data, or on public data to take advantage of novel software or reference data in data re-analysis. However, many of the existing workflows are limited to specific types of studies. We therefore aimed to develop a maximally general workflow, applicable to a wide range of data and analysis approaches and at the same time support research on both model and non-model organisms. Furthermore, we aimed to make the workflow usable also for users with limited programming skills.Results: Utilizing the workflow management system Snakemake and the package management system Conda, we have developed a modular, flexible and user-friendly RNA-Seq analysis pipeline: RNA-Seq Analysis Snakemake Workflow (RASflow). Utilizing Snakemake and Conda alleviates challenges with library dependencies and version conflicts and also supports reproducibility. To be applicable for a wide variety of applications, RASflow supports mapping of reads to both genomic and transcriptomic assemblies. RASflow has a broad range of potential users: it can be applied by researchers interested in any organism and since it requires no programming skills, it can be used by researchers with different backgrounds. RASflow is an open source tool and source code as well as documentation, tutorials and example data sets can be found on GitHub: https://github.com/zhxiaokang/RASflow Conclusions: RASflow is a simple and reliable RNA-Seq analysis workflow which is a full pack of RNA-Seq analysis.

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RNA sequencing: the teenage years

Cited by 1,365 publications

References 282 publications

Cellular and molecular mechanisms of photoreceptor tuning for prey capture in larval zebrafish

Cellular and molecular mechanisms of photoreceptor tuning for prey capture in larval zebrafish

Sex differences: Transcriptional signatures of stress exposure in male and female brains

RASflow: An RNA-Seq Analysis Workflow with Snakemake

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