Author: achamess

Model Articles: Transcriptomic Profiling

Model Articles: Transcriptomic Profiling

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Transcriptomic profiling with RNA-seq is increasingly common. Often, RNA-seq is used a first step to discover genes, followed by manipulation of said genes to show a causal relationship with some phenotype. That’s often the case, but sometimes, just the transcriptomic data are reported without any follow-up perturbations. The volume of data one gets from transcriptomic studies is huge, and reporting the findings in a clear and insightful way can be a challenging.

I’m struggling with this issue right now. But thankfully, there are some good papers to use as models for my own writing. Here are a few that I’ve found helpful.

 

Model Article: A pathway from midcingulate cortex to posterior insula gates nociceptive hypersensitivity (Tan et al 2017)

Model Article: A pathway from midcingulate cortex to posterior insula gates nociceptive hypersensitivity (Tan et al 2017)

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Tan, L. L. et al. A pathway from midcingulate cortex to posterior insula gates nociceptive hypersensitivity. Nat Neurosci 4, 362 (2017).

This is a beautiful and insightful paper from Rohini Kuner’s lab. I’m using this as an exemplary model of how to causally implicate a brain region in some kind of pain behavior. The general approach is to take a region of interest, push and pull it (manipulate) using some kind of selective manipulative method like optogenetics, and then look at various aspects of the output of interest (in this case pain hypersensitivity due to capsaicin).

That’s the general approach to many circuit papers these days. Of course, each biological question will necessitate lots of idiosyncratic variations in how to address the question. But overall, there is a general model of:

Region of interest -> Silence/Activate (Manipulate) Neurons in Region -> Look for Effect on Behavioral Output  -> Iteratively Apply the Manipulation to Find Additional Information about the Circuit

OK. So let’s break this down. I’m going to focus less on the actual results and more on the rationale, approach and question that each part of this paper addresses.

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Series: Model Articles for Pain Researchers

Series: Model Articles for Pain Researchers

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There is a very large variety of kinds of research approaches in pain neuroscience, and science in general. If you read enough papers, you can begin to glean ‘models’ or templates for how certain kinds of research gets done. I’m starting this series to begin to describe and catalog examples of different models of scientific investigations.

Over time, I hope that this catalog can serve to help trainee pain researchers plot out their own investigations using the well-worn models of high quality papers.

 

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