The subfornical organ is a nucleus for gut-derived T cells that regulate behaviour 2025 Wang et al

@jnmaciuch you have explained all that very clearly - I am really grateful. Is there a resourse (eg book) that would explain these sorts of techniques? I am trying to teach myself, but it's not efficient for me, and I am reluctant to burden busy folks at s4me with my endless questions.

Once again, thanks so much.
 
I'll also note that the reason they probably didn't do the additional barcoding here is because it would have been unfeasible for them. 10X is the standard third-party sequencing technology and the machines that most universities/labs have access to only allow for 2 barcodes (one to identify all reads from the same cell, and one to identify all the ones from the same sample). Figuring out how to add an additional barcode would probably have involved investing in an entirely new protocol, which may not have been financially feasible. So I understand why they didn't do it--they were probably banking on the tissue-specific differences surviving batch effect correction, which just didn't happen.

But like I said, without those additional steps, this single-cell analysis is basically useless. They could have acknowledged those limitations and done extensive experimental validation to confirm that the findings weren't batch effect--but as I mentioned in one of my comments last month, the mouse knockout models that they used to validate their most important findings are not at all brain-specific. So a bit of a disappointment all around.
 
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arnoble said:
@jnmaciuch you have explained all that very clearly - I am really grateful. Is there a resourse (eg book) that would explain these sorts of techniques? I am trying to teach myself, but it's not efficient for me, and I am reluctant to burden busy folks at s4me with my endless questions.

Once again, thanks so much.
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No problem! It's a bit of a tricky subject, since most resources for it assume that people have prior knowledge in experimental biology. The youtube channel StatQuest has a few videos on RNA-seq (keep in mind that RNA-seq usually refers to bulk RNA-seq, which involves measuring gene expression from a bunch of cells all together, without separating them by cell). Other than that, you might just have to read a bunch of "Single-cell RNA-sequencing explained" articles and try to get an idea from all of them cumulatively even though many of them will assume too much prior knowledge. I'm happy to answer questions when I have time if you'd like to make a separate thread on it, though!
 
@jnmaciuch you have been a great help to me - thank you so much. ChatGPT/Gemini have been helping me a lot (I apply a reasonable grain of salt). As you suggest, I will try StatQuest and some more scRNA-seq articles and see how that goes. I also use R so will try playing with some libraries and their vignettes.

Can't thank you enough.
 
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