scRNASeq of rare heterogenous population with weak response

Question

[frymor2]

I'm new to scRNA-Seq analysis and would appreciate the help of this community in analyzing my data set.

I have both data from single cell RNA and one of single-nuclei RNA including five different timepoints with duplicates each. all samples were sequenced using the 10x technology. I have five different time-points from Embryo to adult.

As I'm working on a specific organism in the mouse brain for which not a lot is known, I am struggling getting what i need. The cells I'm working on are both rare (meaning also weak expression in general and a low number of cells), as well as very heterogenous in their behavior.

It is known that there are two distinct regions with different behavior and separate (even antagonistic) responsibilities.

My goals are to try and identify marker genes for each of this two regions as well as in the different timepoints, compared to the adult stage. I'm not quote sure if it is better to regard this data set as a different discrete conditions and compare them against each other or is it better to use it to identify trajectories along the developmental timeline (or both???).

I would appreciate some ideas as how to approach this kind of analysis.

thanks in advance

[igor]

Since you have "seurat" as a tag, have you already looked into those vignettes? There are a few different tutorials available that address your questions.

Answer 1

[frymor2]

Thanks @igor for the answer. I have read through some of the vignette of Seurat (There are so many). My most important question is how to know if I need to merge the different timepoints into a one big data set, or is it better to use the IntegratedData analysis method to "align" the different TP ontop of eachother?

all suggestions would be welcome.