My lab is planning to gather scRNA-seq data on some samples and perform some clustering and differential expression analysis. In addition to the scRNA-seq data, we can get either ATAC-seq data or bisulfite-sequencing data. Which type of data (ATAC-seq or bisulfite-sequencing) would better complement the scRNA-seq data, and why?
Edit: more information on my lab's experiment: we are planning to use flow cytometry to sort out a rare subpopulation of immune cells. We then want to use differential expression analysis and either ATAC-seq or bisulfite-sequencing to identify the differences between our rare subpopulation and the more general class of immune cells from which we isolated our subpopulation, and potentially to identify cells that are showing signs of shifting from the more general class of immune cells to our subpopulation. We then would like to see if/how this subpopulation of cells changes in response to receiving a transplant. So the goal is to come away from the experiment with genomic and epigenomic markers for this cell subclass, and with data specifically illuminating how and why these cells change in response to a transplant.
Ok, by looking at the comment below, and with the fact that standard bisulfite will not be sufficient to differentiate between these two regulatory marks, I think your best bet is with ATAC-seq.
That cannot be answered with the provided information and entirely depends on the scientific question.
Examples:
If your scRNA-seq identified the differential expression of transcription factor between two populations of cells and maybe a surface marker than can be enriched by FACS, a meaningful downstream experiment would be to FACS-sort these two populations. With these one could do ATAC-seq to test if the differential TF is involved in chromatin accessability changes. Additionally some ChIP-seq of this TF would probably be informative.
Alternatively, if scRNA-seq suggested that pathways involved in DNA methylation are altered one would better do bisulfite-sequencing to test if indeed this observation can be found on a larger scale, maybe combined with bulk RNA-seq to connect DNA methylation levels with gene expression changes.
It depends on the context. If you provide some more information maybe you'll get better suggestions.
Thank you very much for the fast response, and sorry about the insufficient information - my lab is planning to use flow cytometry to sort out a rare subpopulation of immune cells. We then want to use differential expression analysis and either ATAC-seq or bisulfite-sequencing to identify the differences between our rare subpopulation and the more general class of immune cells from which we isolated our subpopulation, and potentially to identify cells that are showing signs of shifting from the more general class of immune cells to our subpopulation. We then would like to see if/how this subpopulation of cells changes in response to receiving a transplant. So the goal is to come away from the experiment with genomic and epigenomic markers for this cell subclass, and with data specifically illuminating how and why these cells change in response to a transplant. I don't know if this changes your response at all, but thanks again, I found the initial response helpful.
I think what is most important is that you gradually expand your skillsets, making sure you take your time to be comfortable and have substantive understanding of your new technologies.
So, if you don't have a clear reason for wanting to add a new technology, my guess is that it may not be in your best interests to do so. For example, if you have a pilot with multiple data types and your signal is more clear with one data type, then I would probably recommend focusing on maximizing your sample size with the feature with the most clear difference (rather than continuing to process multiple data types for each sample).
Likewise, for some labs, I think regular RNA-Seq and/or FACS with replicates may be a better option than scRNA-Seq (although I certainly believe some labs should be doing scRNA-Seq).
will your bisulfite sequencing be just standard bisulfite (where you can't differentiate 5mC vs 5hmC)?
Yes it will be just standard bisulfite
Ok, by looking at the comment below, and with the fact that standard bisulfite will not be sufficient to differentiate between these two regulatory marks, I think your best bet is with ATAC-seq.