integrated scRNA-seq dataset

Question

[tomas4482]

I read a lot of methods about integration of multiple scRNA-seq datasets from different cohorts, species, or experimental designs. I'm curious about a question.

It seems that almost all of studies try to explore "methodology" of integration rather than "application". Is there any publications using one of these integration methods to combine scRNA-seq data from different studies for downstream analysis?

For instance, if I need to analyze scRNA-seq data in a larger cohort or at different time-points, technically speaking, I can start with an integrated, larger dataset which consists of several different datasets (e.g. with different time points). But I never see any literature doing such thing at least in cancer field.

Does it mean these methods are pre-mature for application or other scientists and reviewers just don't buy it?

Answer 1

[Friederike]

Most of the papers published by bigger consortia such as the Allen Brain Atlas, Human BioMolecular Atlas, and the Human Cell Atlas initiatives make use of integration methods. In fact, most of the papers introducing new methods for data integration demonstrate it using data from different single-cell platforms, labs, even organisms. I actually cannot remember seeing a scRNA-seq paper in the past months that did not make use of integration methods, but maybe I'm not properly understanding the issue you're trying to get at?

[tomas4482]

In fact, most of the papers introducing new methods for data integration demonstrate it using data from different single-cell platforms, labs, even organisms.

That is what I'm saying. If you search for any scRNA-seq integration, a lot of new methods integrating different scRNA-seq datasets come in sight.

Most of the papers published by bigger consortia such as the Allen Brain Atlas, Human BioMolecular Atlas, and the Human Cell Atlas initiatives make use of integration methods.

Thanks for the hint. You've answered my question. I find some papers I need. I'm looking for studies analyzing integrated scRNA dataset like what A multimodal cell census and atlas of the mammalian primary motor cortex just did.