How should I analyze the following dataset (GSE150847)?

Question

[arjuncsubra]

Hi all, new to Bioconductor/scRNA-seq analyses here.

For an upcoming project, I have chosen to analyze this dataset, "Generation of a Broadly Useful Model for COVID-19 Pathogenesis, Vaccination, and Treatment".

I have preprocessed and loaded the .tsv file (from supplemental files in GEO) into a SingleCellExperiment. My understanding is that the row names are the individual mouse genes and the column names are the six samples that were taken.

Here is how my SingleCellExperiment looks in R:

> sc3.sc #what my sce is called
class: SingleCellExperiment 
dim: 55339 6 
metadata(0):
assays(1): counts
rownames(55339): 0610005C13Rik 0610006L08Rik ... n-TStga1 SARS-CoV-2
rowData names(0):
colnames(6): Ad5.Empty.rep1 Ad5.Empty.rep2 ... Ad.hACE2.rep2 Ad.hACE2.rep3
colData names(0):
reducedDimNames(0):
altExpNames(0):

What is your advice going forward/what should my end product be?

Furthermore, can I create a clustering map with this type of data/how applicable will that be with this dataset (individual cells do not seem to be in the columns, as there are only 6)?

Answer 1

[Ram]

Are you asking us what you can do with a publicly available dataset, or do you have a specific hypothesis/scientific question in mind?

[arjuncsubra]

I do not really have a particular hypothesis in mind; I would like to know what end product makes the most sense given this dataset and data type.

[Ram]

That is not really a way to approach a project - you should have some idea of what you're looking for. Without that, the dataset is just a bunch of random data points. Why did you pick this dataset in particular? What about it appeals to you?

[arjuncsubra]

I picked this dataset because I want to do some clustering related to COVID-19 and its effect on the lungs.

[Ram]

What can you tell me about this dataset, the attributes it contains and how it relates to Covid-19 and lungs? What does this dataset have that other Covid-19 datasets don't? What was the process by which you arrived to this dataset?

[arjuncsubra]

To my understanding (I am really new to this), this dataset seems to have mouse genes in the rows and 6 columns which seem to be the test subjects. This dataset seems to involve mice that were gene-edited so they could become susceptible to the effects of COVID-19 respiratorily. I was just looking for COVID-19 datasets on GEO, that is how I found it.

I am still wondering what the practical possibilities are when it comes to graphing this data set (does this mean clustering, etc.).

[Kevin Blighe]

Just some training, I presume? You could try to follow the methods that my colleague and I used here: https://www.biorxiv.org/content/10.1101/271411v1.article-info

We never published that. Publishing already-published data in this way is difficult.

[arjuncsubra]

Yes - it was for training, thank you!