Now it's your time to shine ! We are going to put into pratice what we have just seen. By using a more complicated use case, you are going to reproduce the whole scRNAseq analysis with Seurat.

Dataset test

The dataset for this analysis will be single cell RNAseq from chick embryos from de Lima et al. We are going to analyse only single cells of E10 stage of embryos. You can download the dataset at the GEO accession GSE166981.

Do you need help to find the data ?

Click to reveal spoiler: Hello ! I'm a spoiler !

First tip : Look to supplementary file....
Second tip: To see what's inside the tar archive you can click on (custom)
Still no clue ? : You need the three files with "E10" in the filename. You need to check the three files and then click on download. You will have the archive GSE166981_RAW.tar in your downloads.

Once you download the data, all you have to do is import it onto the Rstudio server.

Biomart is your friend

Don't forget to import biomaRt in order to help you annotate your genes. Make sure to tweak parameters to fit this new dataset.

Trouble to use biomaRt ?

Here is some links to help you with biomaRt :

• Vignette of the R package
• Short presentation of the use of the R package, comparing it with the Ensembl interface

Quizz time !

Before moving on, please take this quiz : Quizz n°1

To complete this quizz you'll need to :

1. Retrieve the chick dataset
2. Import data in Rstudio
3. Import data in your global environment
4. Create a Seurat Object
5. Create an annotation table of chick genes using biomaRt.