add resources

[marypiper]

https://broadinstitute.github.io/2020_scWorkshop/

? https://nbisweden.github.io/workshop-scRNAseq/schedule.html

https://azimuth.hubmapconsortium.org/

Single-nucleus and single-cell transcriptomes compared in matched cortical cell types paper: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6306246/ and https://www.nature.com/articles/s41591-020-0844-1

cellmarker

cellphonedb (https://www.nature.com/articles/s41576-020-00292-x)
spatial transcriptomics
CITE-seq

[mistrm82]

Also, eventually add some info/blurb describing snRNA-seq and how does it work differently from scRNA-seq

[marypiper]

I have added all links above to workshop schedule page, but need to add spatial and CITE-seq to introduction still

[jihe-liu]

Single-nucleus RNA-sequencing (snRNA-seq) analyzes the expression profiles from nuclei, instead of intact cells. In some situations (depending on your research materials and goals), snRNA-seq is the preferred method compared to scRNA-seq. Advantages of snRNA-seq include:

1. Works well with hard-to-isolate samples (for example, adipocytes), as well as frozen tissues;
2. Reduces transcriptional artifacts from the isolation process;
3. Provides less biased cellular coverage;

Typically, less transcripts are detected from the nuclei (~7,000 genes), compared to intact cells (~11,000 genes). In a matched snRNA-seq and scRNA-seq study, cell types are discriminated effectively with both methods, suggesting that snRNA-seq could still maintain rich transcriptional information. A practical workflow, with both experimental and computational aspects, of scRNA-seq/snRNA-seq is proposed in this study. In particular, for snRNA-seq, the paper suggests testing several protocols for corresponding tissue types, to determine the best approach for the sample.

[jihe-liu]

I added some blurbs for snRNA-seq. I am not sure where is the best place to put it, so I leave it as comment here for now @mistrm82

[mistrm82]

Add snRNA-seq blurb into a separate doc - include other similar technologies ie CITE-seq, spatial.

Could be a note as well?

[mistrm82]

Tried adding as a note to pre-reading: #63