Compare transcriptomes to RNA-seq

[ribaribaworking]

Compare transcriptomes of B-ALL cells from our RNA-seq to the transcriptomes from the paper: Single-cell functional genomics reveals determinants of sensitivity and resistance to natural killer cells in blood cancers The data is here: https://github.com/odufva/nk-bloodcancer?tab=readme-ov-file

4 B-ALL cell lines We are interested in tumor cells. Nalm-6, Kasumi, 697, RCHACV

[ribaribaworking]

Here is the site with mouse-human homologs: https://www.informatics.jax.org/homology.shtml

[ribaribaworking]

I Did this to AB and CD populations separately. I extracted expression profiles of cells from https://immunogenomics.shinyapps.io/nkheme/. What I did, was, I just downloaded the DE table from their web tool (co-culture scRNA-seq > cancer sells (volcano plots)). Then I used the table of homologs that you sent me and tried to see what is the overlap of DE genes between Human cells and Mouse cells.

I just subsampled all DE expressed genes with p_adj < 0.05. I didn't check the directionality of the change.

• In addition I added tables that have Human L2FC, padj, etc + our Mouse data.

• added the Fisher test to make sure that the overlap has statistical significance.

  AB: E697 0.0002703 kasumi 0.04833 nalm6 0.96 rchacv 1.885e-05

CD: E697 1.697e-07 kasumi 8.715e-0.7 nalm6 0.2293 rchacv 1.113e-11

[ribaribaworking]

Michelle also asked for ABCD and to see how AB overlaps CD

rstudio-export (14).zip