Extracting specific gene data from mouse/human.tome data set

#1

Hello,
Thanks for the fantastic data.
My supervisor gave me the task to compare the gene expression of 22 specific genes in the 37 matching cells between human and mice to look for differences similar to the approch in Nature 2019, Conserved cell types with divergent features in human versus mouse cortex for Serotonin receptors.
I accessed the data as described in the read.me file in R.
My question is what would be the best method to extracte the data for my 22 genes and the 37 matching cell clusters?
Is there a standarized procedure to get the same clusters or would I have to do the whole Data analysis again to get to the same Cluster results?
I know that it is not possible to download data for specific genes and that the tool to compare mice and human is in the making.

Thanks for your effort

#2

Hello @JoSta95,

Code for reproducing the analyses presented in our manuscript (including how to read the data and cluster calls into R) are included on our GitHub repo. Another option would be to download the data and meta-data directly from our website, where we have gene expression aggregated per cluster, calculated as trimmed means. A final option is to use our RNA-seq Data Navigator, which has much more flexibility in its features and will allow download of many different types of data aggregations for up to 10 genes at once.

I would strongly discourage you from trying to regenerate the cluster results from scratch unless your purpose is to compare different clustering results.

Best,
Jeremy