Using 10X Genomics Mouse Transcriptomic matrix.csv file


I was using the trimmed_means.csv file and the analysis was going great but it seems for the data I am looking for, I need to access the matrix.csv file. I downloaded it and it worked but it the first column is labelled with sample names so it was a bit confusing how to work with it.
I am trying to access L6b data and specifically wanting to access Ctgf+ cells and compare them to all the other cells in L6b. Having filtered by L6b, and Ctgf, I would like to evaluate the values of Hcrt, Hcrtr1 and Hcrtr2 in these selections.
Ultimately, I would like to access the other genes as well but these are my foci right now.


Hi Roksana,
Assuming you mean the mouse whole cortex and hippocampus 10x data set, the raw data (and other info) can be found at the download page here. The hdf5 file may be a bit easier to use than the matrix.csv file, as addressed in this community forum post. Let us know if this doesn’t solve your problem.

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