# Using 10X Genomics Mouse Transcriptomic matrix.csv file

**URL:** <https://community.brain-map.org/t/using-10x-genomics-mouse-transcriptomic-matrix-csv-file/3056>\
**Category:** Technical\
**Tags:** celltype, transcriptomics, analysis, how-to\
**Created:** [February 6, 2024, 9:22am UTC](https://community.brain-map.org/t/using-10x-genomics-mouse-transcriptomic-matrix-csv-file/3056 "2024-02-06T09:22:20Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![R91](https://avatars.discourse-cdn.com/v4/letter/r/54ee81/32.png) [@R91](https://community.brain-map.org/u/R91)\
**Post date:** [February 6, 2024, 9:22am UTC](https://community.brain-map.org/t/using-10x-genomics-mouse-transcriptomic-matrix-csv-file/3056/1 "2024-02-06T09:22:21Z")

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Hi,

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.

Thanks!  
Roksana

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**Author:** ![jeremyinseattle](https://yyz1.discourse-cdn.com/flex027/user_avatar/community.brain-map.org/jeremyinseattle/32/50_2.png) [@jeremyinseattle](https://community.brain-map.org/u/jeremyinseattle)\
**Post date:** [February 6, 2024, 4:26pm UTC](https://community.brain-map.org/t/using-10x-genomics-mouse-transcriptomic-matrix-csv-file/3056/2 "2024-02-06T16:26:27Z")

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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](https://portal.brain-map.org/atlases-and-data/rnaseq/mouse-whole-cortex-and-hippocampus-10x). The hdf5 file may be a bit easier to use than the matrix.csv file, as addressed in [this community forum post](https://community.brain-map.org/t/gene-expression-matrix-cvs-is-too-large-to-load-it/566/17). Let us know if this doesn’t solve your problem.  
Best,  
Jeremy