Viewing cardiomyocyte scRNAseq data online?

Gene-editing Discussion
1

Hi Allen Cell peeps!

I’m wondering if there is a way to view the cardio RNAseq data (with genes and relative expression values) online? I started to do the recommended quilt option, but don’t have 400GB of free space to download all the info. I saw that there are .csv files that are available to download separately, however the counts aren’t available for these (at least with the files I checked… maybe I’m looking at the wrong files?)

Any help you can provide is much appreciated! Thank you!
Maggie Fuqua

2

Hi Maggie!

We don’t have a fully preprocessed object containing the cardiomyocyte scRNA-seq data publicly available, but we do have the count matrix and necessary metadata available in Quilt, which takes up less than a gigabyte of storage. These files can be used to directly make a Seurat object in R. The raw_counts.mtx file can be read into R with readMM() from the Matrix package or potentially into Python with mmread() from the scipy module, though I haven’t tried the latter. I hope this helps!

Kristen Niekamp

3

Thank you for your reply, Kristen! I did download Quilt, and that was fine, but trying to run the data through Quilt (I believe), it started a 400GB download. So I should instead get R? I have never used that, and am frankly a newbie to coding-related things. I will see if some of my teammates can help me with this, and I’ll get back to you to let you know if it worked!

Thanks again,
Maggie

4

As far as I’m aware, Quilt is just an interface to access and download data stored in AWS and there isn’t really anything you can do with the data in Quilt itself. You’ll have to load the data into Python or R to be able to perform any analysis on it. If you click on “< > CODE” at the top of the quilt page, it will show you how to download the data using Python, the command line, or using the URI. If you click the four individual files here, you’ll be able to download them instead of the 400GB of files.

Let me know if you have any more questions!

Kristen Niekamp

5

Sweet! Thanks, Kristen! I’ll try these things out. :slight_smile:

Cheers!
Maggie