List of Cell-Type and/or Cluster Markers

Transcriptomics Explorer
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Hi,

Is there a way to extract marker genes for each cell-type or cluster, or is it required to download the data and perform differential expression testing offline?

Thanks.

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Hi @AndyCGraham. For the “Cell Types Database: RNA-Seq Data” “Explore & Analyze” tools, this is currently possible for human “MTG - SMART-Seq (2018)” and mouse “V1 & ALM - SMART-seq (2018)”, but not yet for more recent data sets. You can find additional posts about the Transcriptomics Explorer (for more recent data sets) in its own Community Forum topic.

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Hi Jeremy,
are there any updates on this topic.

I just wondered if there is some summary of all cell types listed in: Cell Type Knowledge Browser.

This would be a really helpful feature, for adapting and understanding the annotation for our datasets.

All the best
Matthias

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Hi @matthias. All of the data from the Cell Type Knowledge Explorer comes from the package of papers on primary motor cortex summarized in the Flagship Paper. If you scroll down to the “Data Availability” section you can see where to access the raw data (there is a more complete table in the bioRxiv version). Finally, you can get underlying data for nearly all panels on the cell type cards by clicking on the relevant “More Data” button, as shown here for example:
image
That said, we are always looking for feedback about how we can better provide content to the public, and we’ll take this idea of having more prominent data access for future versions of this tool into consideration.

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Thank you souch for your reply @jeremyinseattle !
It is some how overwhelming how much data you share on your site, that I lost sight of the wood for the trees!

(please correct me if I am wrong)
A list with marker genes can also be found in those two publications:
Comparative cellular analysis of motor cortex in human, marmoset and mouse
A transcriptomic and epigenomic cell atlas of the mouse primary motor cortex

Those genes + celltypes listed in the supplementary data would be great to be directly available on the Cell Type Knowledge Explorer, or the Azimuth page. :smiley:

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