Other databases for deposition of scRNA-seq data than NCBI GEO?
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6 weeks ago
mschmid ▴ 180

Are there some other database for the deposition (raw data and/or count data) of scRNA-seq data than NCBI GEO?

EDIT: For clarification: I am looking for data and not submitting at the moment. So I want to make sure I make a complete search.

database scRNA • 341 views
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Thanks, aren't they synced? So if it is deposited at ENA it will appear at NCIB GEO / SRA?

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You don't want your data to appear in GEO? There is also ArrayExpress (not sure if that is linked to NCBI as well): https://www.ebi.ac.uk/arrayexpress/help/single-cell_submission_guide.html

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Sorry, my question is badly worded. I am actually SEARCHING for scRNA-seq datasets and want to make sure I catch all of them :) So where -- in addition to NCBI GEO -- do I have to search?

I basically need raw data.

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GEO/SRA should have you covered. There is variability regarding raw data for scRNAseq depending on technology used. Always look under the Data Access tab in SRA records for files uploaded by submitters.

There are also databases like: https://panglaodb.se/ and https://bioinfo.uth.edu/scrnaseqdb/. Not sure if they provide access to raw data or if that data is also in SRA.

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Thanks! I already found them. But they also just link to GEO/SRA as far as I can tell.

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