I am very much in favor of always providing raw data for any NGS analysis.
However, for one particular project, I was asked to upload only the count matrices of a scRNA-seq and to not provide raw data.
As far as I know, both NCBI GEO and EMBL-EBI ArrayExpress require raw data. Do you know of a trusted repository where one can upload only the count matrices?
We have used FigShare to deposit code and data for reproducible analyses, for example https://www.nature.com/articles/s41597-022-01236-2
FigShare is essentially free, provides a permanent DOI and guarantees more than 10 years of working life. It is a good choice I think for general data types that don't fit into specialist formats such as GEO or ENA.
Looking at FigShare site it appears that only 20G of space is available for free. More than that will require some kind of a subscription?
The fact that our article was published in Scientific Data entitled us to 100GB for free in FigShare. Datasets larger than that can be published with a one-time payment (e.g., 1TB=USD2500).
OP is uploading count data, not raw data, so even the 20GB limit is very unlikely to be reached.
Good to know. I still think your comment below is important. Withholding data from access that is published needs to be discouraged.
One issue is the availability via third party sites may not be (more or less) perpetual, like NCBI/ArrayExpress.