Can I analyze scRNA-seq data produced by Takara Smart-seq method?

Hi, I have scRNA-seq data. I sorted single cells and used Takara Smart-seq for RNA/cDNA and library preparation.
I wonder if I can analyze the data using Bioimage. but in this case, what format of the file is required to upload?

Hi Momoko - welcome to the Cellenics community!

Due to the much smaller number of cells, Cellenics performance may not be optimal with your Takara Smart seq dataset. (Essentially, Cellenics has been optimised for datasets with larger cells, like 10x data.) For example, all filters in the data processing module would likely need to be disabled for your dataset, and the differential expression may not return results if the cell number is too low, and if DE does return results, these results would need to be carefully interpreted. That said, we have had a couple of users with Smart-seq data use Cellenics for exploring gene expression in their data, so it’s worth a go!

In terms of what files to upload, to upload directly to Cellenics using the user interface, the files would need to be in the same format as 10x count matrices (i.e. a features file, a barcodes file and a matrix file). Assuming that your primary processing pipeline for Takara Smart seq data outputs some form of count matrices, it should be possible to extract and/or manipulate the files to make them acceptable to Cellenics. If you need some help, do give us a shout!