How can I compare my neurons basal microarrays transcriptome with a curated neuronal/brain expression database?

13 July 2023 0 4K Report

Hi dear colleagues,

Thank you for reading my question. I'm struggling to compare my basal transcriptome microarray data (Clariom S, human, Affymetrix) versus some brain or neuronal database to confirm neuronal identity gene expression in my iPSC-derived neuronal cultures.

For this purpose, I'm trying to perform a ssGSEA using GenePattern but cannot move forward to transforming my CEL files into GCT files. I know I need to convert the ID of the probes to the same format as in the comparing database, but I don't know how to do it without programming.

I also can't find a brain or neuronal database in a format I could use or an original file that I could convert to GCT.

Does anyone know an easier way to confirm that my cells' transcriptome is neuronal?

Thank you in advanced

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