I am currently working with circRNA microarray data generated using the Arraystar Human circRNA microarray V2 (GPL21825) platform. However, I am facing a critical issue:
The platform only provides internal probe IDs in the format of ASCRPxxxxx (e.g., ASCRP002539, ASCRP001697, etc.), but for downstream functional analysis such as enrichment analysis (GO, KEGG, etc.), I need to obtain the corresponding:
1. hsa_circRNA IDs (e.g., hsa_circRNA_XXXXX)
2. host gene symbols
Unfortunately, I could not find any official or public annotation file that maps these ASCRP probe IDs to hsa_circRNA IDs and host genes.
I have checked: • GEO Platform (GPL21825) page. • Related publications (GSE84655, GSE84656, GSE94520). • circBase and other circRNA databases.
But none of them provides the direct mapping table between ASCRP IDs and circRNA annotations.
My question: Does anyone have access to the full annotation file of Arraystar Human circRNA microarray V2 or know where I can find a mapping between ASCRP IDs and their respective hsa_circRNA IDs and host genes?
Any help would be greatly appreciated.
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ParastooA •
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This appears to be a commercially available array. You could contact Arraystar and see if they would be willing to share the annotations: https://www.arraystar.com/circular-rna-array-service/
You can see ASCRP ID and the circ_RNA ID's in the table here but there is no additional annotation besides sequence for hg19 build : https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?view=data&acc=GPL21825&id=23937&db=GeoDb_blob142
It would be painful to try and blat the sequences to find where they are.