Help with selecting chip platform

[Anna van Koeverden]

Hello, my data is from RNAseq of isolated microglia from mouse retina. A sample of the gene IDs in the dataset I received from the genomic research facility is below. Thank you so much!

Cdca8
Cenpf
Kif15
Knstrn
Knl1
Brca1
Mcm10
Mcm5
Prr11
Lag3
Nusap1
Foxm1
H2bc11
Top2a
Wdr62
Kifc1
Kif20b
Aspm
Brip1
Kif20a
Fignl1
Polq
Aurkb
Cenpe
Cdca2
Anln
Sgo2a
Ccna2
Kif22
Nsd2
Cit
Diaph3
Kif4
Cbx5
Rrm2

[Castanza, Anthony]

Hello,

GSEA can support this data one of two ways, firstly, if you’re using gene sets from our Human collections, you can use the “Mouse_Gene_Symbol_Remapping_Human_Orthologs_MSigDB.v2023.1.Hs.chip” file with Collapse.
Or, if you’re using our Mouse collections, you can use the “Mouse_Gene_Symbol_Remapping_MSigDB.v2023.1.Mm.chip” file with Collapse.

 

Let me know if you have any more questions!

 

-Anthony

 

Anthony S. Castanza, PhD

Department of Medicine

University of California, San Diego

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[Anna van Koeverden]

Thank you so much!