Exclusion of miRNA microarray probes in PDX models

Question

[Juan Cordero]

Hi,

I would like to measure expression of miRNAs from (Affy) Clariom D arrays. cDNA comes from a PDX mouse model. Since extracting human genetic material from the PDX implicates extracting some mouse cDNA too, I am not sure whether I should remove the human probes that may hybridise with mouse cDNA. I know this approach is reasonable when dealing with transcripts, but I have heard the Affy miRNA arrays contain probes for both human and mouse. Under such scenario, I would not expect mouse genetic material to hybridise with human probes, but with their corresponding mouse probes within the array. Thus, it shouldn't be necessary to exclude the probes from the affy library files, right?

Thanks

[Kevin Blighe]

I have heard the Affy miRNA arrays contain probes for both human and mouse.

You have heard that from where?

Have you answered your own question here: What is the specificity of a Microarray for human vs. mouse when completed for a mixed sample? ?

[Juan Cordero]

1) I heard that from a colleague and found out the annotation file from Affy (now Thermofisher) contains probesets for many organisms.

2) Nope. I refers in that question to mRNA. Now what I want to know is whether I need to apply the same procedure to miRNAs.