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Does it matter if I used ON-TARGETplus siRNA in my screen when it comes to selecting seed sibling controls?

Yes, because the seed region has less activity when it carries the ON-TARGETplus siRNA chemical modification pattern, you should use seed siblings with the same modifications. The seed sibling search will automatically select only ON-TARGETplus-modified siRNAs as seed siblings when the input catalog numbers are also ON-TARGETplus.