Because list of probes on the BeadChip contains some of MIR genes (i.e. MIR1-2, MIR1200, MIR1202, MIR1203 etc.) however, as I remember correctly - the mature microRNAs don't contain the polyA tails, so the oligodT primers don't catch them.
Are these probes related to the pre-microRNA transcripts and do they always have polyA tail?
Thank you for any answers and suggestions!
Best regards,
Agata
Yes, expression of some MIR genes can be measured in Illumina Beadchip. There have been evidences that the pri-miRNA precursor contains both 5'-caps and 3'-poly(A) tails. You can have a look at the article in the link below:
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1370684/
It might be possible that the probes against the MIR genes in the beadchip are hybridizing to these pri-miRNA precursors.
Dear Chitra - thank you for your response and publication!
I wrote an email to TechSupport of Illumina so I want to share with their response:
"A subset of miRNAs have poly A tails, not as mature miRNAs but in the preprocessed primary transcript. These are called primary miRNAs or pri-miRNAs (polyadenylated primary transcripts). At the pri-miRNA stage these molecules are much longer than mature miRNAs and should be retained in a standard mRNA extraction kit.
The miRNA content on this chip was designed for these pri-miRNAs which will amplify with for example the Ambion TotalPrep™ RNA Amplification Kit. Please have a look at the manifest to check the miRNA content of the HumanHT-12.
However, I would advise that the HumanHT-12 array is not the best tool to analyze small RNAs. If they are interested in small RNAs I would recommend them to go for small RNA sequencing, and for example to have a look at the following library prep kit:
http://www.illumina.com/products/truseq_small_rna_sample_prep_kit.html."
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