I was wondering if it were possible to combine Small RNA libraries prepared using the Illumina Small RNA kit and mRNA libraries prepared using the TruSeq stranded mRNA kit into the same sequencing reaction?
I noticed that the PCR primer (RP1) used in the small RNA kit is similar up to 20ish nt from the 5' end of the TruSeq Universal Adapter.
RP1 (RNA PCR Primer) | After this point it differs from TruSeq Universal Adapter
5’ AATGATACGGCGACCACCGAGATCTACAC|GTTCAGAGTTCTACAGTCCGA
RPIX (Small RNA Index Primers)
5’ CAAGCAGAAGACGGCATACGAGATXXXXXXGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
vs.
TruSeq Universal Adapter
5’ AATGATACGGCGACCACCGAGATCTACAC|TCTTTCCCTACACGACGCTCTTCCGATCT
TruSeq Index Adapters
5’ GATCGGAAGAGCACACGTCTGAACTCCAGTCACXXXXXXATCTCGTATGCCGTCTTCTGCTTG
Although the Small RNA and TruSeq individual adapters vary widely beginning from the 5' end.
I'm asking because I called Illumina support and they told me that they don't recommend it but didn't specifically say it would be incompatible. Knowing them they would want me to run 2 sequencing reactions separately.
I noticed that the PCR primer (RP1) used in the small RNA kit is similar up to 20ish nt from the 5' end of the TruSeq Universal Adapter.
RP1 (RNA PCR Primer) | After this point it differs from TruSeq Universal Adapter
5’ AATGATACGGCGACCACCGAGATCTACAC|GTTCAGAGTTCTACAGTCCGA
RPIX (Small RNA Index Primers)
5’ CAAGCAGAAGACGGCATACGAGATXXXXXXGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
vs.
TruSeq Universal Adapter
5’ AATGATACGGCGACCACCGAGATCTACAC|TCTTTCCCTACACGACGCTCTTCCGATCT
TruSeq Index Adapters
5’ GATCGGAAGAGCACACGTCTGAACTCCAGTCACXXXXXXATCTCGTATGCCGTCTTCTGCTTG
Although the Small RNA and TruSeq individual adapters vary widely beginning from the 5' end.
I'm asking because I called Illumina support and they told me that they don't recommend it but didn't specifically say it would be incompatible. Knowing them they would want me to run 2 sequencing reactions separately.
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