Can small RNA library be sequenced paired end?

[rnaeye]

Hi all,
I made a library that is compatible with TruSeq Small RNA protocol. In other words, I can sequence it by Miseq using small RNA sequencing option. My libraries contain longer inserts about 200 bp. I need to sequence it from both ends (paired-end). Miseq instrument sample sheet does not give me option for paired end (option is grayed out) when I choose Truseq small RNA.

Now, how do I sequence my small RNA libraries with paired end. Did anyone try it before? I would give a call Illumina tech support but they are in sleep due to different time zone at the moment. Thank you for the help.

[nucacidhunter]

If I understand correctly, the library is not actually a small RNA library. In sample sheet you can put library type as TruSeq DNA library and that should allow paired end sequencing.

[rnaeye]

hi nucacidhunter,
Truseq DNA Adapter sequences are not same as small RNA adapter sequences. It's a small RNA library, except that inserts are not ~22nt small RNA but 200 bp long RNA. I think I have already found a way. Thanks.

[Acrimony]

Hello everyone and rnaeye!
I have the same idea now. I want to sequence long library with adaptors from TruSeq Small RNA protocol. And I noticed that sequences of adapters, especially from P5-side, are not similar to TruSeq Adapters.
Did anyone try to sequence TruSeq Small RNA library from both ends? Is it technically possible to obtain the data from read 2? Is primer for read 2 sequencing compatible with TruSeq Small RNA adapters?
Thank you for the help!