Question: Rna-Seq And Pri-Mirna
2
gravatar for Nicolas Rosewick
9.2 years ago by
Belgium, Brussels
Nicolas Rosewick9.2k wrote:

Hi everybody,

Is it possible to detect pri-miRNA from RNA-seq ? In the literature, I have not found papers talking about such thing.

Thanks,

N.

rna mirna • 3.3k views
ADD COMMENTlink modified 6.4 years ago by Biostar ♦♦ 20 • written 9.2 years ago by Nicolas Rosewick9.2k

any news on your experiments?

ADD REPLYlink written 9.1 years ago by Michael Dondrup48k

the experiment is on is way. Answers in january ;)

ADD REPLYlink written 9.0 years ago by Nicolas Rosewick9.2k

you didn't say which year ;)

ADD REPLYlink written 7.3 years ago by Michael Dondrup48k
1
gravatar for Michael Dondrup
9.2 years ago by
Bergen, Norway
Michael Dondrup48k wrote:

The problem with primary transcripts is that they are processed and degraded, these portions not very likely to yield high coverage in sequencing. They might appear as a weak signal surrounding the mature miRNA. If you know a true miRNA location, one could look for weaker signals surrounding it. If the miRNA is transcribed from an intron, I see marginal chances for separating the signals at all from the background.

ADD COMMENTlink written 9.2 years ago by Michael Dondrup48k
1
gravatar for Steve Lianoglou
9.2 years ago by
Steve Lianoglou5.1k
US
Steve Lianoglou5.1k wrote:

What Michael says is true, but you might have better luck if you design an experiment that gives you a better chance of finding what you're after.

For instance, as part of their work on the ENCODE project, Tom Gingeras' group has run RNA-seq on different sub-fractionations/sub-compartments across different cell lines. They have all different combinations of polyA+ and polyA-, long, and short RNA isolated from cytoplasm, nucleus, nucleolus, etc.

Perhaps you'll have better luck looking at RNA taken from within the nucleus to get what you are after. Unfortunately I can't link directly to the page for this project since their web-site is in (poorly written) flash, but just go to the lab's home page and click on the Projects > ENCODE menu item.

ADD COMMENTlink written 9.2 years ago by Steve Lianoglou5.1k
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