esiRNA sequences in Drosophila
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6.8 years ago
Habil ▴ 80

Hi, I need a fasta file that includes the esiRNA (endogenous small interfering RNA) sequences in Drosophila. I couldn't find it in FlyBase nor UCSC Table Browser. Any ideas on where else to look for this information?

genome alignment • 1.2k views
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Take a look at RNACentral Drosophila entries. I don't see any esiRNA listed for Drosophila but at least it is worth a look.

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6.8 years ago
dyollluap ▴ 310

Try modENCODE Total RNA-seq datasets for Drosophila - much of the higher level analysis results has been long included in FlyBase, however it's based on Total RNA time course series, so it's likely to have many ncRNA if you're looking for it specifically within the bams. Also check if anything more recent has come out of those labs (Celniker and Gravely labs I think generated most of that data).

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Jiayu Wen from Eric Lai lab sent me the esiRNA (a.k.a. TE-siRNA) sequences, which she had annotated "for the modEncode consortium paper".

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