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More next generation sequencing data in miRBase

We have added more next generation sequencing datasets to the read views in miRBase. These include data from 7 metazoan genomes, 5 series of Drosophila sets from GEO and one human GEO series — that’s 56 new next generation sequencing experiments in all. The depth of coverage for some species is now extensive, for example, over 1 million reads map to the mouse mir-17 sequence.

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Posted in data update.


7 Responses

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  1. sam says

    One of the real strengths of these views of deep seq data is the ability to spot sequences which are not likely to be real miRNAs. For example, reads tile across the whole sequence annotated as mir-469 in mouse (Chiang et al. also point out that this sequence is unlikely to be a miRNA.) This “miRNA” will therefore be deleted in miRBase 17.

    We want to hear about sequences that you don’t believe to real miRNAs — please comment here for discussion, or email us.

  2. Paul Gardner says

    This is great work Ana. I’m having a great time browsing the famous miRNAs. The data provides useful QC for the less reliable miRNAs also.

  3. Charlie says

    Is it possible that you will start a section that contains all the deep sequencing data, or at the very least is there a location that lists all species which have this data type so I don’t have to look through each organism to find it for a specific miRNA in multiple species?

    • ana says

      Hi Charlie.
      On miRBAse search page you can search by tissue expression and there you can find listed all the organisms having deep-sequencing data in miRBase.

      At some point we will make database files for deep-sequencing data available on the miRBase ftp site, and so you should be able to download and search those as you want.

      Hope this helps,
      Ana

  4. Jacques says

    Hi,
    Is the NGS data related to human’s miRNAs available currently in miRBase FTP site?
    Thanks!!

    Jacques

    • sam says

      Sorry — it’s not right now. Obviously we want it to be, and we’ll shout here when it is.

      • ana says

        Hi Jacques.
        If you are looking for the entire set of NGS data, every experiment we put in miRBase has a link to GEO from where you can download the data.
        If you are looking for the read count for each microRNA for a given NGS experiment then you can find this by clicking on Number of miRNA of the experiment page.
        Thought this could maybe help.

        Ana