Comments on: More next generation sequencing data in miRBase http://www.mirbase.org/blog/2010/12/more-next-generation-sequencing-data-in-mirbase/ miRBase news and views Thu, 09 May 2013 04:47:03 +0000 hourly 1 http://wordpress.org/?v=3.0.1 By: ana http://www.mirbase.org/blog/2010/12/more-next-generation-sequencing-data-in-mirbase/#comment-1196 ana Tue, 12 Apr 2011 08:46:34 +0000 http://www.mirbase.org/blog/?p=41#comment-1196 Hi Jacques. If you are looking for the entire set of NGS data, every experiment we put in miRBase has <a href="http://mirbase.org/cgi-bin/get_read.pl?acc=MI0000063" rel="nofollow">a link to GEO </a> 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 <a href="http://mirbase.org/cgi-bin/mirna_summary.pl?experiment_mirna=ER0000000104" rel="nofollow">Number of miRNA of the experiment page</a>. Thought this could maybe help. Ana 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

]]> By: sam http://www.mirbase.org/blog/2010/12/more-next-generation-sequencing-data-in-mirbase/#comment-1195 sam Tue, 12 Apr 2011 08:26:36 +0000 http://www.mirbase.org/blog/?p=41#comment-1195 Sorry -- it's not right now. Obviously we want it to be, and we'll shout here when it is. Sorry — it’s not right now. Obviously we want it to be, and we’ll shout here when it is.

]]> By: Jacques http://www.mirbase.org/blog/2010/12/more-next-generation-sequencing-data-in-mirbase/#comment-1194 Jacques Tue, 12 Apr 2011 03:33:10 +0000 http://www.mirbase.org/blog/?p=41#comment-1194 Hi, Is the NGS data related to human's miRNAs available currently in miRBase FTP site? Thanks!! Jacques Hi,
Is the NGS data related to human’s miRNAs available currently in miRBase FTP site?
Thanks!!

Jacques

]]> By: ana http://www.mirbase.org/blog/2010/12/more-next-generation-sequencing-data-in-mirbase/#comment-313 ana Mon, 20 Dec 2010 10:59:05 +0000 http://www.mirbase.org/blog/?p=41#comment-313 Hi Charlie. On <a href="http://mirbase.org/search.shtml" rel="nofollow">miRBAse search page</a> 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 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

]]> By: Charlie http://www.mirbase.org/blog/2010/12/more-next-generation-sequencing-data-in-mirbase/#comment-280 Charlie Fri, 17 Dec 2010 00:12:06 +0000 http://www.mirbase.org/blog/?p=41#comment-280 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? 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?

]]> By: Paul Gardner http://www.mirbase.org/blog/2010/12/more-next-generation-sequencing-data-in-mirbase/#comment-190 Paul Gardner Wed, 08 Dec 2010 21:32:20 +0000 http://www.mirbase.org/blog/?p=41#comment-190 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. 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.

]]> By: sam http://www.mirbase.org/blog/2010/12/more-next-generation-sequencing-data-in-mirbase/#comment-186 sam Wed, 08 Dec 2010 17:27:50 +0000 http://www.mirbase.org/blog/?p=41#comment-186 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, <a href="http://www.mirbase.org/cgi-bin/get_read.pl?acc=MI0002404" rel="nofollow">reads tile across the whole sequence annotated as mir-469 in mouse</a> (<a href="http://dx.crossref.org/10.1101%2Fgad.1884710" rel="nofollow">Chiang et al. also point out</a> 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 <a href="mailto:mirbase@manchester.ac.uk" rel="nofollow">email us</a>. 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.

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