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Old 12-21-2009, 10:38 AM   #1
kumtl
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Default Transcriptome database?

Is there anyone who can tell me where can I find a human transcriptome database? For example,

Chr Gene Exon Start_position End position
========================================
1 X 1 12342214 12342295
1 X 2 12343122 12343821
1 X 3 12344012 12344123
...
M abc 1 1415412 1435412
M abc 2 1445512 1445652

Many thanks,

Kumtl

Last edited by kumtl; 12-21-2009 at 10:40 AM.
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Old 12-23-2009, 12:46 AM   #2
Rao
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from ucsc genome browser...
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Old 12-23-2009, 02:57 AM   #3
yjhua2110
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You can browse transcriptomic data generated by next-generation sequencing technology from deepBase database, which we have developed to map, store, retrieve, annotate, integrate and visualize deep sequencing-derived small RNAs, and facilitate transcriptomic research and the discovery of novel ncRNAs.

deepBase is available at: http://deepbase.sysu.edu.cn/
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Old 12-23-2009, 07:13 AM   #4
kumtl
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Thank you Rao. I got the data.

Last edited by kumtl; 12-23-2009 at 09:36 AM.
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Old 12-23-2009, 08:39 AM   #5
aguffanti
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Hi! you need, to start it, knownTorefSeq (.txt and .sql)

uc009vfk.1 NM_201530
uc009vfo.1 NM_001037748
uc009vfp.1 NM_001037748
uc009vgb.1 NM_001037748
uc009vgc.1 NM_001037748
uc009vgn.1 NM_001037748
uc009vgo.1 NM_001037748
uc009vgz.1 NM_001017393
uc009vhd.1 NM_207162
uc009vhe.1 NM_201530

There are also other known_to mapping files in UCSC db flat files directory

HTH, a very mery xmas

alessandro
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Old 12-23-2009, 07:19 PM   #6
kumtl
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From table menu in UCSC genome browser, I could download what I wanted. Refseq track provided me that information.

Anyway, I appreciate your helps.

Kumtl
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Old 04-05-2010, 06:19 PM   #7
cdragon
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deepBase is a nice database. But you can always find the raw transcriptome or genome data from Short Read Archive (SRA) at NCBI.
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Old 04-05-2010, 09:30 PM   #8
yjhua2110
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Quote:
Originally Posted by cdragon View Post
deepBase is a nice database. But you can always find the raw transcriptome or genome data from Short Read Archive (SRA) at NCBI.
Thanks for your interest in our deepBase( http://deepbase.sysu.edu.cn/ ).

We can't always find the raw transcriptome data from NCBI GEO/SRA at NCBI.

We find the raw transcriptome data by (1) searching new papers about small RNA transcriptomes from Pubmed using some terms, such as "deep sequencing", "next generation sequencing", "microRNA", etc. After we surveyed these papers, we get the raw data at website provided by authors(sometimes, we obtained the raw data by inquiring the authors) or NCBI GEO/SRA database according to the GEO/SRA accession number provided by authors' paper. (2) searching NCBI GEO and SRA database using some terms, such as "illumina genome analyzer", "small RNA",etc.

By now, I can't find a very convenient/automatic approach to get all small RNA transcriptome data. I look forward to anyone's suggestions.

Thank you very much!
Jianhua

Last edited by yjhua2110; 05-09-2010 at 08:54 AM.
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Old 04-09-2010, 07:37 AM   #9
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Yeah, the UCSC tables work like charm! and with BEDtools, its easy to get a lot of numbers related to target regions!
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Old 04-20-2010, 11:21 AM   #10
Ka123$
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Quote:
Originally Posted by yjhua2110 View Post
You can browse transcriptomic data generated by next-generation sequencing technology from deepBase database, which we have developed to map, store, retrieve, annotate, integrate and visualize deep sequencing-derived small RNAs, and facilitate transcriptomic research and the discovery of novel ncRNAs.

deepBase is available at: http://deepbase.sysu.edu.cn/
Can anyone suggest more info in looking into piRNA mappers and analysis?
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Old 04-25-2010, 06:30 PM   #11
yjhua2110
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Quote:
Originally Posted by Ka123$ View Post
Can anyone suggest more info in looking into piRNA mappers and analysis?
Thanks for your interest in our deepBase ( http://deepbase.sysu.edu.cn/ ).

Small RNAs were classified into four categories, including nasRNAs, pasRNAs, easRNAs and rasRNAs at our deepBase database. Many piRNAs overlapped with these small RNAs, especially rasRNAs. We are updating and extending the deepBase, and we will include the detail information for piRNAs at next release version of deepBase. If you want to get the raw data yielded from piRNA-associated small RNA libraries from a specify organism, can you send e-mail to me?

Last edited by yjhua2110; 05-09-2010 at 08:54 AM.
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Old 04-25-2010, 06:47 PM   #12
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THanks so much,
I will take a look at deepbase and get back to you soon.
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Old 05-08-2010, 02:17 PM   #13
aguffanti
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Default small and long ncRNAs analysis resources

Hi. You will find extensive informations on small (and large) ncRNA resources in the review in attach.

Kind regards,

Alessandro
Attached Files
File Type: pdf BriefBioinfo_2009.pdf (285.6 KB, 57 views)
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Old 06-13-2010, 08:59 PM   #14
yjhua2110
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Default computational Rnomics

a review paper focus on "structure identification and functional
prediction of non-coding RNAs in silico".
Attached Files
File Type: pdf Computational RNomics.pdf (725.2 KB, 36 views)
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