piRNA at UCSC
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Jiang,Jinmai
Jan 23, 2017, 11:32:28 AM1/23/17
to gen...@soe.ucsc.edu
Hello,
This is Jinmai Jiang from University of Florida. I am trying to obtain all the human piRNA sequences and get an output BED file from the UCSC Gene database, but no luck at all for the last several days. Could you help me out over there?
Thanks a lot!
Have a great day!
Jinmai
Jinmai Jiang, Ph.D.
Research Assistant Professor
Department of Pharmaceutics
Cancer Genetics Research Complex, Room 470
2033 Mowry Road
Gainesville, FL 32610
Tel 352-273-9119
UNIVERSITY of FLORIDA | College of Pharmacy
Cath Tyner
Jan 23, 2017, 6:26:50 PM1/23/17
to Jiang,Jinmai, gen...@soe.ucsc.edu
Hello Jinmai,
Thanks for using the UCSC Genome Browser. You can obtain this information by using our Table Browser. If you are unfamiliar with the Table Browser, please see the User’s Guide at http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html.
The UCSC Genes track contains piRNAS. To obtain the piRNAs, perform the following steps. For this example, I will use GRCh38/hg38, but you can also choose GRCh37/hg19 if you prefer.
1. Navigate to http://genome.ucsc.edu/cgi-bin/hgTables
2. Select the following options:
3. Next, you will need to create a filter to select only the piRNA records in your output. For the “filter” field, click the “create” button.
4. In the “hg38.kgXref based filters” section (or hg19.kgXref based filters) , the “description” line should read exactly as the following:
description does match *piR-*
Note that you must type
This filter will return transcripts with "piR-#####" id's in the description field of the item. For example,
Th
5. Click the “submit” button to complete the filter.
6. Click the “get output” button from the main form (where you set clade, genome, assembly, etc.).
7. Click the "get BED" button.
You should see results like this:
chr21 45898221 45898271 uc002zfb.3 0 - 45898221 45898221 0 1 50, 0,
chr21 45903703 45903735 uc011afg.2 0 - 45903703 45903703 0 1 32, 0,
chr21 45904163 45904216 uc002zfc.2 0 - 45904163 45904163 0 1 53, 0,
chr21 45911601 45911640 uc011afh.2 0 - 45911601 45911601 0 1 39, 0,
chr21 45913121 45913224 uc002zfd.3 0 - 45913121 45913121 0 1 103, 0,
Thanks for using the UCSC Genome Browser. You can obtain this information by using our Table Browser. If you are unfamiliar with the Table Browser, please see the User’s Guide at http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html.
The UCSC Genes track contains piRNAS. To obtain the piRNAs, perform the following steps. For this example, I will use GRCh38/hg38, but you can also choose GRCh37/hg19 if you prefer.
1. Navigate to http://genome.ucsc.edu/cgi-bin/hgTables
2. Select the following options:
Clade: Mammal
Genome: Human
Assembly: Dec. 2013 GRCh38/hg38 (or you can select Feb. 2009 (GRCh37/hg19)
Group: Genes and Gene Prediction Tracks
Track: GENCODE v24 (or, if you selected hg19 in the above step, choose "UCSC Genes")
Table: knownGene (note, you can click on the "Table Schema" button here to see a table description)
Region: select “genome” for the entire genome, or select “position” and enter the position (e.g., chr21:33031597-33041570) in the text box for a single position, or click the “define regions” button to specify multiple positions.
Output format: select "BED - browser extensible data" from the drop-down list.
3. Next, you will need to create a filter to select only the piRNA records in your output. For the “filter” field, click the “create” button.
4. In the “hg38.kgXref based filters” section (or hg19.kgXref based filters) , the “description” line should read exactly as the following:
description does match *piR-*
Note that you must type
the
asterisk " * " before and after "piR-" for this filter. This filter will return transcripts with "piR-#####" id's in the description field of the item. For example,
ID: uc057com.1mRNA: DQ598170geneSymbol: AL121992.1Description: Homo sapiens piRNA piR-36236, complete sequence. (from mRNA DQ598170)
Th
e
"
description does match *piR-*"
filter will exclude piRNA-related items that do not have the "piR-#####" id, but if you want to ALSO
include items that simply have ""piRNA" in the description, you can change your filter to "*piRNA*" which, in addition to including
the "piR-#####" id items, will
include items such as: ID: uc057kyx.1mRNA: AF227192geneSymbol: TDRKH
Description:Participates in the primary piRNA biogenesis pathway and is required during spermatogenesis to repress transposable elements and prevent their mobilization, which is essential for the germline integrity. The piRNA metabolic process mediates the repression of transposable elements during meiosis by forming complexes composed of piRNAs and Piwi proteins and govern the methylation and subsequent repression of transposons. Required for the final steps of primary piRNA biogenesis by participating in the processing of 31-37 nt intermediates into mature piRNAs. May act in pi-bodies and piP-bodies by transferring piRNA precursors or intermediates to or between these granules (By similarity). (from UniProt Q9Y2W6)
5. Click the “submit” button to complete the filter.
6. Click the “get output” button from the main form (where you set clade, genome, assembly, etc.).
7. Click the "get BED" button.
You should see results like this:
chr21 45898221 45898271 uc002zfb.3 0 - 45898221 45898221 0 1 50, 0,
chr21 45903703 45903735 uc011afg.2 0 - 45903703 45903703 0 1 32, 0,
chr21 45904163 45904216 uc002zfc.2 0 - 45904163 45904163 0 1 53, 0,
chr21 45911601 45911640 uc011afh.2 0 - 45911601 45911601 0 1 39, 0,
chr21 45913121 45913224 uc002zfd.3 0 - 45913121 45913121 0 1 103, 0,
Please respond to this list if you have further questions!
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Cath Tyner
Jan 23, 2017, 7:12:18 PM1/23/17
to Jiang,Jinmai, gen...@soe.ucsc.edu
Hello again Jiang,
Unfortunately, one of our engineers has alerted me to an issue with how we have stored piRNAs, and at this time, I cannot recommend the use of the UCSC Genome Browser to obtain piRNA data. We will be looking into fixing this, and I will alert you when the work is complete. For now, I do not recommend the method that was sent in my earlier post, please disregard those steps.
Cath
. . .
Cath Tyner. . .
UCSC Genome Browser, Software QA & User Support
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