User:Karmella Haynes/Notebook/PcTF Genomics/2014/07/23

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(Autocreate 2014/07/23 Entry for User:Karmella_Haynes/Notebook/PcTF_Genomics)
Current revision (18:30, 23 July 2014) (view source)
(07/23/14)
 
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==mm/dd/yy==
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==07/23/14==
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* Line item 1
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* ChIPseq - bioinformatics
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'''Line item 1'''<br>
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'''Promoters research'''<br>
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> Samples
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* Found free promoters database at the Swiss Institute of Bioinformatics Eukaryotic Promoter Database (EPD) website
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* Retrieved BED file of all human promoters from: http://epd.vital-it.ch/get_promoters.php
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{| class="wikitable" border="0" cellspacing="3" <!-- Rxn. table -->
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** Selected H. sapiens, left all other options blank, clicked [select], downloaded BED file, uploaded to Galaxy as Promoters EPD All
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|-valign="top"
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** Total promoters: 23,316
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| <u>Reagent</u> || <u>Volume</u>
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** Each is only 10 bp long
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** Gene names are included!
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| reagent 1 || # μL
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* Note: Custom-generated promoter file (500 bp TSS regions) = 26,960. This is over 3k more than the EPD.
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| reagent 2 || #
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|-
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| reagent 3 || #
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|-
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| reagent 4 || #
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|-
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| dH<sub>2</sub>O || #
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| &nbsp; || # μL
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|}
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--> Reaction conditions
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'''New Galaxy files'''<br>
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Note: EPD allows selection of promoter sub-classes
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** All EPD promoters - uploaded as Promoters EPD All
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** TATA-box motif - Promoters EPD TATA = 2,007 regions
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** Initiator motif - Promoters EPD Init = 6,538 regions
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** CCAAT-box motif - Promoters EPD CCAAT = 3,838 regions
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** GC-box motif - Promoters EPD GC = 10,695 regions
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** CpG (unable to retrieve...looks like criteria have not been added yet)

Current revision

Pc-TF Genomics Main project page
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07/23/14

  • ChIPseq - bioinformatics

Promoters research

  • Found free promoters database at the Swiss Institute of Bioinformatics Eukaryotic Promoter Database (EPD) website
  • Retrieved BED file of all human promoters from: http://epd.vital-it.ch/get_promoters.php
    • Selected H. sapiens, left all other options blank, clicked [select], downloaded BED file, uploaded to Galaxy as Promoters EPD All
    • Total promoters: 23,316
    • Each is only 10 bp long
    • Gene names are included!
  • Note: Custom-generated promoter file (500 bp TSS regions) = 26,960. This is over 3k more than the EPD.

New Galaxy files
Note: EPD allows selection of promoter sub-classes

    • All EPD promoters - uploaded as Promoters EPD All
    • TATA-box motif - Promoters EPD TATA = 2,007 regions
    • Initiator motif - Promoters EPD Init = 6,538 regions
    • CCAAT-box motif - Promoters EPD CCAAT = 3,838 regions
    • GC-box motif - Promoters EPD GC = 10,695 regions
    • CpG (unable to retrieve...looks like criteria have not been added yet)



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