[Genome] Drosophila ChIP/chip

[Mark Biggin]

Ann, I should perhaps have also provide a link to our own web site,  
which may provide answers to some potential questions.

http://bdtnp.lbl.gov/Fly-Net/chipchip.jsp?w=summary

You'll see our motivation for preferring that you host a visualization  
of our data is that currently we have provided links to the UCSC  
browser for loading files as guest tracks, but to allow quick upload  
times, we only upload crude simplifications of the data that do not  
show much critical detail.

(http://bdtnp.lbl.gov/Fly-Net/SearchChipper?first=12     the links on  
the right).

It would be great to allow folks to quick see the richer data shown in  
the wiggle files in the below message.

thank you for considering our request.


mark



On Mar 6, 2008, at 10:03 AM, Ann Zweig wrote:

> Hello Mark,
>
> 	Our team is looking at your data and discussing the possibility of  
> hosting it on our website.  We will get back to you off-list with  
> any questions.
>
>
> Regards,
>
> ----------
> Ann Zweig
> UCSC Genome Bioinformatics Group
> http://genome.ucsc.edu
>
>
>
> Mark Biggin wrote:
>> Dear UCSC team, we wonder if you would be interested in including  
>> ChIP/ chip data produced by the Berkeley Drosophila Transcription  
>> Network  Project as a track on your browser? For now we would  
>> suggest providing  1% and 25% False Discovery Rate thresholded data  
>> for 7 sequence  specific transcription factors and RNA polymerase.  
>> Wiggle files of the  1% FDR data are at the links below, so you can  
>> get a sense of the  data. (these are to Release 4 of the mel genome  
>> sequence). We could  improve the appearance and add color if you  
>> agree to host these.
>> http://rana.lbl.gov/~smacarth/ChIPChip/Public_Release/wiggle/bcd_1_012505-sym-1.wig
>> http://rana.lbl.gov/~smacarth/ChIPChip/Public_Release/wiggle/bcd_2_092005-sym-1.wig
>> http://rana.lbl.gov/~smacarth/ChIPChip/Public_Release/wiggle/cad_1_020107-sym-1.wig
>> http://rana.lbl.gov/~smacarth/ChIPChip/Public_Release/wiggle/gt_2_020107-sym-1.wig
>> http://rana.lbl.gov/~smacarth/ChIPChip/Public_Release/wiggle/hb_1_012505-sym-1.wig
>> http://rana.lbl.gov/~smacarth/ChIPChip/Public_Release/wiggle/hb_2_092305-sym-1.wig
>> http://rana.lbl.gov/~smacarth/ChIPChip/Public_Release/wiggle/kni_1_092706-sym-1.wig
>> http://rana.lbl.gov/~smacarth/ChIPChip/Public_Release/wiggle/kni_2_092706-sym-1.wig
>> http://rana.lbl.gov/~smacarth/ChIPChip/Public_Release/wiggle/kr_1_113005-sym-1.wig
>> http://rana.lbl.gov/~smacarth/ChIPChip/Public_Release/wiggle/kr_2_113005-sym-1.wig
>> http://rana.lbl.gov/~smacarth/ChIPChip/Public_Release/wiggle/polII_8WG16_092905-sym-1.wig
>> http://rana.lbl.gov/~smacarth/ChIPChip/Public_Release/wiggle/z_2_051504-sym-1.wig
>> Our data are particularly well justified and of high quality. In   
>> addition, our interpretation and analysis of the in vivo DNA  
>> binding  data differ significantly from most others, emphasizing  
>> differences in  the classes of region bound at different levels and  
>> showing that many  weakly bound regions are likely to be non  
>> functional. This is  explained in our recent PLoS Biology paper.
>> http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371%2Fjournal.pbio.0060027
>> I'd be happy to provide any further information you may require.  
>> We  have data on a further 14 factors that we hope to release by  
>> the summer.
>> sincerely
>> mark biggin
>> Mark Biggin
>> Genomics Division
>> Lawrence Berkeley National Laboratory
>> Berkeley CA 94720
>> Phone 	(510) 486 7606
>> Fax 		(510) 486 4229
>> email	mdbiggin at lbl.gov
>> _______________________________________________
>> Genome maillist  -  Genome at soe.ucsc.edu
>> http://www.soe.ucsc.edu/mailman/listinfo/genome

Mark Biggin
Genomics Division
Lawrence Berkeley National Laboratory
Berkeley CA 94720

Phone 	(510) 486 7606
Fax 		(510) 486 4229
email	mdbiggin at lbl.gov