[Genome] Human fetal brain exon array track

Wed May 7 17:29:28 PDT 2008

Dear Donna,

Thank you very much for your reply! We're very pleased that you're
interested in including our data. Please have Andy contact my graduate
student, Matthew Johnson (cc'd here), who will coordinate transferring
the full data set (~1 gb) to you. Feel free to email him or call us at
(203) 737-1435 if you have any questions.

Best regards,
Nenad

Quoting Donna Karolchik <donnak at soe.ucsc.edu>:

> hi Nenad,
>
> We will be happy to add your data to the Genome Browser. Our
> browser engineer Andy Pohl will be working with you on this. It
> may be a few weeks before he can get to it. Andy will contact you
> if he has any questions and will let you know when your data is
> ready to preview.
>
> -Donna
> -----------------------------------
> Donna Karolchik
> Genome Browser Project Manager
> UCSC Genome Bioinformatics Group
> http://genome.ucsc.edu
>
> ----- Original Message -----
> From: "Nenad Sestan" <nenad.sestan at yale.edu>
> To: <genome at soe.ucsc.edu>; "Matt Johnson"
> <matthew.b.johnson at yale.edu>; "Christopher Mason"
> <christopher.mason at yale.edu>; "Yuka Imamura Kawasawa"
> <yuka.imamura at yale.edu>
> Sent: Tuesday, May 06, 2008 10:44 AM
> Subject: [Genome] Human fetal brain exon array track
>
>
> > To whom it may concern,
> >
> > My name is Nenad Sestan and I’m an assistant professor of
> > Neurobiology
> > at Yale School of Medicine. My lab has recently generated a
> > large amount
> > of data on gene expression in the developing (fetal) human brain
> > using
> > Affymetrix Exon Arrays, and we are planning to submit a
> > manuscript
> > shortly to Cell as a resource paper, describing this and related
> > data
> > and providing it as a public resource for the research
> > community. We
> > feel that this data set is an invaluable resource for many
> > reasons, not
> > least of which is the current paucity of published genome-wide
> > expression data from developing human or other primate brain. In
> > addition, as you know, the Exon Array platform provides
> > unparalleled
> > resolution in its coverage of the genome; the prevalence and
> > importance
> > of alternative splicing and other fine transcriptional
> > regulation in the
> > brain is of great interest to a wide audience of researchers,
> > and the
> > Exon Array provides a platform for probing that fine resolution.
> > Our
> > data would be complementary to the existing Affy All Exon track
> > that
> > contains expression data from other, adult tissues. Finally, and
> > most
> > importantly, we have sampled the developing human brain with
> > unprecedented spatial resolution, covering not only major brain
> > structures but also ten distinct areas of cerebral cortex. Thus,
> > these
> > data provide the first comprehensive look at the regional
> > transcriptome
> > of the fetal human brain, and we feel that they will be of great
> > interest to a wide audience of neurobiologists, human
> > geneticists, and
> > many others.
> >
> > Because of the large size of the data set (over 100 arrays from
> > 17
> > regions of four late mid-fetal human brains) and the microarray
> > format
> > of the track, we hope you would be willing to host this track on
> > the
> > genome browser site. We would like to use the microarray (BED
> > 15)
> > format, exactly like the Affy All Exon track, to which our data
> > are
> > directly comparable. We have formatted a sample track using a
> > subset of
> > the data; a link is included below, and matching microarray.ra
> > and
> > trackDb settings are attached to this email. Thank you for your
> > time and
> > attention, and please let me know if there is any other
> > information you
> > need to help you make your decision.
> >
> > Best wishes,
> > Nenad Sestan
> >
> > Sestan lab BED15 sample
> >
>
<http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg18&position=chr1:1004629-1100379&hgt.customText=http://pantheon.yale.edu/%7Embj7/SestanBED15test.txt>
> >
> >
>
(http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg18&position=chr1:1004629-1100379&hgt.customText=http://pantheon.yale.edu/~mbj7/SestanBED15test.txt)
> >
> > --
> > **********************************
> > Nenad Sestan, MD, PhD
> > Assistant Professor
> > Department of Neurobiology
> > Yale University School of Medicine
> > 333 Cedar Street, SHM C323-C
> > New Haven, CT 06510
> >
> > for U.S. postal service:
> > P.O. Box 208001
> > New Haven, CT  06520-8001
> >
> >
> > Office: (203) 737-2190
> > Lab: (203) 737-1435
> > Fax: (203) 785-5263
> > E-mail: nenad.sestan at yale.edu
> > Lab website: www.sestanlab.org
> > **********************************
> >
> >
> >
>
>
>
--------------------------------------------------------------------------------
>
>
> > track HumanBrainAtlas
> > shortLabel Human Brain Atlas
> > longLabel Human Brain Atlas Affymetrix Exon Arrays
> > group regulation
> > priority
> > visibility hide
> > type expRatio
> > expScale 3.0
> > expStep 0.5
> > groupings HBAGroups
> >
>
>
>
--------------------------------------------------------------------------------
>
>
> > name HBAGroups
> > type groupings
> > all HBAAll
> > combine
> >
>
HBAGroupByTissueMean,HBAGroupByTissueMedian,HBAGroupByTissueMeanNctx,HBAGroupByTissueMedianNctx,
> > subset HBASubsetByTissue,HBASubsetByReplicate,
> > combine.default HBAGroupByTissueMedianNctx
> >
> > name HBAAll
> > type all
> > description All Arrays
> > expIds
> >
>
0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,
> > groupSizes
> >
>
1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,
> > names
> >
>
Orbito_19L,Orbito_19R,MPFC_18L,MPFC_18R,MPFC_19L,MPFC_19R,MPFC_21L,MPFC_21R,MPFC_23L,MPFC_23R,DLPFC_18L,DLPFC_18R,DLPFC_19L,DLPFC_19R,DLPFC_21L,DLPFC_21R,DLPFC_23L,DLPFC_23R,VLPFC_18L,VLPFC_18R,VLPFC_19L,VLPFC_19R,VLPFC_21L,VLPFC_21R,VLPFC_23L,VLPFC_23R,MS_18L,MS_18R,MS_19L,MS_19R,MS_21L,MS_21R,MS_23L,MS_23R,Par_18L,Par_18R,Par_19L,Par_19R,Par_21L,Par_21R,Par_23L,Par_23R,Temp_18L,Temp_18R,Temp_19L,Temp_19R,Temp_21L,Temp_21R,Temp_23L,Temp_23R,Aud_18L,Aud_18R,Aud_19L,Aud_19R,Aud_21L,Aud_21R,Aud_23L,Aud_23R,Occ_18L,Occ_18R,Occ_19L,Occ_19R,Occ_21L,Occ_21R,Occ_23L,Occ_23R,Hipp_18L,Hipp_18R,Hipp_19L,Hipp_19R,Hipp_21L,Hipp_21R,Hipp_23L,Hipp_23R,Amyg_19L,Amyg_19R,Striat_18L,Striat_18R,Striat_19L,Striat_19R,Striat_21L,Striat_21R,Striat_23L,Striat_23R,Thal_18L,Thal_18R,Thal_19L,Thal_19R,Thal_21L,Thal_21R,Thal_23L,Thal_23R,VTA_19L,VTA_19R,Pons_19L,Pons_19R,Medulla_19L,Medulla_19R,Cbllm_18NA,Cbllm_19L,Cbllm_19R,Cbllm_21NA,Cbllm_23NA,
> >
> > name HBAGroupByTissueMean
> > type combine mean
> > description Arrays Grouped By Tissue Mean
> > expIds
> >
>
0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,
> > groupSizes 2,8,8,8,8,8,8,8,8,8,2,8,8,2,2,2,5,
> > names
> >
>
oPFC,mPFC,dlPFC,vlPFC,motorsensory,parietal,tempassociation,tempauditory,occip,hippocamp,amygdala,striatum,thalamus,VTA,pons,medulla,cerebellum,
> >
> > name HBAGroupByTissueMedian
> > type combine median
> > description Arrays Grouped By Tissue Median
> > expIds
> >
>
0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,
> > groupSizes 2,8,8,8,8,8,8,8,8,8,2,8,8,2,2,2,5,
> > names
> >
>
oPFC,mPFC,dlPFC,vlPFC,motorsensory,parietal,tempassociation,tempauditory,occip,hippocamp,amygdala,striatum,thalamus,VTA,pons,medulla,cerebellum,
> >
> > name HBAGroupByTissueMeanNctx
> > type combine mean
> > description Arrays Grouped By Tissue Mean and Neocortical Areas
> > Combined
> > expIds
> >
>
0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,
> > groupSizes 66,8,2,8,8,2,2,2,5,
> > names
> > neocortex,hippocamp,amygdala,striatum,thalamus,VTA,pons,medulla,cerebellum,
> >
> > name HBAGroupByTissueMedianNctx
> > type combine median
> > description Arrays Grouped By Tissue Median and Neocortical
> > Areas Combined
> > expIds
> >
>
0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,
> > groupSizes 66,8,2,8,8,2,2,2,5,
> > names
> > neocortex,hippocamp,amygdala,striatum,thalamus,VTA,pons,medulla,cerebellum,
> >
>
>
>
--------------------------------------------------------------------------------
>
>
> > _______________________________________________
> > Genome maillist  -  Genome at soe.ucsc.edu
> > http://www.soe.ucsc.edu/mailman/listinfo/genome
> >
>
>