information about hNCC (Human Neural Crest) data

[dani...@libero.it]

I am italian researcher  and for my research activity  i would need some informations about  the ChIP-seq performed from hNCC  (Human Neural Crest) against p300, H3K4me1 and H3K27ac, which mark active enhancer elements, and H3K4me3 and H3K27me3.

could you explain me in which way can I obtain this information in Genome Browser.

Thanks in advance

Dany

[Christopher Lee]

Hi Dany,

Thank you for your question about hNCC data. Although we do not have any hNCC specific data on the browser, we do have various enhancer data on the browser that you may find useful. In particular, you will probably be interested in the Transcription Factor ChIP-seq track, which illustrates various transcription factor binding sites near genes of interest. Here is a session illustrating EP300 (p300) binding sites, along with H3K4me1, H3K27ac and H3K4me3 data, near the TNFAIP3 gene:
http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=brianlee&hgS_otherUserSessionName=hg19.EP300

To change what transcription factors are selected, click the grey bar to the left of the "Transcription Factor ChIP-seq track, then on the resulting configuration page, click the box underneath "Filter by factor" and select any transcription factors of interest.

For more information on how to find enhancer data around a gene of interest, please see this previously answered mailing list question:
https://groups.google.com/a/soe.ucsc.edu/forum/#!msg/genome/q3OyjSo4Qdk/mhrQtRBhXbYJ

Again, this data is not specific to neural crest cell lines, but may still prove useful. The track description pages for each track goes further into depth on what each track represents and the underlying experiments and data.

Lastly, from a Google search for "human neural crest data", I found the following paper:
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3751405/

which has some excel files in the supplementary section listing hNCC specific enhancer regions for hg18.

Thank you again for your inquiry and using the UCSC Genome Browser. If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Christopher Lee
UCSC Genomics Institute

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