ENCODE histone modification data

[Alessandro Testori]

Greetings!

I'm looking in the goldenPath:
http://hgdownload.cse.ucsc.edu/goldenPath/hg38/database/

for histone modification data. In particular I'm interested in all histone modification data coming from neuroblastoma and melanoma cell lines, but I'm afraid these data are not always available. Alternatively I would like to get data not referred to a single cell line, but general data. Is it possible?

Please let me know.

With kind regards.

Alessandro Testori, PhD

University of Naples

[Cath Tyner]

Hello Alessandro,

Thanks for using the UCSC Genome Browser and for submitting your question regarding how to find certain cell lines and also general data from ENCODE data.

General information about ENCODE at UCSC

​(​

limited until 2012

​).​

Please note: ENCODE results from 2007 until present day are available from the ENCODE Project Portal.

UCSC ENCODE Downloads for hg19 (2007-2012 data):
https://genome.ucsc.edu/ENCODE/downloads.html

For finding certain cell line ENCODE data in the hg19 UCSC Genome Browser, please see this previously answered question, which describes how to use our "track search" function

​.​

Our ENCODE vocab page can also help with picking out a cell type (and interpreting other metaData):

For example, a search of 'melanoma' hits these three samples:
Colo829
RPMI-7951
Mel_2183

From here, you could use the

​ENCODE ​

Experiment Matrix to see experiments on these cell types

​.​

In general, your best option is to go to the new ENCODE portal. For example, at the new ENCODE portal, you can search "melanoma" and then click on "Biosample" under the "Data Type" section in the upper left of the search results and each Biosample will list related experiments on their individual pages

​.​

Please note that the ENCODE portal at www.encodeproject.org is supported separately from the UCSC Genome Browser. For help specific to this portal, please refer to their contact page

​, ​

and email them

​ at​

encod...@lists.stanford.edu

Thank you again for your inquiry and for using the UCSC Genome Browser. 

​Please send new and follow-up questions to one of our UCSC Genome Browser mailing lists below:

  * Post to the Public Help Forum: E

mail 

gen...@soe.ucsc.edu

​ or search the Public Archives

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​Enjoy,​

Cath
. . .

Cath Tyner

UC Santa Cruz Genomics Institute

UCSC Genome Browser

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