Help with interpretation of special data linked to UCSC? Somewhat Urgent
Zinyk, Dawn
I hope you can help me as, although I use the UCSC Genome Browser Gateway for some basic genomic-DNA-sequence stuff, the UCSC link in the attached paper confuses me. And we are trying to quickly clone a construct for use solidifying data of a conditionally approved paper we've submitted.
It is a paper about Human Accelerated Regions (HARs). In Figure 3E (page 26), they identify a Primate-Selective Element (red) that appears to be, by legend, about 4 to 5.6-kb upstream of the transcription start site.
On page 8, they cite that there is "an easily searchable online resource through the UCSC Genome Browser (the HARHub: http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&hubUrl=https://allendiscoverycenter-harhub.s3.us-east-2.amazonaws.com/HAR_hub/hub.txt)"
However, I don't understand it.
Is there any way you might help me with the identification of the sequence of this region from the UCSC site?
Thank you so much for any help you might be able to provide.
Take care, and have a wonderful day!
Dawn :-)
P.S., if the information is easily discernible through that link, I'd also be interested in the sequence of the spike at the beginning of the transcription start site, but I could always just use e.g. the first 1kb. Thanks, regardless. d
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Jairo Navarro Gonzalez
Hello,
Thank you for using the UCSC Genome Browser and sending your inquiry.
If you are new to using the UCSC Genome Browser, you may find the training page useful:
When you view the URL you shared from the paper, the author's hub is connected to the UCSC Genome Browser for the human assembly hg38/GRCh38. Connecting the hub does not automatically take you to the location in Figure 3E, so you can search for the gene mentioned in the caption, PPP1R17.
If you want to obtain the sequence for a genome region, you can use the View --> DNA via the bluebar menu. A video tutorial on obtaining sequences can be found on the training page mentioned above:
https://www.youtube.com/watch?v=6JoUqM1iKxQ&list=UUQnUJepyNOw0p8s2otX4RYQ
If the instructions are not provided in the paper, the paper's lead contact, Christopher A. Walsh (christop...@childrens.harvard.edu), could help interpret the data to obtain the sequence coordinates.
I hope this is helpful. 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 Google Groups forum.
If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.
Jairo Navarro
UCSC Genome Browser
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