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1 Saving and Sharing Sessions on the UCSC Genome Browser In this tutorial we will be discussing the ways to save a session and share the contents of your session with other users or to save it for future reference. An important aspect session, not a static picture. of this feature is that it saves an active genome.ucsc.edu. “ rowser here at the main page, We will start by resetting the B Reset that an individual would who ” so that we start at the same page All User Settings has T he default location on the gateway is the never been to the B rowser before. human genome assembly hg38. [0:30 Set Browser to hg19 UCSC Genes and GTEx tracks. ] is still the best annotated of the human assemblies and We’ll switch to hg19 because it go ] button navigate to our G enome Browser graphic with the [ any dataset s are . M turned on by default so we will use the [ ] button to turn all of them off , cleaning hide all nd turn on just the UCSC G “ up the screen, a enes track to pack .” And the GTEx track, “ full .” U se the [ refresh ] button to turn which is a gene expression track, we’ll set to them on. hemoglobin gene cluster .] Set up interesting view on the [1:01 Now let’s navigate to a that perhaps you’ve picked up from the literature : location Hemoglobin gene, HBB, where you may read that the amino acid lysine 17 in a variant has changed to glutamate. We’ll use enclature. HGVS nom go , we discover that we have in fact navigated to amino acid 17 ] button now Using the [ ysine is at 18 and the B The l us a warning that this but we’re off by one. rowser gives does not match the value. This is because some annotations in the literature for some no t count the m ethionine as one; they count it as zero genes do ’s cle aved off and if it not present in the mature protein. You’ll notice that the highlights and takes us Browser amino acid 17 anyway . to track is for whole blood, as you might You’ll notice that the highest signal in the GTEx expect for hemoglobi n. Let's get a larger view of the genome in this region and see some of the other genes in the hemoglobin cluster. So let ’s zoom out by a factor of [ 100x by another factor of [ 10x ]. This puts two hemoglobin genes in the ] and then HBB BD window: . and H . Let's suppose this is the image that you want to save and share with your colleagues You could try to describe all the steps you took to get here. Or, you could save it as a .pdf image, which is great for publication as it is vector graphics and therefor e scalable to 300 dots per inch, but it is still a static image. Or G oing to you could save a session. an ,” a new user will have My Data, My Sessions “ the top of the screen now , under opportunity to create an account , and existing users can login.

2 [2:33 Create and verify a user account.] Let's “ e’ll call it username: “ videoDemo1 ” and we’ll use my Create an account ”. W for now we’ll leave blank nd we will , and the optional recovery email email address . A create a password. Now we have an account but it's necessary to go check our email and look for the . H ere we see that it tells us that we have created an message from the UCSC system account . We can click the link to confirm we’re not a robot and we’re redirected to a page ted. that tells us that the account has been activa We’ll go back to the original B rowser and “ Login ” using the username “ video Demo1 ” Login] .This i s the only place in the Genome B rowser and my new password and [ whe ’s so the system knows how to access your saved re a login is required, and that s and identify them as uniquely yours. You’ll notice that we have a new section session essions here called “ ” which at the moment is empty and it's our opportunity now to My S Browser view . I create a sessi on for the main t's important to note that you can restore someone else's session without being logged in. Save an active session.] [3:43 So we can save the session as hg19_hemoglobin ” and [ submit. ] Now we have a “ session on our list and if we wish, we can use the right mouse button to keep the link that we can send to someone else or we can open up a mailer using this link her e. Going back to the Genome B rowser you’ll find that we’re at t hat same location . Now to demonstrate , let’s navigate to some other gene in the genome how it works NF1 ” and go. ] If we go to “ My Sessions, ” we can click on our session link [ such as “ r if we navig and we’re taken directly there. O rowser ate to some other place on the B My Dat a, My Sessions ” and we can grab the link if we like, we can go once again to “ the link to someone els e or copy it directly into the B mail rowser and navigate to that page. e a session. ] Updat [4:35 wo gene sets turned on, If we don’t really want to have t eq we can turn off the RefS gene set, w hich came on when we used the HGVS nom enclature. W e can go back to My Data, My Sessions ” and resave the session under the same name, “ ” and [ submit. ] We’re prompted with an opportunity to not hg19_hemoglobin, “ writ over e will overwrit e here and the hit the “ Browser ” link . e our existing session but w It’s important to not e, if I go back here to the session , that the B rowser prompt s you with the name of the genome assembly s very useful to keep in the section for saving. It’ that , so you do not accidentally wind up on a genome assembly you did not expect to . I f you simply name a session by a gene name and you save that session while you are looking at a mouse assembly, then come back a month later you may or may not

3 remember that the session was saved as the mouse hemoglobin gene and you might yourself a bit of confusion. cause the Anyone could restore this session using the link you provided, or simply using in the “Restore” and the session name, hg19_hemoglobin, username, videoDemo1, section. You do not have to be logged in to restore someone else’s session. [5:46 sessions priv ately and publicly Share .] last th e is that you have the option to keep a sess ion The ing to notice about the interfac . It's also possible private so that only the person who has saved the session can view it , it makes the session public so to post in our public website where if you click this box everyone can see it . The person who creates the session is encouraged to document it so that anyone who views it will understand why it was saved. I n a public session you might explain that “ the genes hemoglobin B and hemoglobin D are both expressed in red blood cells but hemoglobin B is also expressed in many other tissues whereas hemoglobin D is expressed in red blood ” Then, [ accept changes ]. cells almost exclusively. My Data , Public Sessions ” and notice that there To view your public sessions go to “ are a lot of sessions that have been made available for the public, and you can find it by typing in a key word . Clicking on that link will activate the session. run- through of how to save a session and share a session with others . That's a quick Thank you for watching our video and thanks for being a G enome Browser user .

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