{"action":"created","issue":{"url":"https://api.github.com/repos/STAT540-UBC/Discussion/issues/107","repository_url":"https://api.github.com/repos/STAT540-UBC/Discussion","labels_url":"https://api.github.com/repos/STAT540-UBC/Discussion/issues/107/labels{/name}","comments_url":"https://api.github.com/repos/STAT540-UBC/Discussion/issues/107/comments","events_url":"https://api.github.com/repos/STAT540-UBC/Discussion/issues/107/events","html_url":"https://github.com/STAT540-UBC/Discussion/issues/107","id":128025448,"number":107,"title":"Team JaWSPR Formed","user":{"login":"shamsbhuiyan","id":12201113,"avatar_url":"https://avatars.githubusercontent.com/u/12201113?v=3","gravatar_id":"","url":"https://api.github.com/users/shamsbhuiyan","html_url":"https://github.com/shamsbhuiyan","followers_url":"https://api.github.com/users/shamsbhuiyan/followers","following_url":"https://api.github.com/users/shamsbhuiyan/following{/other_user}","gists_url":"https://api.github.com/users/shamsbhuiyan/gists{/gist_id}","starred_url":"https://api.github.com/users/shamsbhuiyan/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/shamsbhuiyan/subscriptions","organizations_url":"https://api.github.com/users/shamsbhuiyan/orgs","repos_url":"https://api.github.com/users/shamsbhuiyan/repos","events_url":"https://api.github.com/users/shamsbhuiyan/events{/privacy}","received_events_url":"https://api.github.com/users/shamsbhuiyan/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":{"url":"https://api.github.com/repos/STAT540-UBC/Discussion/milestones/1","html_url":"https://github.com/STAT540-UBC/Discussion/milestones/Team%20formations","labels_url":"https://api.github.com/repos/STAT540-UBC/Discussion/milestones/1/labels","id":1532512,"number":1,"title":"Team formations","description":"","creator":{"login":"santina","id":1039839,"avatar_url":"https://avatars.githubusercontent.com/u/1039839?v=3","gravatar_id":"","url":"https://api.github.com/users/santina","html_url":"https://github.com/santina","followers_url":"https://api.github.com/users/santina/followers","following_url":"https://api.github.com/users/santina/following{/other_user}","gists_url":"https://api.github.com/users/santina/gists{/gist_id}","starred_url":"https://api.github.com/users/santina/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/santina/subscriptions","organizations_url":"https://api.github.com/users/santina/orgs","repos_url":"https://api.github.com/users/santina/repos","events_url":"https://api.github.com/users/santina/events{/privacy}","received_events_url":"https://api.github.com/users/santina/received_events","type":"User","site_admin":false},"open_issues":9,"closed_issues":0,"state":"open","created_at":"2016-01-22T00:15:53Z","updated_at":"2016-01-22T16:16:57Z","due_on":"2016-01-22T08:00:00Z","closed_at":null},"comments":6,"created_at":"2016-01-21T21:39:09Z","updated_at":"2016-02-02T18:05:03Z","closed_at":null,"body":"Our team Members:\r\n\r\nJasleen Grewal | Bioinformatics | @jasgrewal\r\nWendy Zhang | Experimental Medicine |@w-zhang\r\nShamsuddin A. Bhuiyan | Bioinformatics | @shamsbhuiyan\r\nPhillip Richmond | Bioinformatics | @Phillip-a-Richmond\r\nRachelle Farkas | Bioinformatics | @rafarkas\r\n\r\n### Team JaWSPR: Expression Analysis of an Alcohol Tolerance Mouse Model\r\n\r\n **Ja**sleen Grewal, **W**endy Zhang, **S**hams Bhuiyan, **P**hillip Richmond, **R**achelle Farkas\r\nJanuary 29th, 2016\r\n\r\nIn 1981, McClearn greatly impacted the alcohol sensitivity field when he introduced the world to the Inbred Long Sleep (ILS) and Inbred Short Sleep (ISS) mice [MCCLEARN 1981]. The strains were selected for and named by their variable response to a high dose of alcohol, which is measured by a phenomenon known as the Loss of Righting Reflex (LORR).  After roughly 30 generations of selection for this trait, the resultant lines were inbred through brother sister mating to produce an isogenic line. Initial hypotheses regarding metabolic rate were investigated, but were disproven and the sensitivity was linked to differences in the brain [Kakihana 1966].  The ILS and ISS mice were also crossed and inbred to produce the recombinant inbred (RI) panel named LXS—which spans a sleep time spectrum—allowing for mapping of traits in a quantitative trait loci (QTL) manner [Williams 2004].  Presently, we have the unprecedented ability to investigate the gene expression profiles of these mice using RNA-sequencing, which is exactly what Richard Radcliffe at the University of Colorado School of Pharmacology decided to pursue.  Dr. Radcliffe has been studying these mice for the past 15 years, and designed an experiment that includes RNA-sequencing of the brains of the ILS, ISS, and 40 individual LXS strains under both saline and ethanol treatment.  The data generated in the course of this experiment has resulted in a total of 252 RNA-seq libraries from mice whole-brain samples, covering the 2 conditions (saline control and ethanol treatment), with 3 biological replicates for each condition, and a few sets of technical replicates. A bioinformatics based analysis of this dataset will entail identification of significant expression differences between the ILS and ISS cohorts, using the saline treated strains as respective controls for normalizing against batch and technical effects. Additionally, we will look for gene expression trends and patterns in the LXS RI panel.  Since the panel represents a spectrum of phenotypes, we may also expect a subset of genes to be expressed in a spectral manner—modulating across genotypes.  The main intent of this analysis is to identify expression signatures that distinguish the ethanol sensitivity phenotype. The resultant signatures that we observe can then be used by Dr. Radcliffe’s lab in downstream expression-QTL (eQTL) analyses, linking genotypes to expression patterns in an effort to further decode the molecular mechanisms behind sensitivity to alcohol. \r\n\r\n\r\n_References_\r\nKakihana R, Brown DR, McClearn GE, Tabershaw IR. Brain sensitivity to alcohol in inbred mouse strains. Science 154, 1574-1575 (1966) \r\n\r\nMcClearn GE. Genetic differences in the effect of alcohol upon behaviour of mice. In Proceedings of the third international conference on alcohol and road traffic, J. Havard, ed. London: British Medical Association, pp 153-155 (1962) \r\n\r\nMcClearn GE, Kakihana R. Selective breeding for ethanol sensitivity: Short-Sleep and Long-Sleep mice. In Development of Animal Models as Pharmacogenetic Tools, M.G. E., R.A. Deitrich, V.G. Erwin, eds. Rockville, MD: National Institute on Alcohol Abuse and Alcoholism, pp 147-159 (1981) \r\n\r\nWilliams RW, Bennett B, Lu L, Gu J, DeFries JC, Carosone-Link PJ, Rikke BA, Belknap JK, Johnson TE. Genetic structure of the LXS panel of recombinant inbred mouse strains: a powerful resource for complex trait analysis. Mamm Genome 15, "},"comment":{"url":"https://api.github.com/repos/STAT540-UBC/Discussion/issues/comments/178725504","html_url":"https://github.com/STAT540-UBC/Discussion/issues/107#issuecomment-178725504","issue_url":"https://api.github.com/repos/STAT540-UBC/Discussion/issues/107","id":178725504,"user":{"login":"shamsbhuiyan","id":12201113,"avatar_url":"https://avatars.githubusercontent.com/u/12201113?v=3","gravatar_id":"","url":"https://api.github.com/users/shamsbhuiyan","html_url":"https://github.com/shamsbhuiyan","followers_url":"https://api.github.com/users/shamsbhuiyan/followers","following_url":"https://api.github.com/users/shamsbhuiyan/following{/other_user}","gists_url":"https://api.github.com/users/shamsbhuiyan/gists{/gist_id}","starred_url":"https://api.github.com/users/shamsbhuiyan/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/shamsbhuiyan/subscriptions","organizations_url":"https://api.github.com/users/shamsbhuiyan/orgs","repos_url":"https://api.github.com/users/shamsbhuiyan/repos","events_url":"https://api.github.com/users/shamsbhuiyan/events{/privacy}","received_events_url":"https://api.github.com/users/shamsbhuiyan/received_events","type":"User","site_admin":false},"created_at":"2016-02-02T18:05:03Z","updated_at":"2016-02-02T18:05:03Z","body":"Oh I got it! Accepted. Thanks"}}