GRADUATE RESEARCH & TRAINING HANDBOOK 2018 GRADUATE RESEARCH & TRAINING HANDBOOK 2018 Welcome IGMM Graduate Research and Training Contacts Staff Student Liaison Committee/Officer 1 40,000 5.0 0 0 !"#$%&$%'& & 5.0 Number of promoters ()*+&,)-).%+/0-&1(2&,)-0+34) 546)-0+34)&7%44/-,8 & of promoters Proportion & 1 9)-07)&:);")-</-,&6%:&')<07)&.)$%+/=)$3&<6)%4>&%-#&<$0:)&+0&%&7/$$/0-&4)04$)& 30,000 Matched expression Vagina 6%=)&6%#&+6)/.&,)-07)&:);")-<)#8&?0&/-+).4.)+&+6/:&7%::/=)&%70"-+&0@&Divergent expression Neurons Diminished promoter activity Epididymis Ovary, adult Ovary, Testis, adult Testis, CD8+ T cells CD8+ T cells CD4+ T Uterus, adult Uterus, - cerebellum Thymus, fetal Thymus, CD19+ B cells CD19+ B No promoter activity Housekeeping /[email protected]%+/0->&0".&$%'&#)=)$04:&)@@/</)-+&7)+60#:&@0.&7)%:"./-,&%-#&4.)#/<+/-,&+6)& Placenta, adult adly-expressed - hippocampus egulatory T cells T egulatory Inserted promoter sequence Tissue-restricted Cerebellum, adult Cerebellum, adult cord, Spinal Bro onventional T cells onventional )@@)<+:&0@&,)-)+/<&=%./%+/0-8&A)&:3-+6):/B)&$%.,)&<0$$)<+/0-:&0@&7"+%+)#&,)-):>&%-#& adult oblongata, lla Deleted promoter sequence adult Diencephalon, Hippocampus, adult Hippocampus, Ambiguous promoter alignment adult brain, Olfactory Naive r Astrocytes #)=)$04&6/,65+6.0",64"+&%::%3:&+0&7)%:".)&+6)&)@@)<+:&0@&7"+%+/0-:&0-& Medu Naive c 70$)<"$%.&%-#&<)$$"$%.&46)-0+34):>&:"<6&%:&4.0+)/-&%-#&1(2&%'"-#%-<)>Astrocytes &4.0+)/- 5 1(2&/-+).%<+/0-:>&%-#&@/+-)::&CD"<6+%&)+&%$8>&E</)-<)>&FGHIJ8&A)&":)&%&=%./)+3&0@& )*4)./7)-+%$&+)<6-/;"):>&/-<$"#/-,&,)-)&:3-+6):/:>&-)*+ 5,)-).%+/0-&:);")-</-,>& 7/<.0%..%3:>&%-#&%"+07%+)#&7/<.0:<043>&%-#&)*4)./7)-+%$&:3:+)7:&/-<$"#/-,& '%<+)./%>&3)%:+>&%-#&7%77%$/%-&<)$$:8& & & & & & 1 GRADUATE RESEARCH & TRAINING HANDBOOK 2018 Welcome In the first instance you will mainly deal with We are delighted to welcome you to your your supervisors, Graduate Convenor or Nick PhD programme at the Institute of Genetics Gilbert (Director of Graduate Research and and Molecular Medicine. On the following Training for the IGMM). You will also have a pages you will find information relating to thesis committee (normally setup abour 10 the different programmes, timetable for weeks into your PhD) which will be made up the first 6 months, and the assessment of your supervisors, an external advisor and a timetable for the next 3 or 4 years. committee Chair. Formal issues (interruption of studies and so on) are dealt with by the As you probably know, we have a mixture Director of Graduate Research and Training of students on campus, some of whom and the College PG Office. are following a four year programme with rotations and others who are starting a Head of School of MGPHS three year PhD in a specific lab. There Professor Sarah Cunningham-Burley are some teaching elements of the four Director of Graduate Research and Training, year taught course that might be of IGMM: Professor Nick Gilbert interest to other students, for example covering different technologies, computer Graduate Convenor, CRUK Edinburgh programming, aspects of clinical reserach Centre: Professor Val Brunton and research ethics - these are shown Graduate Convenor, MRC Human Genetics in a detailed timetable on page 5 - 8. Unit: Professor Nick Gilbert This teaching is only compulsory for the 4-year HGU students, but other students Graduate Convenor, Centre for Genomic & (and postdocs) are welcome to sign up Experimental Medicine: Dr Kathy Evans and attend any sessions that you find Director of PG Studies, College of MVM useful; you might want to discuss your choice with your supervisor(s). We hope Dr Paddy Hadoke that the IGMM Graduate Research and Staff Student Liaison Officer Training environment will provide a useful Dr Martin Reijns framework for your studies. Please feel free to air your views, and to approach us about Graduate Research and Training any issues you have, and help us to make Administrator the IGMM a huge success! Pauline McDonald Graduate Research and Training Assistant Graduate Research and Training Alana Johnson contacts The IGMM is made up of three centres, the MRC Human Genetics Unit (HGU), the Centre for Genomics and Experimental Medicine (CGEM) and the Cancer Research UK Edinburgh Centre (ECRC), each with their own Graduate Convenor. The IGMM falls within the School of Molecular, Genetic and Population Health Sciences (you will need to know this School affiliation when you apply for Transkills courses amongst other things), and the SMGPHS is within the College of Medicine and Veterinary Medicine or CMVM. 2 GRADUATE RESEARCH & TRAINING HANDBOOK 2018 Staff Student Liaison Committee/ Officer At the IGMM we are committed to ensuring a high-quality student experience. To ensure we are able to deliver this, and to “maximise our students’ potential”, we encourage students to communicate their views and suggestions to help influence any required changes to policies and procedures. The IGMM Staff Student Liaison Committee (SSLC) meets biannually to discuss matters of mutual concern of staff and students. The SSLC is composed of student and staff representatives, and we strongly encourage students at any stage of their graduate degree to consider joining the SSLC. In addition, we introduced a Staff Student Liaison Officer (SSLO) in August 2014. Martin Reijns is an senior research scientist in Professor Andrew Jackson’s laboratory in the Disease Mechanisms section of the Human Genetics Unit. Martin has been a Email: [email protected] member of the Jackson lab since 2007. Telephone: 651 8633 In 2014 we setup a mentoring system for Location: MRC Human Genetics Unit PhD students. This “buddying” programme pairs 1st-year students who wish to be involved with friendly and supportive final What to do if things go wrong year students; and aims to help with their integration into the institute, informally If you have a problem with your project answer any questions and queries and/or supervisor, you should first try regarding starting their PhD, and also to to resolve it between yourselves - it is offer support with beginning a new life in important to keep lines of communication Edinburgh. open where possible and not let things degenerate. If there is still a problem, then If you want to know more, or would like to be please seek advice - you should feel free paired up, please get in touch with Martin; to speak to your second supervisor, your also if you are interested in becoming a thesis committee Chair, the Directors of the representative to the SSLC. Graduate School or the PG Convenor for your building. If in the end problems can’t be solved locally, then official complaints can be made to a committee in the PG Office. These conversations will be in confidence and a strategy will be devised to try and address any problems. Additional meetings of thesis committees can be arranged (subject to members’ availability) if the student and/or supervisors feel that this would help. 3 1 40,000 5.0 0 0 !"#$%&$%'& & 5.0 Number of promoters ()*+&,)-).%+/0-&1(2&,)-0+34) 546)-0+34)&7%44/-,8 & of promoters Proportion & 1 9)-07)&:);")-</-,&6%:&')<07)&.)$%+/=)$3&<6)%4>&%-#&<$0:)&+0&%&7/$$/0-&4)04$)& 30,000 Matched expression Vagina 6%=)&6%#&+6)/.&,)-07)&:);")-<)#8&?0&/-+).4.)+&+6/:&7%::/=)&%70"-+&0@&Divergent expression Neurons Diminished promoter activity Epididymis Ovary, adult Ovary, Testis, adult Testis, CD8+ T cells CD8+ T cells CD4+ T Uterus, adult Uterus, - cerebellum Thymus, fetal Thymus, CD19+ B cells CD19+ B No promoter activity Housekeeping /[email protected]%+/0->&0".&$%'&#)=)$04:&)@@/</)-+&7)+60#:&@0.&7)%:"./-,&%-#&4.)#/<+/-,&+6)& adult Placenta, adly-expressed - hippocampus egulatory T cells T egulatory Inserted promoter sequence Tissue-restricted Cerebellum, adult Cerebellum, adult cord, Spinal Bro onventional T cells onventional )@@)<+:&0@&,)-)+/<&=%./%+/0-8&A)&:3-+6):/B)&$%.,)&<0$$)<+/0-:&0@&7"+%+)#&,)-):>&%-#& adult oblongata, lla Deleted promoter sequence adult Diencephalon, Hippocampus, adult Hippocampus, Ambiguous promoter alignment adult brain, Olfactory Naive r Astrocytes #)=)$04&6/,65+6.0",64"+&%::%3:&+0&7)%:".)&+6)&)@@)<+:&0@&7"+%+/0-:&0-& Medu Naive c 70$)<"$%.&%-#&<)$$"$%.&46)-0+34):>&:"<6&%:&4.0+)/-&%-#&1(2&%'"-#%-<)>Astrocytes &4.0+)/- 5 1(2&/-+).%<+/0-:>&%-#&@/+-)::&CD"<6+%&)+&%$8>&E</)-<)>&FGHIJ8&A)&":)&%&=%./)+3&0@& )*4)./7)-+%$&+)<6-/;"):>&/-<$"#/-,&,)-)&:3-+6):/:>&-)*+ 5,)-).%+/0-&:);")-</-,>& 7/<.0%..%3:>&%-#&%"+07%+)#&7/<.0:<043>&%-#&)*4)./7)-+%$&:3:+)7:&/-<$"#/-,& '%<+)./%>&3)%:+>&%-#&7%77%$/%-&<)$$:8& & & & & & GRADUATE RESEARCH & TRAINING HANDBOOK 2018 GRADUATE RESEARCH & TRAINING HANDBOOK 2018 MRC Human Genetics Unit 4 year programme • Introduction to programme • Projects available 1 40,000 5.0 0 0 !"#$%&$%'& & 5.0 Number of promoters ()*+&,)-).%+/0-&1(2&,)-0+34) 546)-0+34)&7%44/-,8 & of promoters Proportion & 1 9)-07)&:);")-</-,&6%:&')<07)&.)$%+/=)$3&<6)%4>&%-#&<$0:)&+0&%&7/$$/0-&4)04$)& 30,000 Matched expression Vagina 6%=)&6%#&+6)/.&,)-07)&:);")-<)#8&?0&/-+).4.)+&+6/:&7%::/=)&%70"-+&0@&Divergent expression Neurons Diminished promoter activity Epididymis Ovary, adult Ovary, Testis, adult Testis, CD8+ T cells CD8+ T cells CD4+ T Uterus, adult Uterus, - cerebellum Thymus, fetal Thymus, CD19+ B cells CD19+ B No promoter activity Housekeeping /[email protected]%+/0->&0".&$%'&#)=)$04:&)@@/</)-+&7)+60#:&@0.&7)%:"./-,&%-#&4.)#/<+/-,&+6)& adult Placenta, adly-expressed - hippocampus egulatory T cells T egulatory Inserted promoter sequence Tissue-restricted Cerebellum, adult Cerebellum, adult cord, Spinal Bro onventional