NewThis course type is laboratory

Single Cell Technologies and Analysis

20 - 27 July 2018Wellcome Genome Campus, Hinxton, UK
Deadlines (at 23:59 UTC):
  • Deadline for Applications Closed
  • Application Deadline Closed

  • Summary

    The development of robust protocols sensitive enough to measure nucleic
    acids from single cells is revolutionizing biology, enabling the
    interrogation of molecular mechanisms that are not evident from
    measurements that represent the average of thousands of cells.

    Currently, established plate-based protocols (such as Smart-seq2) provide
    scalable and robust measurements of mRNA. However, technologies in this
    field are rapidly evolving, and have recently enabled RNA-seq to be
    conducted on thousands of single cells in parallel (e.g. 3’ end
    sequencing of mRNA in droplets) and for multiple classes of nucleic acid
    to be captured from the same cell (e.g. DNA and RNA with G&T-seq).

    Reliable statistical methods for analysing these data are also being
    developed, though it can be difficult for those new to the field to
    identify the tools most suitable for the analysis of their data.

    This exciting new course will be taught collaboratively by researchers
    from the Wellcome Trust Sanger Institute and staff from the Wellcome Trust Sanger Institute Single Cell Genomics Core
    Facility
    . The programme will provide participants with a broad
    overview of established and cutting-edge single cell methodologies,
    practical experience in the relevant molecular biology and laboratory
    skills, and the computational and statistical skills needed to interpret
    these large data sets.

    The primary focus of the hands-on element of the course will be widely
    applicable protocols for plate-based full-length mRNA sequencing
    (Smart-seq2) and a higher throughput 3’ end based protocol (10x
    chromium/Drop-seq/Seq-well).
    Additional technologies will be demonstrated in sessions for small
    groups. These will be guided by course instructors to maximise the
    breadth of technologies we are able to demonstrate and discuss within the
    time frame of the course.

    The integration of data analysis within the course will allow
    participants to critically evaluate both the technical performance and
    the biological interpretation of single cell data sets that they have
    generated.

    The practical programme will be complemented by seminars from
    distinguished guest speakers.


    Please note new dates (updated 3/4/18): Due to
    unforeseen circumstances the dates for this course have changed slightly
    from the 21-29 July dates originally advertised. The course will now run
    20-27 July 2018.

  • Programme

    The course will include laboratory and computational practical sessions, along with lectures and discussions, covering the following topics:

    • Preparation and isolation of single cells (including preparation of suspensions and single cell sorting with FACS)
    • Cell counting and quality control
    • Full length single cell mRNA sequencing in 96-well plates (Smart-seq2 protocol)
    • 3’ end single cell mRNA sequencing from thousands of cells (10x/Drop-seq/Seq-Well)
    • Multi-omics for single cells (including G&T-seq for DNA/RNA)
    • Automation of single cell protocols
    • Illumina sequencing of single cell libraries
    • Data processing, data handling and QC of single cell data sets
    • Differential expression and clustering of single cell RNA-seq data

    Learning Outcomes

    After attending this course, participants should be able to:
    • Evaluate advanced methodologies for the analysis of nucleic acids from eukaryotic single cells, along with their applications
    • Appreciate different approaches currently in use in the field to address specific research questions
    • Assess the strengths, weaknesses and limitations of different methodologies and approaches, experimental and computational.
    • Integrate and apply the knowledge and training from the course to their own research interests
  • Instructors / Speakers

    The course will be taught collaboratively by researchers from the
    Wellcome Trust Sanger Institute and staff from the Wellcome Trust Sanger Institute Single Cell Genomics Core
    Facility
    . The practical programme will be complemented by seminars
    from distinguished guest speakers.

    Course Instructors
    Lia Chappell Wellcome Sanger Institute,
    UK
    Peter Ellis Wellcome Sanger Institute, UK

    Martin Hemberg Wellcome Sanger Institute,
    UK
    Thierry Voet  Wellcome Sanger
    Institute, UK
    Xi Chen Wellcome Sanger Institute, UK
    Lira Mamanova  Wellcome Sanger
    Institute, UK
    Kedar Nath Natarajan Wellcome Sanger
    Institute, UK

    Guest Speakers
    Garry Nolan
    Stanford University, USA
    Sarah Teichmann Wellcome Sanger Institute
    and EMBL-EBI, UK
    Alex Shalek Institute for Medical Engineering and Science, MIT,
    USA
    Muzlifah Haniffa Newcastle University, UK

    Stein
    Aerts
    Laboratory of Computational Biology, KU Leuven/VIB,
    Belgium

  • How to Apply

    Prerequisites
    Applicants should be researchers or clinicians interested in applying
    advanced laboratory and computational methodologies for the analysis of
    nucleic acids from eukaryotic single cells, with a strong emphasis on
    mammalian systems. It is suitable for PhD students, postdocs and
    clinician scientists, as well as staff from Core Facilities.

    It is expected that participants will be familiar with bulk sequencing
    procedures and that they have basic knowledge of Linux/Unix as well as
    the R programming environment. Numerous online tutorials are available in
    these resources. including:
    http://www.ee.surrey.ac.uk/Teaching/Unix/
    http://tryr.codeschool.com/

    Applications
    Applications
    can be submitted online
    . Places are limited and will be awarded on
    merit. If you have any problems with the online application process,
    please contact
    us
    .

    Please note: Applications
    must be supported by a
    recommendation from a scientific or clinical
    sponsor (e.g. supervisor,
    line manager, or head of department). A
    request for a supporting
    statement will be sent to your nominated sponsor automatically during
    the application process. Applicants must ensure that their sponsor
    provides this supporting statement by the application deadline.
    Applications without a supporting statement cannot be
    considered.

    Deadlines
    Deadline for Applications: Closed

    Travel visas
    Please contact the
    event organiser if you require a letter to support a travel visa
    application to the UK. Note that letters will only be provided to confirmed attendees.

    Non-European Economic Area or Swiss nationals may be required to have a
    visa to enter the UK.
    Early application is strongly advised, as this process can take 6-8 weeks
    or longer.

    Please visit the following websites for further information:
    UK Border Agency website and information for general visitors and business
    visitors.

  • Cost / Bursaries

    Cost
    The course is subsidised by the Wellcome Genome Campus Advanced Courses
    and Scientific Conferences Programme. This is a residential course and
    the fee is £1065, including all accommodation and meals.
    This subsidised fee is available to all non-commercial applicants. Please
    contact us
    for the commercial fee.

    Bursaries
    Advanced Courses are subsidised for non-commercial
    applicants from anywhere in the world. Additional, limited bursaries are
    available (up to a 50% reduction of the course fee) and are awarded on
    merit. If you would like to apply for a
    bursary, please complete the
    bursary section of the online application
    form.

    Please note that both the applicant
    and sponsor are required to provide
    a justification for the
    bursary as part of the application.

    Additional funding opportunities
    Visit
    our Funding webpage
    for additional funding opportunities currently
    available.


    Bursary terms and conditions

    UK Courses (held at the Wellcome Genome Campus, Hinxton,
    Cambridge)
    A
    limited number of bursaries are available for each course. These are
    awarded by the selection committee according to merit. The bursary
    covers a maximum of 50% of the course fee, though in exceptional
    circumstances an application for the total course fee may be considered.
    Where there are many bursary applications, the selection committee may
    issue smaller amounts. We cannot assist with travel costs to attend UK
    courses.