Single Cell Technologies and Analysis

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.

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

• 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

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

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
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.