Modern
DNA
Sequencing
Methods
Duration:
March
14
‐
March
18,
2011.
Location:
CMB
seminar
room,
Berzelius
väg
35,
room
A216.
See
map
below.
Aim:
After
completing
the
course,
the
student
will
understand
the
technology
behind
the
major
DNA
sequencing
platforms
available
today,
and
their
strengths
and
limitations;
and
will
know
the
most
important
applications,
and
how
they
may
apply
to
the
student's
own
research.
Content:
The
course
will
cover
the
following
topics:
The
history
of
DNA
sequencing.
Introduction
to
modern
DNA
sequencing.
Practical
considerations,
cost,
dealing
with
a
deluge
of
data.
Applications
‐
RNA
sequencing,
ChIP
sequencing,
metagenomics.
Future
technologies
and
applications.
Format:
The
course
consists
of
lectures
by
invited
speakers,
and
a
site
visit.
In
addition,
students
will
be
asked
to
prepare
a
presentation
of
how
modern
DNA
sequecning
methods
could
benefit
their
own
research.
Examination:
All
lectures
are
compulsory.
In
case
of
absence,
lectures
can
be
compensated
by
a
literature
assignment
and
written
report.
Oral
examination
is
in
conjunction
with
the
presentation
of
an
individual
project
of
research.
Welcome!
Sten
Linnarsson
Rickard
Sandberg
Assistant
Prof,
MBB
Assistant
Prof,
CMB
Schedule:
Monday,
March
14
9.00
‐
9.30
Introduction
Ass.
Prof.
Rickard
Sandberg
&
Ass.
Prof.
Sten
Linnarsson
9.30
‐
10.15
History
of
DNA
sequencing
Ass.
Prof.
Sten
Linnarsson
10.30
‐
12.00
Applied
Biosystems
SOLiD
Inger
Jonasson,
Lab
Manager,
and
Christian
Tellgren‐Roth,
Bioinformatician,
Uppsala
Genome
Center
13.30
‐
15.00
Enrichment
methods
Dr.
Olle
Ericsson,
Dept
of
Genetics
and
Pathology,
Uppsala
University
15.30
‐
17.00
Bioinformatics
for
next‐generation
sequencing
and
introduction
to
Computer
practises.
Ass.
Prof.
Rickard
Sandberg
Tuesday,
March
15
[in
computer
labs
"Dot"
and
"Enter"]
9.00
‐
12.00
Computer
practise
1:
ChIP‐Seq
data
analyses
13.00
‐
17.00
Computer
practise
2:
RNA‐Seq
data
analyses
Wednesday,
March
16
9.30
‐
10.30
Studying
epigenetics
using
next
generation
ChIP
and
sequencing
technologies
Assoc.
Prof.
Ola
Hermanson,
Neuroscience
department
Karolinska
Institutet
10.45
‐
12.00
Cancer
Genomics
TBD
13.30
‐
15.00
Transcriptome
studies
using
next‐generation
sequencing
Ass.
Prof.
Rickard
Sandberg
15.30
‐
17.00
High‐throughput
single‐cell
RNA‐Seq
Ass.
Prof.
Sten
Linnarsson,
MBB
Thursday,
March
17
10.00
‐
11.00
Genomics
Prof.
Joakim
Lundeberg,
SciLife
Lab,
KTH/KI/SU
11.30
‐
13.00
Site
Visit:
SciLife
lab
Science
for
Life
Laboratory
KISP
(Karolinska
Institutet
Science
Park)
Tomtebodav
23A
14.00
‐
14.45
Studying
genome
organization
and
regulation
using
next‐gen
sequencing
Dr.
Pelin
Akan,
SciLife
lab
Friday,
March
18
9.00
‐
10.30
Project
presentations
(20
min
per
person)
11.00
‐
12.30
Project
presentations
(20
min
per
person)
13.30
‐
14.30
Wrap‐up
and
course
evaluation
Ass.
Prof.
Rickard
Sandberg
&
Ass.
Prof.
Sten
Linnarsson
Additional
Course
Links:
Sequencing
Platforms
Links:
Illumina/Solexa,
SOLiD,
454
Forum:
SEQanswers
