Center for Genomics and Bioinformatics - Indiana CTSI

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Oct 2, 2013 (3 years and 6 months ago)

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CENTER FOR GENOMICS AND BIOINFORMATICS



a multidisciplinary research center serving IUB, with growing
interactions to IUPUI and other institutions



carries out independent research in genomics and bioinformatics



collaborates with faculty to add or enhance a genomic and/or
bioinformatic component in their research projects



promotes interdepartmental and interdisciplinary interactions to
enhance genomics and bioinformatics at IUB



provides access to Roche GS
-
FLX high
-
throughput sequencing and
Nimblegen high
-
density arrays

High
-
throughput sequencing with GS
-
FLX:

We offer both fee
-
for
-
service sequencing
along with opportunities for collaborations using high
-
throughput sequencing
techniques.

Nimblegen high
-
density microarrays:

We offer a variety of options for high
-
density
microarray experiments, including any combination of consultation, experimental
design, and experiments using the high density microarrays.

Characterization of the
Drosophila
Transcriptome

PROJECT DESCRIPTION: This project is an important component of the model
organism ENCODE (modENCODE) project, which aims to identify all of the
sequence
-
based functional elements in the
Drosophila melanogaster

genome. The
project is run as a Research Network. Our role is to produce RNA samples that
include all

D. melanogaster

transcripts. RNA samples are prepared from a variety of
life cycle stages, from dissected tissues, from cell lines and from tissue regions. Many
of these RNA samples are fractionated to enrich small RNAs, nuclear RNAs and poly
-
A+ RNAs. Sample types are chosen to maximize the diversity of transcriptomes.
These samples are then used in experimental and computational work to generate
transcript models and to provide a complete baseline catalog of developmental
(stage
-

and tissue
-
specific) transcription in
Drosophila.0

PROJECT LEADER: Peter Cherbas

FUNDING: National Human Genome Research Institute (NHGRI)


Daphnia pulex

Genome Sequencing & Empirical Annotation

PROJECT DESCRIPTION: The globally distributed zooplankton
Daphnia
(commonly
called the waterflea) is the first crustacean to have its genome sequenced, helping to
create a new model system for ecological genomics. The sequence is produced by
the Joint Genome Institute in collaboration with the
Daphnia
Genomics Consortium.
Investigations of the data are uncovering how the genome's structure, gene inventory
and regulation are products of the many challenges common in aquatic
environments. A surprising result is the genome's impressive catalog of genes; only
half the predicted loci have sequence similarity to other characterized eukaryotic
proteomes. The large number of orphan genes is due to the phylogenetic distances
between Crustacea and insect model species, variable rates of evolutionary change,
and gene family expansions specific to the
Daphnia
lineage. Experimental
annotations are required to understand how the genome's organization is coupled to
the animal's biology. Our characterization of gene functions is based on genome
-
wide expression profiling using ESTs and microarrays, generated by challenging
Daphnia
to ecologically relevant conditions. We further study transcriptional profiles
from more modern conditions that threaten zooplankton populations: environmental
pollutants, the depletion of essential elements and nutrients. Overall, these data
suggest that many of the novel components of the genome reflect physiological and
adaptive responses of
Daphnia
to its complex environments.

PROJECT LEADER: John Colbourne

FUNDING: NSF, NIH, US DOE,


Microbial Systems Biology Pipeline

PROJECT DESCRIPTION: Our current understanding of bacterial cell function is
based on a few very powerful model systems. However, studies on alternative, non
-
model, microbial systems in recent years clearly indicate that restricting our focus on
a few model systems is insufficient and in some cases misleading, for understanding
the amazing diversity of mechanisms and properties of microbial cells. Furthermore,
recent comparisons of true natural isolates with "wild
-
type" laboratory strains has
revealed that many domesticated laboratory models have in fact evolved towards
optimal laboratory growth and often differ considerably from their environmental
counterparts. The study of natural isolates is often hampered by the concurrent loss
of genetic tractability. A paradigm shift is required to launch a new era in the study of
the microbial world in which high
-
throughput technologies combined with powerful
bioinformatics analysis allows the study of non
-
model systems at a level of detail
previously unimaginable.

PROJECT LEADERS: Qunfeng Dong (CGB, Bioinformatics), Jeong
-
Hyeon Choi,
Keithanne Mockaitis, Zhao Lai, in collaboration with Y. Brun and all IU
B
microbiologists

FUNDING: The Indiana Metabolomics and Cytomics Initiative (METACyt)

Director:

Peter Cherbas (cherbas@indiana.edu / 812
-
855
-
6273)

Deputy Director:

Jennifer Steinbachs (
stein@cgb.indiana.edu

/ 812
-
856
-
1858)

Genomics Director:

John Colbourne (
jcolbour@cgb.indiana.edu

/ 812
-
856
-
0099)

Bioinformatics Director:

Qunfeng Dong (
qfdong@cgb.indiana.edu

/ 812
-
855
-
3373)

Computing Director:

Phillip Steinbachs (
pds@cgb.indiana.edu

/ 812
-
856
-
5081)

Nimblegen High
-
Density Arrays:
During a microarray experiment, we perform
QC in every step, as recommended in the NimbleGen manual. Measures
include NanoDrop readings for checking the quantity of ds
-
cDNA synthesis,
Agilent Bioanalyzer readings for checking the quality and quantity of ds
-
cDNA
synthesis, and NanoDrop readings for checking the efficiency of cDNA labeling.
We also perform sample tracking control analysis for data analysis assessment.

High
-
throughput Sequencing:


Sample assessment:


DNA quality and quantity
are assessed by spectrophotometry, fluorometry, and gel
electrophoresis.

These assays reveal potential contaminants (such as RNA,
protein, other small molecules) that would interfere with sample sequencing
and also reveals the extent to which the sample DNA is intact or degraded from
handling.

Library assessment:


A sequencing library that is prepared from the sample
DNA is composed of fragments that are smaller than the sample DNA, and
carefully size
-
selected.

To assess the concentration, size range and quality of
the library, we use fluorometry and an Agilent Bioanalyzer LabChip, designed
for highly sensitive detection.

Library titration:


We test a library by actually doing a trial
-
run of emulsion PCR,
performed in the same manner as if the library were to be sequenced.

For the
high throughput of pyrosequencing to yield successful results, we must ensure
that the vast majority of templates are captured and amplified individually
-

one template per bead.

If more than one template is amplified on a bead,
sequence reads imaged off that bead will be "mixed" and therefore
uninterpretable, and will be discarded in the data analysis.

The CGB employs 30 full
-
time scientists at various levels of expertise who
engage faculty in their genomics and bioinformatics projects. Our
genomics staff have access to a variety of cutting edge equipment in the
lab, some highlights include:



Roche GS
-
FLX
-

capable of generating between 125
-
150 million bases of
sequence in a single run;


GeneMachines Hydroshear DNA Shearing Device;


Veritas Microdissection Instrument model 704 with IR capture laser and
UV cutting laser with epifluorescence;


Beckman Coulter Biomek FX, an automated liquid handling robot;


2 MJ Research Tetrad thermal cyclers and 10 Eppendorf Mastercyclers,
with 18 96
-
well blocks and 1 384
-
well block capable of incubating 2112
thermal cycle reactions simultaneously;


GeneMachines Omnigrid microarry printer, capable of printing 300
microarrays simultaneously with over 14,000 elements per array;


Axon Instruments GenePix 4000A microarray scanner (10 µm resolution)
and GenePix 4200A microarray scanner (5 µm resolution, 3 channels);


NanoDrop ND
-
1000 Spectrophotometer, designed with high absorbance
capability, 50 times that of traditional spectrophotometers.


The CGB designed and maintains its own dedicated Core Computing
Facility (CCF) to support day
-
to
-
day operations and a growing number of
computational and storage intensive research projects.

The CCF consists
of about 54 enterprise class systems from Sun Microsystems.

Dedicated
research systems include two 8
-
core and four 16
-
core systems for
interactive serial jobs, sequencing/microarray analysis, and relational
database services, and 14 dual
-
CPU cluster nodes for batch serial and
parallel jobs.

Another 26 single and dual dual
-
core systems provide
development and production web, database, authentication,
collaboration, and Unix/Windows desktop services.

Production storage is
provided by multiple X4500 "Thumper" systems each serving up 24
-
48TB
of raw capacity, which is combined into a single large pool on high
-
availability head nodes and shared out via NFS and iSCSI.

All filesystems
built on top of this use Sun's Zetabyte File System (ZFS) and a dual parity
RAID scheme (raidz2) for redundancy. Backup storage is provided by a SAN
consisting of several 8
-
24TB Fibre channel/SATA JBOD disk arrays.
Altogether, the CGB has approximately 232TB of total raw disk capacity .


OVERVIEW

RESOURCES

RESEARCH CONTRIBUTION HIGHLIGHTS

LIST OF SERVICES

QUALITY CONTROL AND ASSURANCES

CONTACT INFORMATION

CENTER FOR GENOMICS

AND BIOINFORMATICS