Genomics & Bioinformatics Core Facility

News

Scientists reveal new and improved genome sequence of Daphnia pulex

For many, experience with Daphnia, commonly known as water fleas, ends in high school. The organism is often used for science experiments exploring water toxicity, because of its sensitivity to environmental factors. But the tiny, transparent microcrustaceans have been studied intensively for more than 150 years, and new research published and featured on the cover of the journal G3 reveals scientists can now take a closer look at its genome.

Researchers have completed a new and improved genome sequence of Daphnia pulex (D. pulex), providing a clearer roadmap of the organism’s genome so they can identify the genes and pathways that make this organism so successful in freshwater ecosystems.

Populations of Daphnia, barely visible to the naked eye, can be found in virtually every standing body of water on the planet, including Antarctica. They evolve quickly and are masters of responding to the conditions in their environment. Sensing the chemical cues of nearby predators, some species of Daphnia develop elaborate defensive structures such as spines and helmets that make them harder to eat. While scientists have gained a thorough understanding of what these tiny water fleas do to adapt to varying conditions, they don’t yet know how they do it.

“That’s why a system like this is so powerful,” said Michael E. Pfrender, director of the Genomics & Bioinformatics Core Facility and associate professor in the Department of Biological Sciences and the Environmental Change Initiative at the University of Notre Dame. “We need this genomic infrastructure to add to the ecological context we already have to gain a better understanding of how Daphnia adapt. Because we have an improved genome sequence, we can get a more accurate catalog of genes and when thinking about response to the environment and chemical cues, it’s the turning on and off of genes and pathways that’s important. The picture is much more complete than it was before.”

Calling it the “Portland Arch” genome after the Indiana Nature Preserve where the Daphnia was collected, the new assembly comes six years after the first sequence of D. pulex in 2011. The current study describes how scientists used the latest technology as part of a thorough and methodical process the result of which led to the identification of 18,440 genes.

D. pulex plays a vital role in Earth’s ecology. Feeding off of algae and phytoplankton in standing freshwaters, they are the primary grazer in those environments, the “cows of lakes,” said Pfrender. They’re also primary forage, transferring all of that energy to the fish that eat them. By understanding how species of Daphnia respond to toxic elements like industrial contaminants, toxic algae blooms or thermal stress, scientists can look at how environmental changes caused by agriculture and road runoff or warming temperatures and climate change could impact populations in lakes, rivers and standing bodies of water.

“What happens to this vital part of the ecosystem when conditions change very rapidly? What genes allow some populations to cope with these changes while others fail?” Pfrender said. “That’s what we want to find out. This genome sequence provides the toolkit.”

Co-authors of the study include Pfrender, Jacqueline Lopez and Brent Harker of the Notre Dame Genomics and Bioinformatics Core Facility; Zhiqiang Ye, Ken Spitze, Xiaoqian Jiang, Matthew S. Ackerman and Michael Lynch at the Department of Biology at Indiana University; Sen Xu at the Department of Biology at Indiana University and the University of Texas at Arlington; Jana Asselman, Laboratory for Environmental Toxicology at Ghent University; R. Taylor Raborn at the Department of Biology and School of Informatics and Computing at Indiana University; and W. Kelley Thomas and Jordan Ramsdell at the Hubbard Center for Genome Studies at the University of New Hampshire.

The study was funded through a grant from the National Institutes of Health to Michael Lynch at Indiana University, Bloomington and Notre Dame Research.

Contact: Michael Pfrender, 574-631-0591, michael.pfrender.1@nd.edu

ND GBCF Acquires New Equipment

Published: April 24, 2017

Author: Brandi Klingerman

THE NEW SYSTEM FOR HIGH-THROUGHPUT SEQUENCING SUPPORTS HEALTH AND ENVIRONMENTAL RESEARCH

From cancer to vector-borne diseases, and from drug development to monitoring invasive species, DNA sequencing is vital to the research being done at the University of Notre Dame. To support these research efforts, the Genomics and Bioinformatics Core Facility (GBCF) has acquired an illumina NextSeq 500 Sequencing System, for next generation high-throughput genomics sequencing.

The new machine supports a broad range of applications that can sequence millions of DNA fragments. To explain the benefits of the new equipment, Michael Pfrender, associate professor of biological sciences and director of the GBCF, said, “By providing the research community access to industry-leading technology, the GBCF will be able to better support researchers who increasingly rely on high-throughput DNA sequencing to complete their work. This equipment increases sequencing availability and flexibility, further expanding research and collaborative potential.”

The illumina NextSeq 500 Sequencing System will complement existing GBCF equipment with key applications including whole genome, exome, or transcriptome sequencing, thereby providing exceptional data accuracy at any coverage level. Additionally, the facility now has the capability to perform high throughput next generation sequencing in house at a low-cost per base with faster results. This will allow faculty to utilize the GBCF staff’s expertise in data generation throughout the entirety of their experiments. 

The GBCF is a resource accessible to the Notre Dame research community, external academic institutions, and industry. It is also anIndiana Clinical and Translational Sciences Institute (CTSI) approved core facility with services available to all Indiana CTSI partners. Funding for the system was provided through the Notre Dame Research Equipment Restoration and Renewal internal grant program, the Eck Institute for Global Health, and the Harper Cancer Research Institute

To learn more about illumina sequencing services, please visit http://genomics.nd.edu/illumina-sequencing-services

Contact:

Melissa Stephens / Assistant Director

Genomics and Bioinformatics Core Facility / University of Notre Dame

stephens.49@nd.edu / 574.631.0338

genomics.nd.edu 

About Notre Dame Research:

The University of Notre Dame is a private research and teaching university inspired by its Catholic mission. Located in South Bend, Indiana, its researchers are advancing human understanding through research, scholarship, education, and creative endeavor in order to be a repository for knowledge and a powerful means for doing good in the world. For more information, please seeresearch.nd.edu or @UNDResearch

NEW Computational Training Program Intiative (REACT)

The REACT program (Rapid Exposure to Advanced Computational Training) is a short-term initiative to support graduate students to receive the latest training in computational tools and techniques in their field. REACT is a joint effort between the Environmental Change Initiative (ECI), The Eck Institute for Global Health (EIGH), and the Genomics and Bioinformatics Core Facility (GBCF). REACT will provide up to $1,500 to cover student tuition, registration, and board required to attend nationally-recognized workshops that provide the latest training in computational approaches.

For more details on the program and student eligibility, application instructions, and a list of available workshops, please visit http://genomics.nd.edu/react-program

GBCF Holiday Closure Schedule

Dear Sequencing Users,

The Genomics Core Facility will be closed for the holidays from Tuesday Dec 20- Monday Jan 2nd. We will re-open on Tuesday Jan 3rd, 2017

Last day to submit samples for full service Sanger sequencing will be Wednesday December 14, 2016
All order forms must be submitted no later than 12:00 noon
Samples dropped off to the core no later than 2:00pm

Ready-to-run and fragment analysis plates can be submitted through Friday December 16, no later than 12:00 noon. Please contact genomics core staff in advance to arrange times for drop off.

Please remember to place your CORES orders, and e-mail order forms to genomics@nd.edu

Thank you and a very happy holidays from all of us here at the GBCF!

Join Us! Indiana CTSI Notre Dame Retreat

Please Join Us For The: Indiana CTSI Notre Dame Retreat 2016

Time: Fri Oct 21, 2016, 9:00AM - 3:30PM

Location: Jordan Hall of Science

Presentation Topics: Community Health Engagement Program • Global Health • Molecular Therapeutics • Rare & Neglected Diseases • Team Science • Core Facilities

All are welcome to attend the Indiana CTSI Notre Dame Retreat on Friday, October 21, 2016 in the Jordan Hall of Science from 9:00 A.M to 3:30 P.M. To register, please complete the form here: https://redcap.uits.iu.edu/surveys/?s=N73HXPAELM.

The keynote lecture will be given by James Inglese, Principal Investigator, Division of Pre-Clinical Innovation, National Center for Advancing Translational Sciences (NCATS)
National Institutes of Health.

Funding Opportunity! Indiana CTSI Pilot Funding for Research Use of Core Facilities

Indiana CTSI Pilot Funding For Research Use of Core Facilities

SUBMISSION DEADLINE- OCT 07, 2016

Description:  The Indiana CTSI Pilot Funding program is intended to promote the use of technologies and expertise afforded by the Indiana CTSI Core Facilities available at all partner institutions. Successful proposals will demonstrate outstanding scientific merit that can be linked to generating extramural funding or novel intellectual property (IP). Success of the program will be viewed, in part, by the fostering of new funded grants or providing significant contributions to grant renewals. Therefore, proposals will be judged with equal measure on scientific merit and the likelihood of generating new IP or extramural grant support. See the program guidelines for more information: www.indianactsi.org

For questions, please contact Melanie DeFord, using the information below.

Melanie E. DeFord
Director, Grants Business Management
Notre Dame Research
940 Grace Hall
E: mdeford@nd.edu
P: 574-631-8805
W: research.nd.edu

Please contact Michael Pfrender to secure letters of support.

Michael Pfrender, Ph.D.
Director, Genomics & Bioinformatics Core Facility
Associate Professor Department of Biological Sciences
109B Galvin Life Science Center
E: mpfrende@nd.edu
P: 574-631-0591
W: genomics.nd.edu

Interested in a hands-on analysis workshop?

We are considering offering an analysis workshop in Spring 2016. If you are interested in taking part in an upcoming workshop, or just have suggestions for future traning and workshop topics, please take a few minutes to provide your input on this brief questionnaire so that we can tailor the next workshop to meet your needs. It is very breif and should only take a few minutes of your time. We thank you for participating and offering your feedback.

Please provide some input by following this link: https://www.surveymonkey.com/r/D8LL9MY

Funding Opportunity! HCRI-ACS Research Grant

American Cancer Society Institutional Research Grant

SUBMISSION DEADLINE- MARCH 3, 2016

Description:  The Harper Cancer Research Institute is pleased to announce the availability of funds for new pilot projects to assist new investigators who hold the rank of Assistant Professor (tenure track). These funds are from the American Cancer Society Instiutional Research Grant (ACS IRG). This grant provides support for beginning investigators to enable them to initiate their independent research program. Faculties from all disciplines, with any project relating to cancer research, are especially encouraged to apply.: More Information

For questions regarding proposal development and eligibility, please contact Rob Stahelin (rstaheli@nd.edu)

For GBCF related questions, or to discuss your project ideas please contact Michael Pfrender, Director, Genomics & Bioinformatics Core Facility (mpfrende@nd.edu

New wiki page for CRC biomodules

The core, in conjunction with the CRC, has added new biomodules to the CRC. A wiki page for these tools can be accessed here: http://wiki.crc.nd.edu/wiki/index.php/Installed_Applications#Biology

The module currently contains eleven pieces of software; FastQC, Trimmomatic, BWA, Bismark, Bowtie-2, TopHat, Samtools, GATK, Picard tools, Trinity, HTSeq, and Cutadapt. All of this software can be accessed with the command “module load bio” on the command line when logged into the CRC. Any questions on usage or requests for additional software can be directed to Joe Sarro (jsarro@nd.edu).

Join Notre Dame Research at the Core Facility Fair!

On Wednesday, September 16th, 2015, Notre Dame Research will host its annual Core Facility Fair from 10:00 a.m. to 2:00 p.m. in the Jordan Hall of Science Galleria.

The event is open to all interested undergraduate students, graduate students, post-docs, faculty, and staff, as well as external customers, who wish to learn more about what the core facilities are and how their state-of-the-art instrumentation and expertise can benefit research projects or work areas.

Personnel from the core facilities will be there to answer questions and there will be a chance to win great prizes, like an iPad mini and Notre Dame Research items. The following core facilities are participating:

- Center for Research Computing
- Center for Social Research
- Chemical Synthesis and Drug Discovery Facility
- Computer Aided Molecular Design
- Engineering Machine Shops
- Fluorescence Assisted Cell Sorting Facility
- Freimann Life Science Center
- Genomics and Bioinformatics Core Facility
- Magnetic Resonance Research Center
- Mass Spectrometry and Proteomics Facility
- Materials Characterization Facility
- Molecular Structure Facility
- Notre Dame Integrated Imaging Facility
- Notre Dame Linked Experimental Ecosystem Facility
- Notre Dame Nanofabrication Facility
- Notre Dame Turbomachinery Facility
- Physics Machine Shop
- Radiation Laboratory: Glassblowing and Machine Shops

For more information, please contact Kara Primmer (khuegel1@nd.edu).

ND Genomics Gets A New Look

In order to bring you a better genomics experience, we've reached out to Monkeyhouse Creative Group to design and implement a new site design. It is our goal to make accessing information related to the Notre Dame Genomics and Bioinformatics Department easier, faster, and friendlier to our students and faculty.

Ordering full-service capillary sequencing?

We have a new order form for full-service capillary sequencing services. Please use this form for all full-service orders and follow the instructions on the order form.

Roche NimbleGen has stopped accepting orders for their microarray platform

News text here.

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