Genomics Laboratory,Biological Sciences 81.434/ 81.534, UMass Lowell, Fall 2013
Instructor: Dr. Jessica Garb, Assistant Professor, Department of Biological Sciences
Email: Jessica_Garb@uml.edu
Office Hours: 12-2pm Olsen 520
Graduate Student Teaching Instructor: Sarah Atherton
Email: Sarah_Atherton@student.uml.edu
Office Hours:TBA
Meeting Time: Thursdays: 12:30-3:30 pm
Room: Location will alternate between the Olsen Hall 6th floor computer lab (610) and
the Olsen 509 teaching laboratory asscheduled below.
Course Description:This one-credit course covers a series of molecular laboratory and
computer-based bioinformatics exercises providing practical experience in the collection
and analysis of genomic-level data. Students will gain experience working with
published data, and have the opportunity to collect new data themselves using
molecular techniques (e.g., gene cloning, PCR and sequencing) and will use a variety of
analytical tools and databases to make biologically meaningful interpretations of their
data (e.g., gene predictions, genome annotation, homology searches, sequence
alignment and phylogenetic analyses).
Course Prerequisites: Genetics 81.235 or Principles of Genetics 81.335; Co-requisite
– Genomics Lecture81.432/ 81.532
Text: The laboratory does not require students to purchase books. In class exercises
and readings will be distributed through the blackboard course website or in class.
Webserver Access: To retrieve lab-related documents you will need to access the
biology lab server by logging into vlabs with your email login in ID and password,
choose Biological Sciences,click on the “Biology File Share” icon on the desktop and
navigate to the GenomicsLab folder This folder will contain lab materials you can copy
to the desktop (temporarily), but it is recommended to copy them, and any new
documents you create to your thumbdrive. Work cannot be saved long-term to the
desktop or any other disk space of the computer you are working on, which will be
erased after 60 minutes of inactivity. When you log out, all documents you created will
be erased so be sure to save anything important to a thumbdrive.
Course Learning Objectives:
At the completion of this course:
1.Students will be able to performvaried analyses of genomic data (e.g., sequence
assembly, genome annotation, gene modeling, batch blasting), using a diversity of
bioinformatics tools.
2. Students will become more proficient at manipulating genetic data using different
computer software programs.
3. Students will strengthen their molecular laboratory skills by collecting new genomiclevel data (e.g., using cloning, primer design, PCR, and sequencing).
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4. Students will be able to determine which analytical tools aremost appropriate to
analyze differentgenomic data sets in order to make biologically meaningful
conclusions.
5. Students will deeply appreciatethe role of technology in the collection and analysis of
genomic data.
Achievement of learning objectives 1-5 will be assessed through graded laboratory
exercises and assignments,along with one final lab report.
Tentative Schedule of Laboratory exercises
Week 1
Date: Thursday, Sept.5
No lab this week.
Week 2
Date: Thursday, Sept. 12
Location: Computer lab
Topic: Introduction to sequence databases and analytical tools (NCBI, SwissProt,
BLAST suite, EMBOSS, ExPasy, Genome Browsers, Register for DNA Subway)
Week 3
Date: Thursday, Sept. 19
Location: Computer Lab
Topic: Annotation of Arabadopsis synthetic contig using DNA Subway Part 1
(Annotation, gene prediction, gene modeling)
Week 4
Date: Thursday, Sept. 26
Location: Computer Lab
Topic: Annotation of Arabadopsis chromosome 5 100 kb sequence using DNA
Subway Part 2.Preparation for next week’s trip
Week 5
Date: Thursday, Oct.3
Location: Computer Lab
Tentative: workshop on finding scientific literature for genomics research
Week 6
Date: Thursday, Oct. 10
Location:Molecular Lab (pants and shoes required)
Topic: Collection of gene expression data part I: black widow spider venom gland
EST library construction lecture and size screening
Week 7
Date: Thursday, Oct. 17 Location: Molecular Lab (pants and shoes required)
Topic: Collection of gene expression data part II: black widow spider venom gland
ESTs sequence preparation and restriction digest
Week 8
Date: Thursday, Oct. 24
Location: Broad Institute in Cambridge
Class Trip 1:30-3:30pm: Guided tour of the Broad Institute of MIT and Harvard –
the nation’s premier genome sequencing institute.
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Week 9
Date: Thursday, Oct. 31
Location: Computer Lab
Topic: Introduction to multiple sequence alignment and phylogenetic analysis
Week 10
Date: Thursday, Nov. 7
Location: Computer Lab
Topic: Editing and analysis of black widow spider venom ESTs, identifying
homologs via batch blasting, primer design for PCR of genomic DNA
Week 11
Date: Thursday, Nov. 14
Location: Computer Lab
Topic: Assembly of black widow genomic sequence & annotation of fosmid insert
using DNA Subway, annotation with ESTs
Week 12
Date: Thursday, Nov. 21
Location: Molecular Lab(pants and shoes required)
Topic: Testing student primers on genomic DNA
Week 12
Date: Thursday, Nov. 28 – No lab Thanksgiving
Week 14
Date: Thursday, Dec. 5
Location: Computer Lab/Molecular Lab
Topic: Editing andannotation of black widow PCR products or repeat of PCR.
Course Assignments:
Weekly laboratory assignments - Each week students will participate in the laboratory
exercises described above in class. Exercises will be accompanied by specific
assignments to be completed both in class and after class as homework. These
assignments will largely consist of written answers to questions related to the laboratory
exercise, or may require completion of the exercise outside of class. These
assignments will be graded by the teaching assistant and will count towards 60% of the
final grade.
Final Lab Report–Students will write a final lab report, due at the end of the class,
which will report the results of the black widow genomic data collection and analyses.
The report will take the standard format of a scientific paper with an abstract,
introduction, methods, results and discussion. More details will be forthcoming. This
report will count towards 20% of the final grade.
Attendance & participation – Given the small size of the class, and that several
exercises build on top of previous ones, attendance at each laboratory class is required
and full participation is expected. This counts towards 20% of the final grade of the
course, and each lab missed will result in the deduction of points from your final grade.
Important Dates to Remember:
Last day to add or drop this course: September 17
Withdrawal deadline: November 13
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