Texas Tech UniversitySPRING2016

CenterforBiotechnologyand Genomics

BTEC 5312: Gene ExpressionAnalysis

When:Wednesday2:00-4:50PM

Where: Experimental Sciences Building,Room105

Instructors: Room 108 (officehoursbyappointment)

:806-834-0592

Description:Thisclasswillintroduce studentstotechniquesof gene expression analysisand itsapplications.

LearningOutcomes: Students successfullycompleting thiscoursewill have anunderstanding ofvariousmethodsof quantifying geneexpression and application of these techniques. Studentswill isolateRNA and studydifferential geneexpressionbyRNA-Sequencing usingNextGeneration sequencing. Quantitative realtime PCR will be used to validate thegene expression results.Studentswill be introducedtotopics likeregulation of gene expression, gene annotation,andpathwaymapping.

Course Project:

Students will be required to complete a course project. Students should work either in a topic of their interest or in groups of two or three, combining different background and expertise in each team, when possible. Start discussing project ideas you are interested in with your fellow students and with me as soon as possible - you need to have selected a project by the 6th week and a proposal has to be submitted by the 9th week. The proposal should be about 2-4 pages long and needs to reflect your understanding of the problem, briefly discuss existing and related work, describe the proposed work, specify a work schedule, and list relevant literature. The project proposals and reports will be reviewed and evaluated according to standard criteria for research proposals/research papers. A preliminary list of possible project topics is as follows:

  • Identification of differentially expressed genes in various tissues
  • RNA-Seq experiment to understand the mechanisms of stress response
  • Small RNA-Sequencing to understand post-transcriptional gene regulation.
  • Understanding the mechanisms of disease resistance by RNA-Seq

If you have other ideas for potential projects, come talk to me - I look forward to hearing about your ideas!

Tentative Schedule:

1/27IntroductiontoRNA and geneexpression.Methods ofRNA extraction–total RNA, mRNA,small RNA. Linux OS introduction.

2/3RNA Extraction, quantification and qualityanalysis.

2/10Gene expression Profiling–RNA-Sequencingprinciples,methods,and applications.

2/17RNA-SequencingcDNA librariespreparation. Neoprep library preparation.

2/24RNA-SequencingcDNA libraryqualityanalysisandquantification. Sequencing of libraries

3/2BCL to fastq conversion,Sequence read QC, assembly principles, and assembly algorithms. Case study using Trinity.

3/9Expression profiling bysequencing–ClassSeminar

3/16SPRINGBREAK

3/23RNAseqdata analysis,calculation offold changesandgenerationofdifferentially expressedgene lists.

3/30Small RNA andEpigenetic regulation of geneexpression.

4/6Small RNA extraction, quantification, and quality analysis

4/13Gene annotationand pathway mapping.

4/20Gene expression validation. Quantitative real-time PCR –principles.Semi-quantitative

PCR. BasicQuantitative real-time PCR considerations, primer and probe designing.Design of experiments.

4/27Absolutequantification andRelative quantification –Dataanalysis.

5/4RNA-Seq Applications– Case study.

5/17Final - Class Seminar and projectsubmission.

Methodsofassessmentoflearningoutcomes:

Learning outcomewill be assessedthrough written examination andreports.Participation in discussionsandquestioningduring classwill also beusedforassessinglearning outcomes. Course Assignment/Description ofhowgradesare determined:

Participation/presentation/reports/quiz:75% Final exam/project:25%

Afinal letter gradewill be determined byperformance onthe above criteria,with consideration given to performance of the class asa whole.Agrade of“I” (Incomplete) will be awarded bythe instructorprior totheendofthesemesteronlywhenfailuretocompletethe workhasbeendueto causesbeyond the student’s control andwhen classperformancehasbeen satisfactory. TexasTechregulations requirethataformexplaining thereasonfor theIncompleteandthe methodtobe usedtomakeupthemissedworkbe submitted,afterbeingsigned byboththe student and instructor, totheRegistrar.Incompletegradesthat arenot replaced byan A, B or C grade within one year areautomaticallyreplaced byan F.

SpecialConditions: Anystudent who,becauseofadisability,mayrequire special arrangements in order tomeet thecourserequirementsshould contact theinstructorassoonas possible tomakeanynecessaryarrangements. Studentsshould presentappropriate

verificationfrom Student Disability Services (AccessTECH).Norequirementexiststhat accommodationsbemade prior tocompletion of thisapproved universityprocess.

Academic Integrity: It is theaim ofthefacultyof Texas Tech University tofosteraspiritof completehonestyandahigh standardofintegrity. Theattemptof studentstopresentastheir own anyworknothonestlyperformed isregardedbythefacultyand administration asamost serious offenseandrendersthe offenders liable toseriousconsequences, possiblysuspension.

“Scholastic dishonesty”includes,butnotlimitedto,cheating, plagiarism, collusion, falsifyingacademic records, misrepresentingfacts, andanyactdesigned togive unfairacademicadvantagetothestudent or the attempttocommit such and act.

Cheating: Dishonesty inexaminations, quizzes,orhome workassignments,illegal possession of examinations,theuseof unauthorized notesduring anexamination or quiz,obtaininginformation during an examinationfromthe examinationpaperorotherwisefromanotherstudent,assistingothers to cheat, alteration of grade records, illegal entry to or unauthorized presence in an officeare instances ofcheating.

Plagiarism: Offering theworkofanother as one’sown,withoutproperacknowledgement, isplagiarism; thereforeanystudentwhofailstogive creditfor quotationsoran essentially identical expression of material takenfrombooks,encyclopedias, magazines,internet web sites,and other reference works,or from thethemes, reportsorotherwritingsofafellowstudentisguiltyofplagiarism.

Civilityin the Classroom: Studentsareexpected toassist inmaintaining a classroom environment that isconducive tolearning.In order toensurethatall studentshave anopportunitytogainfrom time spentinclass,unless otherwise approved bythe instructorstudentsare prohibitedfromusingcellular phones or beepersorengageinanyother formof distraction.Inappropriate behaviorin theclassroom will resultin arequest toleave the class.

Attendance: It isexpectedthat youwillattend and participatein everyscheduled class.There arenomakeupclasses. If thereisareasonfor missing a classyou must contacttheinstructoras soon aspossible tomake necessaryarrangementsto discussthe outcome oftheabsence.You may need toprovide a notefromyourphysician excusingyourabsence ifyouare absent fromaclassmore than adaydue toanillness.

ReligiousHolyDay: Astudent who intendsto observe a religiousholydayshould makethat intentionknown totheinstructorpriortothe absence.Astudentwho isabsent from classesfor the observance ofareligiousholydayshall be allowed to takean examination orcompletean assignment scheduledfor that daywithin a reasonable timeaftertheabsence.

Ombudsmanforstudents: TheOmbudsmanforstudents isavailable toassiststudentswith any conflictorproblemthathas todo with beingastudentat TexasTechUniversity.Youmay visitthe Ombudsmanat Student Union Buildingorcall 742-4791.