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   Location:Home > Announcement > Trainings
June 9-12, 2017: Environmental Microbiomes: Amplicon sequencing from sample preparationto publication
Author: Liu Jingxin
Update time: 2017-05-24
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Title: Environmental Microbiomes:  Amplicon sequencing from sample preparationto publication

Venue: Meeting room 1 (XTBG headquarter at Menglun Town, Mengla County, Yunnan)  

Dates: 9– 12 June  2017 (4 days)

Organiser: Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences

Registration: application will be closed on 6 June 2017

Sponsors: Forest Ecology Group ofKey Laboratory of Tropical Forest Ecology and Training Department of theXishuangbanna Tropical Botanical Garden, CAS

Registration fee: 600 RMB

About the workshop: Advances in sequencing technologies provide researchers with the capacityto profile large numbers of diverse environmental microbial communities at lowcost.  These technologies yield molecularsequence datasets ranging in size from millions to trillions of reads. Thereare substantial challenges in determining how to best prepare samples, processresulting datasets, and test hypotheses for amplicon sequencing.

In this interactive seminar class, participantswill be encouraged to explore course ideas using sample datasets in hands onlearning modules.  In total, participantsin this course will become familiar with important considerations in hypothesistesting, experimental design, sample preparation, and various approaches foramplicon sequence processing, data analysis, and presentation. This four-dayworkshop will consist of informal lectures (50%) and hands-on tutorials(50%).  

Student number: a maximum of 20

Instructor: Dr. SONG Zewei (University of MinnesotaTwin Cities, Department of Plant Pathology)  

                                 Researchgate: https://www.researchgate.net/profile/Zewei_Song

If youhave any questions about the workshop, please email huyuehua@xtbg.org.cn and/or liujx@xtbg.org.cn


Tentative Schedule:

DAY 1:June 9th, 2017


Lecture 1: General principle of ampliconsequencing: history and future

Lecture 2: Experimental design for studyingenvironmental microbiomes


Lecture 3: Sequencing platforms and librarypreparation



Practice 1: Set up working environmental forbioinformatics

Practice 2: Basic commands in Linux

DAY 2:June 10th, 2017


               Lecture 1: Data processing –Part I

               Lecture 2: Data processing –Part II


               Lecture 3: OTU clustering andtaxonomy assignment




               Practice: Data processing

               Practice: OTU clustering

DAY 3:June 11th, 2017


               Lecture 1: Analyze the OTUtable: diversity

               Lecture 2: Analyze the OTUtable: multivariate analysis


               Lecture 3: analyze the OTUtable: functions


               Lunch break


               Practice: Measure diversity

               Practice: Multivariate analysis

DAY 4:June 12th, 2017


               Lecture 1: Network analysis

               Lecture 2: How to do troubleshooting


               Lunch break


               Practice: Network analysis


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Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences. Menglun, Mengla, Yunnan 666303, China
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