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CNC Cores - PDBEB 2016/2017 Edition
October 10 - 21
Doctoral Program in Experimental Biology and Biomedicine (PDBEB)
2016/2017 Edition

CNC Cores

October 10-21

UC-Biotech and CNC (FMUC, POLO I building)

BEB CNC-Cores:
10th – 14th October, UC-Biotech

Monday, October 10th
Life Sciences Mass Spectrometry
Bruno Manadas


9:30 – 11:00
Introduction to Mass spectrometry and Proteomics
Protein Identification and Characterization

11:15 – 12:30
Clinical Proteomics

14:00 – 15:00
Interactomics - IP and Pull-down experiments

15:00 – 16:00
Small molecule

16:00 – 17:00
Translational mass spectrometry

Tuesday, October 11th
Transcriptomics to characterize cellular mechanisms
Conceição Egas

9h30m - 17h
•    Next-generation sequencing technologies (NGS)
•    RNA, transcriptomes and RNA-Seq
•    Experimental design for RNA-Seq
•    RNA-Seq data processing
•    RNA-Seq data analysis methods
•    Differential expression and functional analysis

Module description
The transcriptome is the complete set of RNA transcripts in a given cell for a specific time point, physiological condition, developmental stage or response to an external stimulus. Understanding the transcriptome is important for interpreting the functional elements of the genome.  Transcriptome profiling experiments (RNA-Seq) can identify differentially expressed genes between different stages or between healthy and diseased groups identify of alternative splicing events and post-transcriptional RNA editing events.

Next-generation sequencing (NGS) is now the preferred method for high throughput transcriptional profiling over microarrays or real-time-PCR.  NGS produces millions of short DNA fragments during one sequencing run and per sample. Analysis of this complex data is only possible through the use of combined sets of bioinformatics tools for the different steps.
This module aims to help students to gain a better understanding of RNA-Seq techniques and their applications. RNA-Seq experimental planning, performing and analyzing will be addressed.

Learning outcomes
By the end of this module participants should understand the principles of next generation sequencing technologies, design RNA-Seq experiments, identify the main steps in RNA-Seq data processing and learn bioinformatics tools for raw data quality control, processing, read alignment, transcripts expression quantification and differential expression analysis.

Wednesday, October 12th
Functional genomics
Miguel Mano

9.00-10.00 – High-throughput/high-content screening: from basic principles to emerging technologies
10.00-11.00 – Case studies: RNAi screenings for gene and microRNA function
11.00-11.30 – Break
11.30-12.30 – Principles of automated image analysis
12.30-14.00 – Lunch
14.00-16.00 – Hands-on (sample processing, image acquisition)
16.00-18.00 – Hands-on (image analysis)

Thursday, October 13th
Production and purification of recombinant proteins
Ricardo Pires

9:30 – 11:00
Expression systems for production of recombinant proteins
Soluble proteins vs Membrane proteins

11:00 – 11:15 - Break
11:15 – 12:30
New cloning methods
Multi-tiered protein expression and purification approaches in E.coli

12:30 – 14:00 – Lunch
14:00 – 15:30
Molecular visualization of protein structures: PyMOL basics - I
16:00 – 17:30
Molecular visualization of protein structures: PyMOL basics – II

Notes for students:
Pymol basics tutorials
Please have your laptop computer ready with PyMOL software (Schrödinger);
An educational version can be obtained at:
A temporary version of Pymol (only for Windows) will also be provided during the course;
Two workstations will also be available during the tutorials.

Friday, October 14th

Course Evaluation

Morning – free time to prepare project and presentations
14:00 –Presentations and evaluation

Monday, October 17th - Friday, October 21st

Microscopy (Luisa Cortes & Margarida Caldeira) and Flow Cytometry (Isabel Nunes)
CNC, FMUC Building, pólo I, Coimbra

i)    Basics on Fluorescence Microscopy and on Flow Cytomety;
ii)   Live Cell Imaging Approaches;
iii)  Introduction to Image Analysis using FIJI software;
iv)  Cell Sorting Fundamentals;
v)   Practical session I –Visualization and Quantification of Cell Death;
vi)  Practical session II –Visualization and Quantification of Protein Traffic in Transfected Cells;
vii)  Practical session III – Live cell imaging and 3D imaging;
viii)  Data Analysis.

Monday, 17th October 2016

09:30 – 11:00: Basics on Fluorescence Microscopy (Luisa Cortes)
11:15 – 12:30: Basics on Flow Cytomety (Isabel Nunes)
14:00 – 15:00: Measuring oxygen and acidification rates on living cells – Seahorse (Margarida Caldeira)
15:00 – 16:00: Live Cell Imaging Approaches (Luisa Cortes)
16:30 – 17:30: Experimental Design

Tuesday, 18th October 2016

09:30 – 10:30: Cell Sorting Fundamentals and Applications (Filipe Pereira)
10:45 – 12:00: Introduction to Image Analysis using FIJI software (Luisa Cortes)

14:30 – 18:00: Practical session I – Quantification and Visualization of Cell Death (Microscopy and Flow Cytometry)  

Wednesday, 19th October 2016

9:30 – 12:45: Practical session II – Quantification and Visualization of Transfected Cells (Microscopy and Flow Cytometry)  
14:30 – 17:30: Practical session III – Live cell imaging and 3D imaging (Microscopy) 

Thursday, 20th October 2016

9:30 – 12:30: Data Analysis   

Friday, 21th October 2016

9:30 – 12:30: Presentation and Discussion
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