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PDBEB Courses 2019/2020 - Core Technologies @ CNC
January 20 - 31
Coordinator: Luísa Cortes - lcortes@cnc.uc.pt

Doctoral Program in Experimental Biology and Biomedicine (PDBEB)

2019/2020 Edition

Core Technologies @ CNC

January 20 – January 31, 2020


Registration is mandatory here.


Deadline for registration: January, 10 2020


Coordinator: Luísa Cortes (lcortes@cnc.uc.pt); CNC, University of Coimbra



Bruno Manadas (bmanadas@cnc.uc.pt); CNC, University of Coimbra

Cátia Santa Cátia Santa (catiajmsanta@gmail.com); CNC, University of Coimbra

Conceição Egas (cegas@biocant.pt); CNC, University of Coimbra

Hugo Froufe (hugo.froufe@biocant.pt); Biocant

Isabel Nunes (inunes@cnc.uc.pt); CNC, University of Coimbra

Isaura Simões (isimoes@biocant.pt); CNC, University of Coimbra

Luisa Cortes (lcortes@cnc.uc.pt); CNC, University of Coimbra

Margarida Caldeira (mcaldeira@cnc.uc.pt); CNC, University of Coimbra

Maria José Simões (mjs@biocant.pt); Biocant

Marta Pinto (mlaranjeiro.pinto@gmail.com); CNC, University of Coimbra

Miguel Mano (mano@ci.uc.pt); CNC, University of Coimbra

Pedro Curto (pedrocurtobioq@gmail.com): CNC, University of Coimbra

Ricardo Vieira Pires (ricardo.pires@biocant.pt); CNC, University of Coimbra

Sandra Anjo (sandra.isabel.anjo@gmail.com); CNC, University of Coimbra

Susana Pedreiro (susanapedreiro@gmail.com); CNC, University of Coimbra

Tatiana Catarino (tatianacatarino@gmail.com); CNC, University of Coimbra

Vera Mendes (vera3m@gmail.com); CNC, University of Coimbra


Date: January 20 – January 31, 2020

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



The aim of this course is to provide an overview of the technological platforms available at CNC.

This two-week course will focus on the principles and high-end applications of the different methodologies and students will gain a theoretical understanding and hands-on experience on state-of-the-art equipment and on data processing and analysis.




Week I – 20th -24th January 2020 – UC-Biotech

Monday, 20th January 2020

9h30 - Welcome Session – Luisa Cortes (UC-Biotech Auditorium)


Transcriptomics to characterize cellular mechanisms: RNA-Seq (UC-Biotech)

10h00 -11h20: RNA-Seq: NGS and experimental design – Conceição Egas

11h40 – 13h00: RNA-Seq analysis. Data processing and analysis - Hugo Froufe

14h30 - 17h00: Hands on RNA extraction and QC- I - Maria José Simões


Tuesday, 21st January 2020

Transcriptomics to characterize cellular mechanisms: RNA-Seq (UC-Biotech)

10h00 - 12h30: Hands on RNA extraction and QC- I - Maria José Simões

14h00 - 17h00: Hands on data processing and analysis – Hugo Froufe


Wednesday, 22nd January 2020

High-throughput/high-content screening

9h00-10h00 – High-throughput/high-content screening: from basic principles to emerging technologies – Miguel Mano

10h00-11h00 – Case studies: RNAi screenings for gene and microRNA function - Miguel Mano

11h30-12h30 – Principles of automated image analysis - Miguel Mano

14h00-16h00 – Hands-on (sample processing, image acquisition)

16h00-18h00 – Hands-on (image analysis)


Thursday, 23th January 2020

Recombinant protein expression and purification (UC-Biotech)

09h30-10h45 – Cloning strategies: the old and the new – Isaura Simões

11h15-12h30 – Protein expression and purification: there is no such thing as a “one size fits all solution” - Isaura Simões

14h00-18h30 – Hands-on protein purification- Pedro Curto (please bring lab coats)


Friday, 24th January 2020

R&D Antibodies

9h30-10h30 – Developing antibodies for research, diagnostics and therapy using birds – Ricardo Pires

11h00-12h00 – Visiting CNC’s Avian Facility


14h00- Mass Spectrometry

-Introduction to Mass Spectrometry and Liquid chromatography coupled to Mass spectrometry     - Bruno Manadas

- Small Molecules Quantification by Mass Spectrometry (Targeted and Untargeted approaches) - Vera Mendes  

- Introduction to LC-MS/MS based proteomics- Bruno Manadas

- Drug induced neuroproteomic changes - Cátia Santa

- Translational biomarker research - Sandra Anjo


Week II – 27th January – 31st January – CNC polo I

Monday, 27th January 2020

Fluorescence Microscopy

(*) Students will be divided in 2 groups for the hands-on sessions.

 9h30 - 10h30: Fundamentals of Fluorescence Microscopy – Margarida Caldeira

11h00 - 12h00: Optical Sectioning – Luísa Cortes

14h00 - 15h00: Live Cell Imaging – Luísa Cortes

15h15 - 17h45: Hands on microscopy session I (*)


Tuesday, 28th January 2020

Fluorescence Microscopy

 9h30 - 12h00: Hands on microscopy session II (*)

14h30 - 17h00: Hands on microscopy session III (*)


Wednesday, 29th January 2020

Fluorescence Microscopy

10h00 - 12h00: Hands on microscopy session IV (*)

14h30 - 15h30: Fundamentals of Imaging Processing with FIJI – Luísa Cortes

15h45 - 17h00: Hands on imaging processing session


Thursday, 30th January 2020 – UC-Biotech

Flow Cytometry

10h00 - 11h00: Principals of flow cytometry – Isabel Nunes

11h15 - 12h00:  Flow Cytometry applications – Isabel Nunes

14h00 - 15h00: Fluorescence-activated cell sorting (FACS): principles and applications – Marta Pinto (@ UC-Biotech)

15h00 – 17h30: Hands on cell sorting session – Susana Pedreiro (@ UC-Biotech)


Friday, 31st January 2020

15h00 - 16h00: Students Presentations

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