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Single-Cell Transcriptomics is improving the quality of biological investigations by enhancing the dissection of heterogeneity in complex tissues and cell cultures.

This 3-day course aims to provide an overview of a complete Single-Cell RNA sequencing workflow:

  • A theoretical overview of all existing methods to perform Single-Cell RNA sequencing libraries with a focus on individual features and weaknesses;
  • A practical hands-on laboratory training to produce 10X Genomics 3’ Single-Cell RNA sequencing libraries;
  • A practical bioinformatics training that will provide guidelines and tools to process and analyze Single-Cell RNA sequencing libraries from raw sequences to visualization.

Important Dates

Deadline for applications: 16 March 2019
Chosen participants will be notified by: 01 April 2019
Payment deadline: 10 April 2019
Course date: 07-09 May 2019


Telethon Institute of Genetics and Medicine (TIGEM)
Via dei Campi Flegrei, 34
80078 Pozzuoli (NA) - Italy

Registration fee:

Academic 350€ - Non-academic 500€

Registration fee includes course material, coffee breaks, lunchs and dinner buffets, transfer from the partner hotels. A maximum of 25 candidates will be accepted in the course. Priority will be given to candidates from ELIXIR-IIB member institutions (see the list at the bottom) and ELIXIR nodes. Incomplete applications or applications for only parts of the course will not be accepted.

Travel Grants

Five travel grants of EUR 200 will be available for candidates that will be accepted. If you are interested in applying for a travel grant please state it in the application form.


We suggest the three options listed below for acccomodation. Transfer between hotels and the course venue will be available for free.

hotel website booking code single occupancy twin occupancy
Villa Avellino www.villaavellino.it TIGEM 115 EUR 121 EUR
Miramare www.miramareresidence.com TIGEMMAY19 66 EUR 71 EUR
Maison Toledo www.maisontoledopozzuoli.it TIGEMMAY19 80 EUR 80 EUR

Selection criteria

The requirement for this course is knowledge of RNA-sequencing theory and practice. Participants will be selected based on a solid background in RNA sequencing. Applicants already working on a research project that involves single-cell sequencing will be given priority.

Application form


Wet-lab specialists

Anna Manfredi - TIGEM, Pozzuoli (NA), IT
Antonio Grimaldi - TIGEM, Pozzuoli (NA), IT
10X Genomics Specialist - TBA


Annamaria Carissimo - National Research Council, Naples, IT
Gennaro Gambardella - TIGEM, Pozzuoli (NA), IT
Francesco Panariello - TIGEM, Pozzuoli (NA), IT

Abstract guidelines

Participants will be required to submit an abstract (max 1500 characters). Abstracts should describe participants’ research projects. Applications without abstract will not be considered.


Davide Cacchiarelli (TIGEM & University of Naples “Federico II”, IT)
Vincenza Colonna (CNR-IGB, Naples, IT)
ELIXIR-IIB Training Platform


Barbara Zimbardi and Marica Giovannini course2019@tigem.it

Pdf of lectures can be found here


Tuesday 07 May 2019

Single-Cell RNA sequencing Theory
14:00-14:30 Coffee and registration
14:30-15:00 Welcome session Organizers, Trainers and Participants Introduction to the course, presentation of the course website and repository with all the material for the course. Trainers and participants presentation: current position in science, course motivations, objectives and expectations.
15:00-16:30 Lecture Bashir Sadet Chromium Single Cell 3’ Application and Protocol Overview
16:30-17:00 Coffee break
17:00-17:30 Presentation Mattler Toledo
17:30-18:00 Practical Participants and Trainers Organization for the practical section of the next day
18:00-19:30 Dinner Buffet sponsored by Mettler-Toledo

Wednesday 08 May 2019

Hands-on laboratory training to produce 10X Genomics 3’ Single-Cell RNA sequencing libraries
09:00-09:30 Recap session Participants and Trainers Quick recapitulation of concepts from the previous day
09:30-12:00 Practical Participants and Trainers Cell Preparation, Application Setup, Start run: Each Trainee Performs One Real Chip loading. Post Cycling Recovery, Dynabeads Cleanup
12:00-12:30 Practical Participants and Trainers Review and discussion
12:30-14:00 Lunch
14:00-15:30 Practical Visualization of QC (examples of Bioanalyzer results)
15:30-16:00 Coffee break
16:00-17:30 Lecture Chiara Reggio Latest Application of 10x Genomic
17:30-18:30 Dinner Buffet sponsored by 10X genomics

Thursday 09 May 2019

Practical bioinformatics training to process and analyze Single-Cell RNA sequencing libraries from raw sequences to visualization
09:00-09:30 Recap session Participants and Trainers Quick recapitulation of concepts from the previous day
09:30-10:30 Lecture Francesco Panariello Theory Refresher and Software Overview: Cell Ranger
10:15-10:30 Coffee break
10:30-12:30 Practical Gennaro Gambardella Visualizing Single Cell Data
12:30-13:30 Lunch
13:30-14:30 Lecture AnnaMaria Carissimo Statistical analysis of Single Cell data
14:30-17:30 Practical Practical exercises
17:30- 20:30 Dinner Buffet

ELIXIR-IIB member institutions

  • CNR (ELIXIR-IIB coordinator)
  • CRS4
  • Fondazione Edmund Mach, Trento
  • INFN
  • GARR
  • Sapienza University of Roma
  • University of Bari
  • University of Bologna
  • University of Firenze
  • University of Milano
  • University of Milano Bicocca
  • University of Padova
  • University of Parma
  • University of Roma "Tor Vergata"
  • University of Salerno
  • University of Tuscia