#  1 Introduction

PROSEQO participates in the Open Research Data Pilot in Horizon 2020 thus
contributing to improve and maximize access to and re-use of research data
generated by the project. This deliverable describes datasets that are planned
to be generated and released during the project. Further data may however
arise through the lifetime of the project and will lead to updates of the Data
Management Plan.

Following the Guidelines on FAIR Data Management in Horizon2020  1  the
description of each dataset (DS) includes the following information as far as
appropriate and applicable for the respective data:

  * __Data set reference and name_ _

  

Identifier for the data set to be produced

  * __Data set description_ _

  

Description of the data that will be generated or collected

  * __Fair data: Findable_ _

  

Indication of the metadata, documentation or other supporting information that
will accompany the data for it to be interpreted correctly

  * __Fair data: Accessible_ _

  

Information on whether and how it is planned to make data openly available

  * __Fair data: Interoperable_ _

  

Information on how the interoperability of the dataset will be guaranteed

  * __Fair data: Re-usable_ _

  

Information on how it will make sure to increase the data re-use

#  2 Datasets: overview

The consortium has identified N°12 datasets to be generated and released
during the project implementation. The table below gives an overview on the
datasets:  
  
<table>  
<tr>  
<th>

**ID**

</th>  
<th>

**Name**

</th>  
<th>

**Responsible partner**

</th>  
<th>

**PROSEQO Task(s)**

</th> </tr>  
<tr>  
<td>

DS#1

</td>  
<td>

Data needed to validate results in scientific publications

</td>  
<td>

UPSud

</td>  
<td>

All tasks

</td> </tr>  
<tr>  
<td>

DS#2

</td>  
<td>

Scientific publications

</td>  
<td>

UPSud

</td>  
<td>

All tasks

</td> </tr>  
<tr>  
<td>

DS#3

</td>  
<td>

DNA_sequence

</td>  
<td>

AB Analitica

</td>  
<td>

Task 5.2

</td> </tr>  
<tr>  
<td>

DS#4

</td>  
<td>

Research data

</td>  
<td>

ALACRIS

</td>  
<td>

Task 5.1-2

</td> </tr>  
<tr>  
<td>

DS#5

</td>  
<td>

Analysis algorithms

</td>  
<td>

ALACRIS

</td>  
<td>

Task 5.4

</td> </tr>  
<tr>  
<td>

DS#6

</td>  
<td>

Proof of concept using a standard (Rayleigh limited) focused beam for optical
trapping

</td>  
<td>

UB

</td>  
<td>

Task 4.1

</td> </tr>  
<tr>  
<td>

DS#7

</td>  
<td>

Design new microfluidic chambers

</td>  
<td>

UB

</td>  
<td>

Task 2.3

</td> </tr>  
<tr>  
<td>

DS#8

</td>  
<td>

Study of the translocation of DNA and Protein through the nano capillarities
using electrical measurements

</td>  
<td>

UB

</td>  
<td>

Task 4.2

</td> </tr>  
<tr>  
<td>

DS#9

</td>  
<td>

Low speed polymer translocation

</td>  
<td>

UB

</td>  
<td>

Task 4.2

</td> </tr>  
<tr>  
<td>

DS#10

</td>  
<td>

Plasmonic trap

</td>  
<td>

UB

</td>  
<td>

Task 4.4

</td> </tr>  
<tr>  
<td>

DS#11

</td>  
<td>

Polymer translocation control via surface plasmon

</td>  
<td>

UB

</td>  
<td>

Task 4.5

</td> </tr>  
<tr>  
<td>

DS#12

</td>  
<td>

Spectroscopy of DNA sequence

</td>  
<td>

IIT

</td>  
<td>

Task 3.3

</td> </tr> </table>

#  3 Dataset Management Tables

We established an on-line form for data management  2  . It addresses the
elements for data management listed in Section 1. The form supports the
process of data collection, alignment of data collection with the workplan,
communication across partners, and data publication. In the following, the
data sets expected to be collected in the runtime of PROSEQO are listed in
tabular structure. One dataset is listed per page.

##  3.1 1  
  
<table>  
<tr>  
<th>

Data set name

</th>  
<th>

Data needed to validate results in scientific publications

</th> </tr>  
<tr>  
<td>

Responsible partner

</td>  
<td>

UPSud

</td> </tr>  
<tr>  
<td>

Description

</td>  
<td>

Data needed to validate results in scientific publications

</td> </tr>  
<tr>  
<td>

PROSEQO Task

</td>  
<td>

All tasks

</td> </tr>  
<tr>  
<td>

File formats

</td>  
<td>

Various

</td> </tr>  
<tr>  
<td>

Metadata

</td>  
<td>

Protocols

</td> </tr>  
<tr>  
<td>

Access

</td>  
<td>

Open

</td> </tr>  
<tr>  
<td>

Data repository

</td>  
<td>

Institutional: University repository

</td> </tr>  
<tr>  
<td>

Supporting tools

</td>  
<td>

\-

</td> </tr>  
<tr>  
<td>

Interoperability

</td>  
<td>

\-

</td> </tr>  
<tr>  
<td>

Copyright and IP issues

management

</td>  
<td>

As defined in the Consortium Agreement

</td> </tr>  
<tr>  
<td>

Availability

</td>  
<td>

Directly to all partners

</td> </tr>  
<tr>  
<td>

Duration

</td>  
<td>

As long as publication platform runs

</td> </tr>  
<tr>  
<td>

Expected re-use

</td>  
<td>

Everybody

</td> </tr> </table>

##  3.2 Dataset # 2  
  
<table>  
<tr>  
<th>

Data set name

</th>  
<th>

Scientific publications

</th> </tr>  
<tr>  
<td>

Responsible partner

</td>  
<td>

UPSud

</td> </tr>  
<tr>  
<td>

Description

</td>  
<td>

Public access version of scientific publication

</td> </tr>  
<tr>  
<td>

PROSEQO Task

</td>  
<td>

All tasks

</td> </tr>  
<tr>  
<td>

File formats

</td>  
<td>

Pdf

</td> </tr>  
<tr>  
<td>

Metadata

</td>  
<td>

Link to original publication

</td> </tr>  
<tr>  
<td>

Access

</td>  
<td>

Open

</td> </tr>  
<tr>  
<td>

Data repository

</td>  
<td>

Institutional: University repository

</td> </tr>  
<tr>  
<td>

Supporting tools

</td>  
<td>

\-

</td> </tr>  
<tr>  
<td>

Interoperability

</td>  
<td>

\-

</td> </tr>  
<tr>  
<td>

Copyright and IP issues

management

</td>  
<td>

UPSud

</td> </tr>  
<tr>  
<td>

Availability

</td>  
<td>

Directly after publication of the manuscript

</td> </tr>  
<tr>  
<td>

Duration

</td>  
<td>

As long as publication platform runs

</td> </tr>  
<tr>  
<td>

Expected re-use

</td>  
<td>

Everybody

</td> </tr> </table>

##  3.3 3  
  
<table>  
<tr>  
<th>

Data set name

</th>  
<th>

DNA_sequence

</th> </tr>  
<tr>  
<td>

Responsible partner

</td>  
<td>

AB Analitica

</td> </tr>  
<tr>  
<td>

Description

</td>  
<td>

  * Data originated from a NGS platform (Illumina MySeq) 

  

  * large dimension computer files 

  

  * similar data can be obtained with other instrumentation starting from the same bio-material (DNA/RNA) 

  

</td> </tr>  
<tr>  
<td>

PROSEQO Task

</td>  
<td>

Task 5.2

</td> </tr>  
<tr>  
<td>

File format

</td>  
<td>

.FASTQ

</td> </tr>  
<tr>  
<td>

Metadata

</td>  
<td>

The data will regard genetic information obtained from nucleic acids
sequencing. No label are foreseen up to now

</td> </tr>  
<tr>  
<td>

Access

</td>  
<td>

PROSEQO consortium only

Justification: Data strictly related to the technology development. To be
shared only within the consortium

</td> </tr>  
<tr>  
<td>

Data repository

</td>  
<td>

Data repository shared folder

</td> </tr>  
<tr>  
<td>

Supporting tools

</td>  
<td>

A suitable software will be developed in order to read and interprete the data

</td> </tr>  
<tr>  
<td>

Interoperability

</td>  
<td>

The data will be generated in a standard and well-known format (.FASTQ)

No standard vocabulary will be used

No mapping will be provided to more commonly used ontologies

</td> </tr>  
<tr>  
<td>

Copyright and IP issues

management

</td>  
<td>

No copyright and IPR issues are expected

</td> </tr>  
<tr>  
<td>

Availability

</td>  
<td>

No data embargo is expected

</td> </tr>  
<tr>  
<td>

Duration

</td>  
<td>

Project duration

</td> </tr>  
<tr>  
<td>

Expected re-use

</td>  
<td>

All the partners can be interested in re-use the data

</td> </tr> </table>

##  3.4 Dataset # 4  
  
<table>  
<tr>  
<th>

Data set name

</th>  
<th>

Research data

</th> </tr>  
<tr>  
<td>

Responsible partner

</td>  
<td>

ALACRIS

</td> </tr>  
<tr>  
<td>

Description

</td>  
<td>

Experimental results in form of measurements, images, accompanying description
files, eventually sequencing data

</td> </tr>  
<tr>  
<td>

PROSEQO Task

</td>  
<td>

Task 5.1-2

</td> </tr>  
<tr>  
<td>

File format

</td>  
<td>

Data in form of facts and experimental results in a presentation

</td> </tr>  
<tr>  
<td>

Metadata

</td>  
<td>

Experiment description

</td> </tr>  
<tr>  
<td>

Access

</td>  
<td>

PROSEQO consortium only – Justification: commercial

</td> </tr>  
<tr>  
<td>

Data repository

</td>  
<td>

Institutional: a common repository folder on an internal IIT-server

</td> </tr>  
<tr>  
<td>

Supporting tools

</td>  
<td>

\-

</td> </tr>  
<tr>  
<td>

Interoperability

</td>  
<td>

Standard vocabulary for all data types present in the data set will be used to
allow inter-disciplinary interoperability

</td> </tr>  
<tr>  
<td>

Copyright and IP issues

management

</td>  
<td>

According to the CA IP definition

</td> </tr>  
<tr>  
<td>

Availability

</td>  
<td>

Upon publication

</td> </tr>  
<tr>  
<td>

Duration

</td>  
<td>

Project duration + 5 years

</td> </tr>  
<tr>  
<td>

Expected re-use

</td>  
<td>

Project partners and external researchers (after being published)

</td> </tr> </table>

###  3.5 5  
  
<table>  
<tr>  
<th>

Data set name

</th>  
<th>

Analysis algorithms

</th> </tr>  
<tr>  
<td>

Responsible partner

</td>  
<td>

ALACRIS

</td> </tr>  
<tr>  
<td>

Description

</td>  
<td>

Program for sequencing data analysis

</td> </tr>  
<tr>  
<td>

PROSEQO Task

</td>  
<td>

Task 5.4

</td> </tr>  
<tr>  
<td>

File format

</td>  
<td>

File with a program code

</td> </tr>  
<tr>  
<td>

Metadata

</td>  
<td>

Accompanying file with program description; presentation of program
performance

</td> </tr>  
<tr>  
<td>

Access

</td>  
<td>

PROSEQO consortium only – Justification: commercial

</td> </tr>  
<tr>  
<td>

Data repository

</td>  
<td>

Institutional: a common repository folder on an internal IIT-server

</td> </tr>  
<tr>  
<td>

Supporting tools

</td>  
<td>

\-

</td> </tr>  
<tr>  
<td>

Interoperability

</td>  
<td>

Standard vocabulary for all data types present in the data set will be used to
allow inter-disciplinary interoperability

</td> </tr>  
<tr>  
<td>

Copyright and IP issues

management

</td>  
<td>

According to the CA IP definition

</td> </tr>  
<tr>  
<td>

Availability

</td>  
<td>

Upon publication

</td> </tr>  
<tr>  
<td>

Duration

</td>  
<td>

Project duration + 5 years

</td> </tr>  
<tr>  
<td>

Expected re-use

</td>  
<td>

Project partners and external researchers (after being published)

</td> </tr> </table>

###  3.6 6  
  
<table>  
<tr>  
<th>

Data set name

</th>  
<th>

Proof of concept using a standard (Rayleigh limited) focused beam for optical
trapping

</th> </tr>  
<tr>  
<td>

Responsible partner

</td>  
<td>

UB

</td> </tr>  
<tr>  
<td>

Description

</td>  
<td>

Use of an infrared trap at the entrance of the single nanopore structure and
test it with several beads and molecules, first tested with DNA and next with
RNA and proteins.

Use of existing methods that avoid adsorption of molecules on beads

</td> </tr>  
<tr>  
<td>

PROSEQO Task

</td>  
<td>

Task 4.1

</td> </tr>  
<tr>  
<td>

File formats

</td>  
<td>

Notebooks

</td> </tr>  
<tr>  
<td>

Metadata

</td>  
<td>

Notebooks, web pages, papers

</td> </tr>  
<tr>  
<td>

Access

</td>  
<td>

Open

</td> </tr>  
<tr>  
<td>

Data repository

</td>  
<td>

Project website

</td> </tr>  
<tr>  
<td>

Supporting tools

</td>  
<td>

\-

</td> </tr>  
<tr>  
<td>

Interoperability

</td>  
<td>

Via mail contact

Standard vocabulary for all data types present in the data set will be used to
allow inter-disciplinary interoperability

</td> </tr>  
<tr>  
<td>

Copyright and IP issues

management

</td>  
<td>

The data obtained in this set up will be open and it is not necessary any
license because there are a lot of references and papers published regarding
the topic

</td> </tr>  
<tr>  
<td>

Availability

</td>  
<td>

Indefined

</td> </tr>  
<tr>  
<td>

Duration

</td>  
<td>

n/a

</td> </tr>  
<tr>  
<td>

Expected re-use

</td>  
<td>

Project partners and external researchers related to the field

</td> </tr> </table>

###  3.7 7  
  
<table>  
<tr>  
<th>

Data set name

</th>  
<th>

Design new microfluidic chambers

</th> </tr>  
<tr>  
<td>

Responsible partner

</td>  
<td>

UB

</td> </tr>  
<tr>  
<td>

Description

</td>  
<td>

Design of new microfluidic chambers to control the translocation through the
nano pipette using our mini tweezers set up

</td> </tr>  
<tr>  
<td>

PROSEQO Task

</td>  
<td>

Task 2.3

</td> </tr>  
<tr>  
<td>

File formats

</td>  
<td>

Notebooks, web pages, papers

</td> </tr>  
<tr>  
<td>

Metadata

</td>  
<td>

Notebooks, web pages, papers

</td> </tr>  
<tr>  
<td>

Access

</td>  
<td>

Open

</td> </tr>  
<tr>  
<td>

Data repository

</td>  
<td>

Project website

</td> </tr>  
<tr>  
<td>

Supporting tools

</td>  
<td>

\-

</td> </tr>  
<tr>  
<td>

Interoperability

</td>  
<td>

Standard vocabulary for all data types present in the data set will be used to
allow inter-disciplinary interoperability

</td> </tr>  
<tr>  
<td>

Copyright and IP issues

management

</td>  
<td>

The data obtained in this set up will be open and it is not necessary any
license because there are a lot of references and papers published regarding
the topic

</td> </tr>  
<tr>  
<td>

Availability

</td>  
<td>

Indefined

</td> </tr>  
<tr>  
<td>

Duration

</td>  
<td>

n/a

</td> </tr>  
<tr>  
<td>

Expected re-use

</td>  
<td>

Project partners and external researchers related to the field

</td> </tr> </table>

##  3.8 Dataset # 8  
  
<table>  
<tr>  
<th>

Data set name

</th>  
<th>

Study of the translocation of DNA and Protein through the nano capillarities
using electrical measurements

</th> </tr>  
<tr>  
<td>

Responsible partner

</td>  
<td>

UB

</td> </tr>  
<tr>  
<td>

Description

</td>  
<td>

Characterizing the translocation of DNA and protein through the nano
capillarities by means of electrical signal measurements

</td> </tr>  
<tr>  
<td>

PROSEQO Task

</td>  
<td>

Task 4.2

</td> </tr>  
<tr>  
<td>

File formats

</td>  
<td>

Notebooks, web pages, papers

</td> </tr>  
<tr>  
<td>

Metadata

</td>  
<td>

Notebooks, web pages, papers

</td> </tr>  
<tr>  
<td>

Access

</td>  
<td>

Open

</td> </tr>  
<tr>  
<td>

Data repository

</td>  
<td>

Project website

</td> </tr>  
<tr>  
<td>

Supporting tools

</td>  
<td>

\-

</td> </tr>  
<tr>  
<td>

Interoperability

</td>  
<td>

Standard vocabulary for all data types present in the data set will be used to
allow inter-disciplinary interoperability

</td> </tr>  
<tr>  
<td>

Copyright and IP issues

management

</td>  
<td>

The data obtained in this set up will be open and it is not necessary any
license because there are a lot of references and papers published regarding
the topic

</td> </tr>  
<tr>  
<td>

Availability

</td>  
<td>

Indefined

</td> </tr>  
<tr>  
<td>

Duration

</td>  
<td>

n/a

</td> </tr>  
<tr>  
<td>

Expected re-use

</td>  
<td>

Project partners and external researchers related to the field

</td> </tr> </table>

##  3.9 Dataset # 9  
  
<table>  
<tr>  
<th>

Data set name

</th>  
<th>

Low speed polymer translocation

</th> </tr>  
<tr>  
<td>

Responsible partner

</td>  
<td>

UB

</td> </tr>  
<tr>  
<td>

Description

</td>  
<td>

Use an optical fiber laser mechanically coupled to a wiggler to produce a
steerable beam. Verify the translocation of the polymer via V-clamp signal
measurement

</td> </tr>  
<tr>  
<td>

PROSEQO Task

</td>  
<td>

Task 4.2

</td> </tr>  
<tr>  
<td>

File formats

</td>  
<td>

Report

</td> </tr>  
<tr>  
<td>

Metadata

</td>  
<td>

Notebooks, web pages, papers

</td> </tr>  
<tr>  
<td>

Access

</td>  
<td>

PROSEQO consortium only – Justification: because these data set will be novel

</td> </tr>  
<tr>  
<td>

Data repository

</td>  
<td>

Project website

</td> </tr>  
<tr>  
<td>

Supporting tools

</td>  
<td>

\-

</td> </tr>  
<tr>  
<td>

Interoperability

</td>  
<td>

Standard vocabulary for all data types present in the data set will be used to
allow inter-disciplinary interoperability

</td> </tr>  
<tr>  
<td>

Copyright and IP issues

management

</td>  
<td>

Copyright and Project partners

</td> </tr>  
<tr>  
<td>

Availability

</td>  
<td>

One year

</td> </tr>  
<tr>  
<td>

Duration

</td>  
<td>

As long as publication platform runs

</td> </tr>  
<tr>  
<td>

Expected re-use

</td>  
<td>

Project partners

</td> </tr> </table>

##  3.10 Dataset # 10  
  
<table>  
<tr>  
<th>

Data set name

</th>  
<th>

Plasmonic trap

</th> </tr>  
<tr>  
<td>

Responsible partner

</td>  
<td>

UB

</td> </tr>  
<tr>  
<td>

Description

</td>  
<td>

The nanotrap will be generated provided by a second nanostructure illuminated
by a secondary wavelength at the entrance of the nanochannel. Design of the
second nanostructure and test of its trapping capabilities with microspheres
of few tens until hundreds of nanometers

</td> </tr>  
<tr>  
<td>

PROSEQO Task

</td>  
<td>

Task 4.4

</td> </tr>  
<tr>  
<td>

File formats

</td>  
<td>

Reports

</td> </tr>  
<tr>  
<td>

Metadata

</td>  
<td>

Notebooks, web pages, papers

</td> </tr>  
<tr>  
<td>

Access

</td>  
<td>

PROSEQO consortium only – Justification: because these data set will be novel

</td> </tr>  
<tr>  
<td>

Data repository

</td>  
<td>

Project website

</td> </tr>  
<tr>  
<td>

Supporting tools

</td>  
<td>

\-

</td> </tr>  
<tr>  
<td>

Interoperability

</td>  
<td>

Standard vocabulary for all data types present in the data set will be used to
allow inter-disciplinary interoperability

</td> </tr>  
<tr>  
<td>

Copyright and IP issues

management

</td>  
<td>

Copyright and Project partners

</td> </tr>  
<tr>  
<td>

Availability

</td>  
<td>

One year

</td> </tr>  
<tr>  
<td>

Duration

</td>  
<td>

As long as publication platform runs

</td> </tr>  
<tr>  
<td>

Expected re-use

</td>  
<td>

Project partners

</td> </tr> </table>

##  3.11 Dataset # 11  
  
<table>  
<tr>  
<th>

Data set name

</th>  
<th>

Polymer translocation control via surface plasmon

</th> </tr>  
<tr>  
<td>

Responsible partner

</td>  
<td>

UB

</td> </tr>  
<tr>  
<td>

Description

</td>  
<td>

Developing a plasmonic trap device to control the biomolecule translocation
through a nano capillarity

</td> </tr>  
<tr>  
<td>

PROSEQO Task

</td>  
<td>

Task 4.5

</td> </tr>  
<tr>  
<td>

File formats

</td>  
<td>

Reports

</td> </tr>  
<tr>  
<td>

Metadata

</td>  
<td>

Notebooks, web pages, papers

</td> </tr>  
<tr>  
<td>

Access

</td>  
<td>

PROSEQO consortium only – Justification: because these data set will be novel

</td> </tr>  
<tr>  
<td>

Data repository

</td>  
<td>

Project website

</td> </tr>  
<tr>  
<td>

Supporting tools

</td>  
<td>

\-

</td> </tr>  
<tr>  
<td>

Interoperability

</td>  
<td>

Standard vocabulary for all data types present in the data set will be used to
allow inter-disciplinary interoperability

</td> </tr>  
<tr>  
<td>

Copyright and IP issues

management

</td>  
<td>

Copyright and Project partners

</td> </tr>  
<tr>  
<td>

Availability

</td>  
<td>

One year

</td> </tr>  
<tr>  
<td>

Duration

</td>  
<td>

As long as publication platform runs

</td> </tr>  
<tr>  
<td>

Expected re-use

</td>  
<td>

Project partners

</td> </tr> </table>

##  3.12 Dataset # 12  
  
<table>  
<tr>  
<th>

Data set name

</th>  
<th>

Polymer translocation control via surface plasmon

</th> </tr>  
<tr>  
<td>

Responsible partner

</td>  
<td>

IIT

</td> </tr>  
<tr>  
<td>

Description

</td>  
<td>

Optical data recorded as wavelength spectrum

</td> </tr>  
<tr>  
<td>

PROSEQO Task

</td>  
<td>

Task 3.3

</td> </tr>  
<tr>  
<td>

File formats

</td>  
<td>

Spectrum

</td> </tr>  
<tr>  
<td>

Metadata

</td>  
<td>

Any spectrum will has a ID

</td> </tr>  
<tr>  
<td>

Access

</td>  
<td>

PROSEQO consortium only – Justification: novel data

</td> </tr>  
<tr>  
<td>

Data repository

</td>  
<td>

Project repository folder

</td> </tr>  
<tr>  
<td>

Supporting tools

</td>  
<td>

Computer software for spectrum reading

</td> </tr>  
<tr>  
<td>

Interoperability

</td>  
<td>

The data are generic, i.e. intensity versus wavelength / energy

</td> </tr>  
<tr>  
<td>

Copyright and IP issues

management

</td>  
<td>

IIT

</td> </tr>  
<tr>  
<td>

Availability

</td>  
<td>

A data embargo can be expected for IP reason

</td> </tr>  
<tr>  
<td>

Duration

</td>  
<td>

n/a

</td> </tr>  
<tr>  
<td>

Expected re-use

</td>  
<td>

All the related scientific community

</td> </tr> </table>