**Deliverable content**

**1\. Purpose of the MAGNEURON Data Management Plan (DMP)**

MAGNEURON is a Horizon 2020 project participating in the Open Research Data
Pilot. This pilot is a part of the Open Access to Scientific Publications and
Research Data programme in H2020. The goal of the program is to foster access
to the data generated in H2020 projects.

The purpose of the DMP is to analyse the main elements of the European data
management policy that will be used by the consortium regarding all the
datasets that will be generated by the project. The DMP as a not fixed
document, has been evolving during the lifespan of the project.

This last version of the DMP includes an overview of the datasets generated by
the project, and the specific conditions that are attached to them.

The MAGNEURON project DMP primarily lists the different datasets generated by
the project and the main actions that the project implemented to manage these
datasets.

**2\. Register of the data sets generated or collected in MAGNEURON**

The register must be understood as a dynamic document, which has been updated
regularly during project lifetime.

The information listed below reflects the conception and design of the
individual work packages at the end of the project.

The data register delivers information according to Guidelines on Data
Management in Horizon 2020:

  * Data set reference and name; 

  

  * Data set description; 

  

  * Standards and metadata; 

  

  * Data sharing; 

  

  * Archiving and preservation. 

    1. **Datasets collected within WP1**

  
  

  

Not relevant for this work package.

  2. **Datasets collected within WP2 - Preparation of synthetic and recombinant MNPs (Phenix – Christine M.)**

  

  
  
<table>  
<tr>  
<th>

**Data set reference and name: WP2 dataset**

Person in charge: Christine Ménager (CNRS)

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

**Data type**

</td>  
<td>

**Data standards**

</td>  
<td>

**Data generation software**

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

Images (TEM pictures)

</td>  
<td>

Format: TIFF

</td>  
<td>

ImageJ (open source image processing program

designed for scientific multidimensional images)

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

Video tapes

</td>  
<td>

Format: AVI,

STK

</td>  
<td>

MetaMorph Microscopy

Automation and Image

Analysis Software

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

Analysis files (text, calculation) for magnetism, DLS, zeta potential,

hyperthermia, spectroscopy (UV-visible

absorption, fluorescence)

</td>  
<td>

Format:

Different text and calculation formats

</td>  
<td>

Different text processing and calculation software

(excel, kaleidagraph, Igor)

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

A dataset containing electronic microscopy imaging of the optimized particles
and

their main characterizations (size analysis, hydrodynamic diameter, magnetism
properties) used by the different partners

of the project

</td>  
<td>

Format of the data: TIFF,

JPEG and PDF

</td>  
<td>

The dataset was made using imageJ, excel, word,

Malvern zetasizer software

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

**Estimated data size**

</th>  
<th>

**Data sharing**

</th>  
<th>

**Data storage and archiving**

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

~500 gigabytes per year will be

generated by WP2.

</td>  
<td>

The generated data have been shared only with the team of Christine Ménager
and the MAGNEURON project partners.

The MAGNEURON partners have used Dropbox for data sharing in WP2, internal
reports and EC

deliverables

</td>  
<td>

The data generated in

WP2 have been stored only in the digital

format, no physical

support will be kept.

The data have been stored on the Phenix local servers. The

scientific data have

been stored during all

the project, and 5 years after the project

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

25 Mb

</td>  
<td>

The dataset is shared on the website zenodo: with

DOI: 10.5281/zenodo.3587537

https://zenodo.org/record/3587537#.XhL6kvxCc2w

</td>  
<td>

The dataset will be stored on zenodo, and

on the PHENIX internal servers.

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

  3. **Datasets collected within WP3 - Biofunctionalization and intracellular delivery of MNPs (UOS – Jacob P.)**

  

  
  
<table>  
<tr>  
<th>

**Data set reference and name: WP3 dataset**

Person in charge: Jacob Piehler (UOS)

</th>  
<th>

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

**Data type**

</td>  
<td>

**Data standards**

</td>  
<td>

**Data generation software**

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

Maps of Plasmids Used for Magnetogenetic Manipulation

</td>  
<td>

Format: .cm5

</td>  
<td>

Clone Manager

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

Tools & Microscope-Setup for Magnetogenetic Manipulation of Cells

</td>  
<td>

Format: .docx

</td>  
<td>

MS-Word

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

Protocol for Production of MagIcS

Nanoparticles

</td>  
<td>

Format: .docx

</td>  
<td>

MS-Word

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

Probing Magnetic Manipulation of MagIcS Nanoparticles Inside Living Cells

</td>  
<td>

Format: .docx, .AVI, .TIFF

</td>  
<td>

MS-Word, Image-J,

AxioVision

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

Tools for Probing Magnetogenetic

Activation of GTPases

</td>  
<td>

Format: .docx, .AVI, .TIFF

</td>  
<td>

MS-Word, Image-J,

AxioVision

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

Script for Analysis of FRET-Ratio Images

</td>  
<td>

Format: .cmv

</td>  
<td>

Matlab

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

**Estimated data size**

</th>  
<th>

**Data sharing**

</th>  
<th>

**Data storage and archiving**

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

~10-50 gigabytes per

year have been generated by WP3.

</td>  
<td>

The generated data have been shared only with the team of Jacob

Piehler and the MAGNEURON project partners. The MAGNEURON partners have used
two software types for data sharing in WP3:

  * UOS own software for sharing 

  

the scientific data;

  * Dropbox for sharing internal reports and EC deliverables. 

  

</td>  
<td>

The data generated in WP3 have been stored only in the digital format, no
physical has been kept.

The data have been stored on the UOS local servers using OMERO software. The
scientific data will be stored during all the project, and for 10 years
thereafter.

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

All data

described above are about 10-50 gigabytes in sizes

</td>  
<td>

These data will be published on  _https://zenodo.org_

</td>  
<td>

These data will be stored on  _https://zenodo.org_

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

including data files

</td>  
<td>

raw

</td>  
<td>

</td>  
<td>

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

  1. **Datasets collected within WP4 - Tools for MNP manipulation in single-cell assays**

  

  
  
<table>  
<tr>  
<th>

**Data set reference and name: WP4 dataset** Person in charge: Mathieu Coppey
(Institut Curie)

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

**Data type**

</td>  
<td>

**Data standards**

</td>  
<td>

**Data generation software**

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

Maps of molecular plasmids

</td>  
<td>

Format: JDK

</td>  
<td>

Curie Institute application

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

Document presenting the tools for magnetic manipulation

</td>  
<td>

document docx

</td>  
<td>

Word & PowerPoint

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

Videos: raw data of manipulation of magnetic nanoparticles in single cells

</td>  
<td>

Tiff videos

</td>  
<td>

Recorded with

Metamorph

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

Scripts for analysis

</td>  
<td>

MATLAB scripts, csv file with quantification, tracks.

</td>  
<td>

Coded with MATLAB

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

Videos: Cellular magneticmanipulation with an endosomal

approach

</td>  
<td>

AVI, TIFF,

</td>  
<td>

Metamorph, ImageJ,

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

Analysis: Cellular magneticmanipulation with an endosomal

approach

</td>  
<td>

PowerPoint, Excel files

</td>  
<td>

PowerPoint, Excel

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

**Estimated data size**

</th>  
<th>

**Data sharing**

</th>  
<th>

**Data storage and archiving**

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

~1-2 terabytes per year

generated by WP4.

</td>  
<td>

The generated data have been shared only with the team of Mathieu Coppey and
the MAGNEURON project partners.

The MAGNEURON partners have used two software types for data sharing in WP4:

  * Xfer – Institut Curie own software – for sharing the scientific data; 

  

  * Dropbox for sharing internal reports and EC deliverables. 

  

</td>  
<td>

The data generated in WP4 have been stored only in the digital format, no
physical support have been kept.

The data have been stored on the Curie Institute local servers. The scientific
data have been stored during all the project, and the after-project scientific
data storage is to be discussed.

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

Tool for magnetic

manipulation:

20kB

</td>  
<td>

Open data will be published on  _https://zenodo.org_

</td>  
<td>

Word document

published directly on  _zenodo.org_

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

Magnetic manipulations in single cells:

10GB – 50GB of raw data

</td>  
<td>

The dataset is shared on the website zenodo: with DOI 10.5281/zenodo.3579322
_https://zenodo.org/record/3579322#.Xigz52hKhPY_

</td>  
<td>

The data will be stored directly on  _zenodo.org_ with a backup on the NAS of
the team.

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

Scripts for the analysis:

100Mo

</td>  
<td>

The dataset is shared on the website zenodo: with DOI 10.5281/zenodo.3582962
_https://zenodo.org/record/3582962#.XigzFmhKhPY_

</td>  
<td>

Scripts will be stored directly on  _zenodo.org_ with a backup on the NAS of
the team.

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

Endosomal approach:

80GB

</td>  
<td>

Raw data will be published with description of the published experiments on
_https://zenodo.org_

</td>  
<td>

The data will be stored directly on  _zenodo.org_ with a backup on the NAS of
the team.

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

  1. **Datasets collected within WP5 - Biomagnetic control of stem cell differentiation (Keele – Neil T. / Michael R.)**

  

  
  
<table>  
<tr>  
<th>

**Data set reference and name: WP5 dataset** Person in charge: Alicia El Haj
(Birmingham University)

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

**Data type**

</td>  
<td>

**Data standards**

</td>  
<td>

**Data generation software**

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

Video files

</td>  
<td>

Format: AVI, WMV

</td>  
<td>

Microscopy Automation and

Image Analysis Software

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

Still images

</td>  
<td>

Format: TIF, JPEG

</td>  
<td>

ImageJ (open source image processing program

designed for scientific multidimensional images)

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

Graphing and statistics files

</td>  
<td>

Format: various software specific

</td>  
<td>

Microcal Origin, SPSS, PRISM, GraphPad, Minitab

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

Analysis files

</td>  
<td>

Format: MS Excel spreadsheets

</td>  
<td>

MS Excel

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

Data summary files

</td>  
<td>

Format: ppt, docx, pdf

</td>  
<td>

MS PowerPoint, MS Word,

Adobe acrobat

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

**Estimated data size**

</th>  
<th>

**Data sharing**

</th>  
<th>

**Data storage and archiving**

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

~1-2 terabytes per year will be generated by WP5.

</td>  
<td>

The generated data will be shared only with the team of

Alicia El Haj, and the MAGNEURON project partners.

The MAGNEURON partners will use Dropbox for data sharing in WP5.

Processed data associated with published work will be made open access via a
suitable data repository (e.g. EPrints / Keele Research repository).

</td>  
<td>

The data generated in WP5 will be stored in the digital format, and in
physical copies in laboratory notebooks.

The data will be stored on the Keele University local servers and hard drives.
The scientific data will be stored during the project and for 10 years
thereafter. Place for after-project scientific data storage is to be
discussed.

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

In more details, the following datasets have been identified in WP5  
  
<table>  
<tr>  
<th>

**Data Ref**

</th>  
<th>

**Name**

</th>  
<th>

**Type and size**

**(Standards / metadata)**

</th>  
<th>

**Sharing**

</th>  
<th>

**Storage / Archiving**

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

WP5.1 SH active b-catenin expt.

</td>  
<td>

Active bcatenin fluorescent images

</td>  
<td>

PPT, Spreadsheet (<10Mb), JPG, <1Mb per image (150+ images), Minitab file

(<1Mb per file)

</td>  
<td>

Processed images and data

shared with Magneuron consortia and disseminated at conferences

</td>  
<td>

Digital

(University hard

drives), Physical

(Poster)

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

WP5.1 SH bcatenin ELISA expt.

</td>  
<td>

B-cat ELISA

</td>  
<td>

PPT, Spreadsheet

(<10Mb), Minitab file

(<1Mb per file)

</td>  
<td>

Processed data shared with Magneuron consortia and disseminated at conferences

</td>  
<td>

Digital

(University hard drives)

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

WP5.1 SH MNP

labelling

</td>  
<td>

UM206-MNP and TREKMNP

fluorescent images

</td>  
<td>

PPT, TIF, <3Mb per image (100+ images)

</td>  
<td>

Processed images shared with Magneuron consortia and disseminated at
conferences

</td>  
<td>

Digital

(University hard drives)

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

WP5.1 / WP5.2

Receptor expression (PCR)

</td>  
<td>

SH and Rat receptor PCR gels and qPCR

</td>  
<td>

PPT, TIF 3-13Mb per image (15+ images), spreadsheets (<10Mb

per file), Minitab files

(<2Mb per file)

</td>  
<td>

Processed images shared with Magneuron consortia and disseminated at
conferences

</td>  
<td>

Digital

(University hard drives),

Physical (MSc dissertation)

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

WP5.1/5.2 MNP and PMA IF expt.

</td>  
<td>

TH and DAT fluorescent images

</td>  
<td>

PPT, Spreadsheet (<10Mb), TIF (100+ images, <25Mb per image), JPG (50+ images,
<2Mb), OIB files (20+ files, <10Mb per file), Minitab file

(<1Mb per file)

</td>  
<td>

Processed images shared with Magneuron consortia and disseminated at
conferences

</td>  
<td>

Digital

(University hard

drives), Physical

(Poster),

Physical (MSc dissertation)

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

WP5.1/5.2 Diff.

media +/- MNP IF expt.

</td>  
<td>

TH and DAT fluorescent images

</td>  
<td>

PPT, JPG, (220+ images, (<2Mb per image), OIB files (20+ files, <10Mb per
file)

</td>  
<td>

Processed images shared with Magneuron consortia and disseminated at
conferences

</td>  
<td>

Digital

(University hard drives),

Physical (MSc dissertation)

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

**Data Ref**

</th>  
<th>

**Name**

</th>  
<th>

**Type and size**

**(Standards / metadata)**

</th>  
<th>

**Sharing**

</th>  
<th>

**Storage / Archiving**

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

WP5.1/5.2 Diff.

media +/- MNP PCR expt.

</td>  
<td>

Neuro. and Dopa. gene expression with Diff. media with/without

MNP

</td>  
<td>

PPT, Spreadsheets

(<10Mb per file), Minitab files (<1Mb

per file)

</td>  
<td>

Processed data shared with Magneuron consortia and disseminated at conferences

</td>  
<td>

Digital

(University hard drives),

Physical (Poster and MSc

dissertation)

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

WP5.2 Target receptor

homology study (Human vs Rat)

</td>  
<td>

Rat Frizzled and TREK receptor homology

</td>  
<td>

PPT (<10Mb)

</td>  
<td>

Processed data shared with Magneuron consortia

</td>  
<td>

Digital

(University hard drives)

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

WP5.1 Receptor expression during differentiation

</td>  
<td>

Frizzled, TREK

and BIII Tubulin fluorescent images

</td>  
<td>

PPT, TIF <10Mb per image (100+ images),

JPG <5Mb per image

(50+ images)

</td>  
<td>

Processed images shared with Magneuron consortia and disseminated at
conferences

</td>  
<td>

Digital

(University hard drives),

Physical (MSc dissertation)

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

WP5.1 Stress response gene expt.

</td>  
<td>

Stress response gene expression

with TREKMNP

</td>  
<td>

PPT, Spreadsheets

(<10Mb per file), Minitab files (<1Mb

per file)

</td>  
<td>

Processed data shared with Magneuron consortia and disseminated at conferences

</td>  
<td>

Digital

(University hard drives),

Physical (MSc dissertation)

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

WP5.1 Wnt response gene expt.

</td>  
<td>

Wnt associated gene expression

with UM206MNP

</td>  
<td>

PPT, Spreadsheets

(<10Mb per file), Minitab files (<1Mb

per file)

</td>  
<td>

Processed data shared with Magneuron consortia and disseminated at conferences

</td>  
<td>

Digital

(University hard drives),

Physical (MSc dissertation)

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

WP5.1 Wnt reporter expt.

</td>  
<td>

SH TCF/LEF

reporter

</td>  
<td>

PPT, Spreadsheets

(<10Mb per file), Minitab files (<1Mb

per file)

</td>  
<td>

Processed data shared with Magneuron consortia and disseminated at conferences

</td>  
<td>

Digital

(University hard

drives), Physical

(Poster)

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

WP5.2 SH Neurite extension study

</td>  
<td>

SH neurite extension fluorescent microscopy

</td>  
<td>

PPT, TIFF, <10Mb per image (100+ images), Spreadsheet (<2Mb

per file)

</td>  
<td>

Processed images shared with Magneuron consortia

</td>  
<td>

Digital

(University hard drives)

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

WP5.2 hDNP with MNP study

</td>  
<td>

hDNP neurite extension microscopy

</td>  
<td>

PPT, JPG, <2Mb per image (40+ images), Spreadsheets (<5Mb

per file), Neurite trace

file (ImageJ format,

<1Mb)

</td>  
<td>

Processed images shared with Magneuron consortia

</td>  
<td>

Digital

(University hard drives)

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

**Data Ref**

</td>  
<td>

**Name**

</td>  
<td>

**Type and size**

**(Standards / metadata)**

</td>  
<td>

**Sharing**

</td>  
<td>

**Storage / Archiving**

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

WP5.2/WP5.3 Rat

slice expt’s

</td>  
<td>

Rat slice fluorescent images

</td>  
<td>

PPT, TIF, <15Mb per image (300+ images)

</td>  
<td>

Processed data shared with Magneuron consortia and disseminated at conferences

</td>  
<td>

Digital

(University hard

drives), Physical

(Poster)

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

WP5.2 Rat VM / N27 cells

</td>  
<td>

Rat VM / N27 in vitro diff.

Expt’ and MNP labelling

</td>  
<td>

PPT, TIFF, JPG,

<10Mb per image

(800+ images), Spreadsheet (<2Mb

per file)

</td>  
<td>

Processed images shared with Magneuron consortia

</td>  
<td>

Digital

(University hard drives)

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

WP2/WP3 MNP and Ferritin

samples

characterisation

</td>  
<td>

ACS (100F1,

Dahan MNP,

Ferritin Sample

K)

</td>  
<td>

Spreadsheets (<5Mb each)

</td>  
<td>

Processed data shared with Magneuron consortia

</td>  
<td>

Digital

(University hard drives)

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

WP5 MNP

characterisation

</td>  
<td>

Micromod

250nm MNP

TEM images

</td>  
<td>

PPT, TIF, <2Mb per image (100+ images)

</td>  
<td>

Processed data shared with Magneuron consortia

</td>  
<td>

Digital

(University hard drives)

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

  2. **Datasets collected within WP6 - Directed fibre outgrowth of neuronal cells (RUB – Rolf H.)**

  

  
  
<table>  
<tr>  
<th>

P

</th>  
<th>

**Data set reference and name: WP6 dataset** erson in charge: Rolf Heumann
(Ruhr-University Bochum)

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

**Data type**

</td>  
<td>

**Data standards**

</td>  
<td>

**Data generation software**

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

Video tapes

</td>  
<td>

Format: AVI, MP4

</td>  
<td>

Olympus Cell Sense Dimensions Image

Analysis Software

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

Still images

</td>  
<td>

Format: TIF, JPEG

</td>  
<td>

ImageJ (open source image processing program designed for scientific
multidimensional images) Bio-Rad Image Lab

Olympus Cell Sense Dimensions Image

Analysis Software

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

Maps of molecular plasmids

</td>  
<td>

Format: XDNA, DNA

</td>  
<td>

Serial Cloner, SnapGene

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

Graphing and statistics files

</td>  
<td>

Format: XLSX, PZF, PZFX,

OPJ and further software specific formats

</td>  
<td>

Microsoft Excel, Microcal Origin,

GraphPad PRISM

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

Analysis files

(text, calculation)

</td>  
<td>

Format: Different text and calculation formats

</td>  
<td>

Different text processing and calculation software

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

**Estimated data size**

</th>  
<th>

**Data sharing**

</th>  
<th>

**Data storage and archiving**

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

~1.0 terabytes per year have been

generated by WP6.

</td>  
<td>

The generated data have been shared only with the team of Rolf Heumann and the
MAGNEURON project partners.

The MAGNEURON partners will use two software types for data sharing in WP6:

  * FileShare (Ruhr-University Bochum 

  

internal)

  * Dropbox for sharing internal reports and EC deliverables. 

  

</td>  
<td>

The data generated in WP6 have been stored only in the digital format, no
physical support have been kept.

The data have been stored on the Ruhr-University Bochum local servers. The
scientific data have been stored during all the project, and the afterproject
scientific data storage is to be discussed.

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

5.9 Mb

</td>  
<td>

The dataset is shared on the website zenodo: with DOI: 10.5281/zenodo.3606263

https://zenodo.org/record/3606263#.XhyPQ

yNCdaQ

</td>  
<td>

The dataset will be stored on

zenodo, and on the RUB internal servers.

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

  1. **Datasets collected within WP7 - Magnetic manipulation of cellular signalling in organotypic brain slices and in vivo models of Parkinson’s disease**

  

  
  
<table>  
<tr>  
<th>

**Data set reference and name: WP7 dataset**

Person in charge: Monte Gates (Keele)

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

**Data type**

</td>  
<td>

**Data standards**

</td>  
<td>

**Data generation software**

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

Video tapes

</td>  
<td>

Format: AVI, MPEG

</td>  
<td>

Microscopy Automation and Image Analysis Software

Ethovision and Tracksys processing software

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

Still images

</td>  
<td>

Format: TIF, JPEG,

JPEG2000

</td>  
<td>

NIS elements (NIKON), and ImageJ (open source image processing) programs
designed for scientific multidimensional images

MatLab Image Processing Toolbox

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

Statistics files

</td>  
<td>

Format: SPSS and Prism formats (PZF)

</td>  
<td>

SPSS, GraphPad Prism

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

Analysis files (excel files, word docs)

</td>  
<td>

Format: Different text and spreadsheet formats

</td>  
<td>

Microsoft Office

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

Video of slice culture protocol / embryo dissection and imaging

</td>  
<td>

Combination of video (AVI) and images (JPG, TIFF)

</td>  
<td>

Video and images edited in Movie Maker

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

**Estimated data size**

</th>  
<th>

**Data sharing**

</th>  
<th>

**Data storage and archiving**

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

~1-2 terabytes per year will be generated by WP7.

</td>  
<td>

The generated data have been shared only with the team of

Monte Gates and the MAGNEURON project partners.

The MAGNEURON partners have used Dropbox for data sharing in WP7:

</td>  
<td>

The data generated in WP6 have been stored in the digital format, and in
physical copies in laboratory notebooks.

The data have been stored on the Keele University local servers and hard
drives. The scientific data have been stored during the project and will for
10 years thereafter. Place for after-project scientific data storage is to be
discussed.

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

~up to 1-2 gigabytes

</td>  
<td>

Video/images/description of some protocols (e.g. the tissue slicing protocol,
preparation of VM cells and imaging) will be made openly available.

</td>  
<td>

Video and images will be stored on Keele University servers and the final
version will be made openly available.

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

A video outlining some of the protocols developed in WP7 will be made openly
available. Furthermore, any accepted manuscripts arising from work in WP7 will
be made open access.

In more details, the following datasets have been identified in WP7  
  
<table>  
<tr>  
<th>

**Data Ref**

</th>  
<th>

**Name**

</th>  
<th>

**Type and size**

**(Standards / metadata)**

</th>  
<th>

**Sharing**

</th>  
<th>

**Storage / Archiving**

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

WP Task 7.1

Optimisation of slice culture model of

Parkinson’s disease

</td>  
<td>

Optimisation of slice cutting angle

</td>  
<td>

PPTX, JPG,

TIFF, ND2, <3GB

</td>  
<td>

Processed summary

shared with Magneuron consortia,

disseminated at conference

</td>  
<td>

Digital

(University hard

drives),

physical

(poster)

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

WP Task 7.1

Optimisation of slice culture model of

Parkinson’s disease

</td>  
<td>

Cell death analysis in slices

</td>  
<td>

PPTX, JPG,

TIFF, ND2, XLS

Excel spreadsheets,

PZF GraphPad

Prism spreadsheet,

<15GB

</td>  
<td>

Processed summary

shared with Magneuron consortia,

disseminated at conference

</td>  
<td>

Digital

(University hard

drives),

physical

(poster)

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

**Data Ref**

</th>  
<th>

**Name**

</th>  
<th>

**Type and size**

**(Standards / metadata)**

</th>  
<th>

**Sharing**

</th>  
<th>

**Storage / Archiving**

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

WP Task 7.1

Optimisation of slice culture model of

Parkinson’s disease

</td>  
<td>

Retrograde labelling with FluoroGold and

FluoroRuby

</td>  
<td>

PPTX, JPG, TIF,

ND2,

<36GB

</td>  
<td>

Processed summary

shared with

Magneuron consortia

</td>  
<td>

Digital

(University hard drives)

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

WP Task 7.1

Optimisation of slice culture model of

Parkinson’s disease

</td>  
<td>

Degeneration of TH in slices

</td>  
<td>

PPTX, JPG, TIF,

ND2,

<10GB

</td>  
<td>

Processed summary

shared with Magneuron consortia,

disseminated at conference

</td>  
<td>

Digital

(University hard

drives),

physical

(poster)

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

WP Task 7.1

Optimisation of slice culture model of

Parkinson’s disease

</td>  
<td>

Removal of cortex to improve slice health

</td>  
<td>

PPTX, JPG, TIF,

ND2, XLS Excel spreadsheets,

PZF GraphPad

Prism spreadsheet,

<3GB

</td>  
<td>

Processed summary

shared with

Magneuron consortia

</td>  
<td>

Digital

(University hard drives)

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

WP Task 7.1

Optimisation of slice culture model of

Parkinson’s disease

</td>  
<td>

Optimisation of slices derived from older

rats

</td>  
<td>

PPTX, JPG, TIF,

ND2,

<15GB

</td>  
<td>

Processed summary

shared with Magneuron consortia,

disseminated at conference

</td>  
<td>

Digital

(University hard

drives),

physical

(poster)

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

WP Task 7.1

Optimisation of slice culture model of

Parkinson’s disease

</td>  
<td>

Transplantation of embryonic VM tissue

into slices

</td>  
<td>

PPTX, JPG,

TIFF, ND2, XLS

Excel spreadsheets,

PZF GraphPad

Prism files,

<15GB

</td>  
<td>

Processed summary

shared with Magneuron consortia,

disseminated at conference

</td>  
<td>

Digital

(University hard

drives),

physical

(poster)

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

**Data Ref**

</th>  
<th>

**Name**

</th>  
<th>

**Type and size**

**(Standards / metadata)**

</th>  
<th>

**Sharing**

</th>  
<th>

**Storage / Archiving**

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

WP Task 7.1

Optimisation of slice culture model of

Parkinson’s disease

</td>  
<td>

Functional connections between

transplanted tissue and slices

</td>  
<td>

PPTX, JPG, TIF,

ND2,

<20GB

</td>  
<td>

Processed summary

shared with Magneuron consortia,

disseminated at conference

</td>  
<td>

Digital

(University hard

drives),

physical

(poster)

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

WP Task 7.2/7.3

Transplantation of

MNP-loaded dopaminergic

neurons/precursors to slice cultures

</td>  
<td>

Microinjection of SH-

SY5Y cells into slices

</td>  
<td>

PPTX, JPG TIF,

ND2,

<6GB

</td>  
<td>

Processed summary

shared with

Magneuron consortia

</td>  
<td>

Digital

(University hard drives)

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

WP Task 7.2/7.3

Transplantation of

MNP-loaded dopaminergic

neurons/precursors to slice cultures

</td>  
<td>

Injection of MNPs directly into slices

</td>  
<td>

PPTX, JPG TIF,

ND2,

<32GB

</td>  
<td>

Processed summary

shared with

Magneuron consortia

</td>  
<td>

Digital

(University hard drives)

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

WP Task7.2/7.3

Transplantation of

MNP-loaded dopaminergic

neurons/precursors to slice cultures

</td>  
<td>

Optimisation of protocol for getting

MNPs into cell line and primary cells

</td>  
<td>

PPTX, JPG TIF,

ND2,

<1GB

</td>  
<td>

Processed summary

shared with

Magneuron consortia

</td>  
<td>

Digital

(University hard drives)

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

WP Task 7.2/7.3

Transplantation of

MNP-loaded dopaminergic

neurons/precursors to slice cultures

</td>  
<td>

Injection of MNPloaded cells into slices (in

collaboration with

WP5)

</td>  
<td>

PPTX, JPG TIF,

ND2, XLS Excel spreadsheets,

PZF GraphPad

Prism files,

<1GB

</td>  
<td>

Processed summary

shared with

Magneuron consortia

</td>  
<td>

Digital

(University hard drives)

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

WP Task 7.2/7.3

Transplantation of

MNP-loaded dopaminergic

neurons/precursors to slice cultures

</td>  
<td>

Establishment of E12

VM dopaminergic precursors

(neurospheres)

</td>  
<td>

PPTX, JPG TIF,

ND2,

<1GB

</td>  
<td>

Processed summary

shared with

Magneuron consortia

</td>  
<td>

Digital

(University hard drives)

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

**Data Ref**

</th>  
<th>

**Name**

</th>  
<th>

**Type and size**

**(Standards / metadata)**

</th>  
<th>

**Sharing**

</th>  
<th>

**Storage / Archiving**

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

WP Task 7.2/7.3

Transplantation of

MNP-loaded dopaminergic

neurons/precursors to slice cultures

</td>  
<td>

Images for quantification of TH

and Tuj1 outgrowth in slices and SN/VTA

explants grafted into

slices

</td>  
<td>

PPTX, JPG TIF,

ND2,

<1GB

</td>  
<td>

Processed summary

shared with

Magneuron consortia

</td>  
<td>

Digital

(University hard drives)

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

WP Task 7.2/7.3

Transplantation of

MNP-loaded dopaminergic

neurons/precursors to slice cultures

</td>  
<td>

Incubation of nanorods with cells to test compatibility

</td>  
<td>

PPTX, JPG TIF,

ND2,

<1GB

</td>  
<td>

Processed summary

shared with

Magneuron consortia

</td>  
<td>

Digital

(University hard drives)

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

WP Task 7.2/7.3

Transplantation of

MNP-loaded dopaminergic

neurons/precursors to slice cultures

</td>  
<td>

Comparison of use of

E11 and E13 rat embryos to generate neurospheres

</td>  
<td>

PPTX, JPG TIF,

ND2,

<1GB

</td>  
<td>

Processed summary

shared with

Magneuron consortia

</td>  
<td>

Digital

(University hard drives)

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

WP Task 7.2/7.3

Transplantation of

MNP-loaded dopaminergic

neurons/precursors to slice cultures

</td>  
<td>

Comparison of use of cell penetrating

peptide-linked MNPs and endosomal

MNPs in cells

</td>  
<td>

PPTX, JPG TIF,

ND2,

<1GB

</td>  
<td>

Processed summary

shared with

Magneuron consortia

</td>  
<td>

Digital

(University hard drives)

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

WP Task 7.2/7.3

Transplantation of

MNP-loaded dopaminergic

neurons/precursors to slice cultures

</td>  
<td>

Comparison of

effects/efficacy of different

concentrations of

endosomal MNPs on

SH-SY5Y and primary cells

</td>  
<td>

PPTX, JPG TIF,

ND2,

<1GB

</td>  
<td>

Processed summary

shared with

Magneuron consortia

</td>  
<td>

Digital

(University hard drives)

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

WP Task 7.2/7.3

Transplantation of

MNP-loaded dopaminergic

neurons/precursors to slice cultures

</td>  
<td>

Testing the effects of the magnet

microarray on MNPs

</td>  
<td>

PPTX, JPG TIF,

ND2, AVI

<1GB

</td>  
<td>

Processed summary

shared with

Magneuron consortia

</td>  
<td>

Digital

(University hard drives)

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

**Data Ref**

</th>  
<th>

**Name**

</th>  
<th>

**Type and size**

**(Standards / metadata)**

</th>  
<th>

**Sharing**

</th>  
<th>

**Storage / Archiving**

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

WP Task 7.2/7.3

Transplantation of

MNP-loaded dopaminergic

neurons/precursors to slice cultures

</td>  
<td>

Use of GIRK2 and

Calbindin to differentiate between

SN and VTA dopaminergic neurons

</td>  
<td>

PPTX, JPG TIF,

ND2,

<1GB

</td>  
<td>

Processed summary

shared with

Magneuron consortia

</td>  
<td>

Digital

(University hard drives)

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

WP Task 7.2/7.3

Transplantation of

MNP-loaded dopaminergic

neurons/precursors to slice cultures

</td>  
<td>

Use of E17 cortical neurons to test uptake of MNPs

</td>  
<td>

PPTX, JPG TIF,

ND2,

<1GB

</td>  
<td>

Processed summary

shared with

Magneuron consortia

</td>  
<td>

Digital

(University hard drives)

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

WP Task 7.2/7.3

Transplantation of

MNP-loaded dopaminergic

neurons/precursors to slice cultures

</td>  
<td>

Assessing the effects of size and position

of magnets on MNPloaded cells

</td>  
<td>

PPTX, JPG TIF,

ND2,

<2GB

</td>  
<td>

Processed summary

shared with

Magneuron consortia

</td>  
<td>

Digital

(University hard drives)

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

WP Task 7.2/7.3

Transplantation of

MNP-loaded dopaminergic

neurons/precursors to slice cultures

</td>  
<td>

Injection of neurospheres into striatum of slices

</td>  
<td>

PPTX, JPG TIF,

ND2,

<1GB

</td>  
<td>

Processed summary

shared with

Magneuron consortia

</td>  
<td>

Digital

(University hard drives)

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

WP Task 7.2/7.3

Transplantation of

MNP-loaded dopaminergic

neurons/precursors to slice cultures

</td>  
<td>

tempMode

experiments using

neurospheres in

slices (in

collaboration with

WP5)

</td>  
<td>

PPTX, JPG TIF,

ND2,

<20GB

</td>  
<td>

Processed summary

shared with

Magneuron consortia

</td>  
<td>

Digital

(University hard drives)

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

WP Task 7.2/7.3

Transplantation of

MNP-loaded dopaminergic

neurons/precursors to slice cultures

</td>  
<td>

Optimisation of D1 and D2 receptor antibody staining

</td>  
<td>

PPTX, JPG TIF,

ND2,

<1GB

</td>  
<td>

Processed summary

shared with

Magneuron consortia

</td>  
<td>

Digital

(University hard drives)

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

**Data Ref**

</td>  
<td>

**Name**

</td>  
<td>

**Type and size**

**(Standards / metadata)**

</td>  
<td>

**Sharing**

</td>  
<td>

**Storage / Archiving**

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

WP Task 7.2/7.3

Transplantation of

MNP-loaded dopaminergic

neurons/precursors to slice cultures

</td>  
<td>

Optimisation of growth of primary

cells in microfluidic devices

</td>  
<td>

PPTX, JPG TIF, ND2, PZF

GraphPad Prism

files

<30GB

</td>  
<td>

Processed summary

shared with

Magneuron consortia

</td>  
<td>

Digital

(University hard drives)

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

WP Task 7.2/7.3

Transplantation of

MNP-loaded dopaminergic

neurons/precursors to slice cultures

</td>  
<td>

Improving the loading of MNPs in free-

floating primary cells

(for injection into slice)

</td>  
<td>

PPTX, JPG TIF,

ND2,

<1GB

</td>  
<td>

Processed summary

shared with

Magneuron consortia

</td>  
<td>

Digital

(University hard drives)

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

WP Task 7.2/7.3

Transplantation of

MNP-loaded dopaminergic

neurons/precursors to slice cultures

</td>  
<td>

Loading of primary

VM cells into SN area of the slice

</td>  
<td>

PPTX, JPG TIF,

ND2,

<1GB

</td>  
<td>

Processed summary

shared with

Magneuron consortia

</td>  
<td>

Digital

(University hard drives)

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

WP Task 7.2/7.3

Transplantation of

MNP-loaded dopaminergic

neurons/precursors to slice cultures

</td>  
<td>

spaceMode

experiments using

the magnetic device

(made by Koceila at

IC) to promote outgrowth of

transplanted MNP-

loaded primary VM

cells

</td>  
<td>

PPTX, JPG TIF, ND2, PZF

GraphPad Prism

files

<20GB

</td>  
<td>

Processed summary

shared with

Magneuron consortia

</td>  
<td>

Digital

(University hard drives)

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

**3\. Conclusion**

Over the last reporting period, a great effort was made to open our Data to
the general public. We decided to share them mostly through the open
repository Zenodo (https://zenodo.org/).

This repository can be linked to the European Commission Funded Research
(OpenAIRE). A DOI (Digital Object Identifier) is attributed to each dataset.
See for example  _https://zenodo.org/communities/locco_ for the IC partner. We
will continue this effort over the coming months to ensure that all results
and products of the Magneuron project are being shared on an open repository.
Regarding the archiving of the numerous data that have been produced, diverse
solutions have been proposed to ensure backups and accessibility (NAS, zenodo,
dropbox, hard drives).