Published October 31, 2024 | Version v1
Dataset Restricted

SYSTACT CyTOF dataset associated with Multiomics approaches disclose very-early molecular and cellular switches during insect-venom allergen-specific immunotherapy: an observational study

  • 1. ROR icon Luxembourg Institute of Health

Description

This dataset contains all the raw mass cytometry (CyTOF) fcs files associated with Pogorelov et al. 'Multiomics approaches disclose very-early molecular and cellular switches during insect-venom allergen-specific immunotherapy: an observational study', Nature Communications, 2024, in Press. The dataset contains all the raw fcs files generated by CyTOF analysis of 199 time-series samples including ~200 million of deeply characterized immune cells, either from patients with insect-venom allergy or patients with pollen allergy following allergen-specific immunotherapy (AIT) or from healthy controls (HC), who did not receive any AIT or other immunotherapy. As specified in the manuscript, we sampled different individuals up to seven times (0h, 8h, 24h, Day 7, Week 2, Week 6 and Week 12) over a three-month period. All the samples from insect-venom allergy patients are stored in the zipper folder called "Venom" and all the samples from pollen allergy patients are in the zipper folder called "Pollen" while all the samples from HC are placed in the zipper folder called "Control". We also provide the following annotation files (metadata) to help the readers to better understand, validate and re-analyze our immunological dataset.

1, In addition to the Supplementary Tables in our manuscript, we also attached one Word table file mapping the 36 specific metal isotypes and the specific Ab target markers.

2, The Excel file with the list of 199 samples, showing the correct group and time point information (of note, the manually input sample information in the file name might be wrong for some samples). The correct time point information is in the column "Timepoint Detail" and "Timepoint Final".

Associated with these raw fcs files, our processed results of all the CyTOF data are deposited in another webpage. Our large-scale interactive interlinked immunological Data resource (i3Dare) allows investigators to more effectively explore or reuse our immunological datasets of each immune subset from each participant at each time point (please refer to https://public.tableau.com/app/profile/lihpublicdata/viz/i3Dare_SYSTACT_Database/SYSTACTHome). OF note, to further protect privacy, the pseudoIDs within groups in i3Dare were re-labelled again. 

Please read the accompanying information/metadata files, our main manuscript and Supplementary Information, our processed data on the i3Dare webpage and the published Source Data together with the raw fcs files in order to reproduce our published results.

Files

Restricted

The record is publicly accessible, but files are restricted to users with access.

Request access

If you would like to request access to these files, please fill out the form below.

You need to satisfy these conditions in order for this request to be accepted:

If you are an academic and would like to request access to these files, please fill out the application form below with your institutional email address. IF YOU ARE A COMMERCIAL ENTITY WISHING TO ACCESS THE DATASET, PLEASE CONTACT BDO@LIH.LU OUTSIDE OF THE ZENODO REPOSITORY.

You need to satisfy these conditions AND the conditions specified in the Data Use Agreement below in order for this request to be accepted:

This dataset is available through this repository for ACADEMIC NON-COMMERCIAL USE ONLY.

If you are an academic looking to access the dataset please contact Luxembourg Institute of Health. You must submit an application detailing your academic status and providing an overview of your intended use of the dataset as part of the justification section of your application request. This will be reviewed by the SYSTACT data committee of the Luxembourg Institute of Health and access will be granted, to bonefide academic, non-commercial institutions. 

The dataset can only be used by the applicants named on the application and for the intended use specified in the application. COPY OR DISTRIBUTION OF THIS DATASET IS STRICTLY PROHIBITED.

 

Data Use Agreement

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Date of Publication: 31/10/2024

Date of Current Version: 1.0

Digital Object Identifier (DOI): https://doi.org/10.5281/zenodo.14001917

Dataset Title: SYSTACT CyTOF dataset associated with Multiomics approaches disclose very-early molecular and cellular switches during insect-venom allergen-specific immunotherapy: an observational study

Corresponding author: Feng Hefeng (feng.hefeng@lih.lu) or Markus Ollert (Markus.Ollert@lih.lu)

1. Introduction

The SYSTACT CyTOF dataset contains all the raw fcs file generated by CyTOF analysis of 199 time-series samples either from patients with insect-venom allergy or pollen allergy following allergen-specific immunotherapy (AIT) or from healthy controls (HC), who did not receive any AIT or other immunotherapy. As specified in the manuscript, we sampled different individuals up to seven times over a three-month period. By accessing the SYSTACT CyTOF dataset, users agree to comply with the terms outlined in this Data Use Agreement.

2. Prohibited Use of the SYSTACT CyTOF data

a. Re-identification and Participant Privacy

  • Users are strictly prohibited from attempting to re-identify participants through the SYSTACT CyTOF data. This includes, but is not limited to, combining the SYSTACT CyTOF data with other datasets or external information that could potentially be used to identify individual participants.
  • Users must ensure that the SYSTACT CyTOF data is used solely for the purposes outlined in this agreement and not for any activities that could compromise the anonymity or privacy of the participants.

b. Data Security and Handling

  • Users must implement appropriate security measures to protect the SYSTACT CyTOF data from unauthorized access, disclosure, alteration, or destruction.
  • The SYSTACT CyTOF data should be stored securely, and access should be limited to authorized personnel involved in the approved research activities.

c. Prohibited Derivative Works

  • Users are prohibited from creating or using derivative works derived from the SYSTACT CyTOF data that could potentially reveal identifiable information about participants.
  • This includes transforming or analyzing the SYSTACT CyTOF data in ways that might lead to the extraction of sensitive information or patterns unique to individual participants.

d. No Distribution or Sharing

  • Users must not distribute, share, or otherwise make the SYSTACT CyTOF data available to third parties unless explicitly authorized under this agreement.
  • Any sharing of data within a research team must ensure that all team members are aware of and comply with the terms of this Data Use Agreement.

e. Ethical Use of Data

  • Users must adhere to all applicable laws, regulations, and ethical guidelines governing the use of the SYSTACT CyTOF data in research.
  • Any use of the SYSTACT CyTOF data outside the scope of this agreement requires prior written consent from the SYSTACT CyTOF administrative team.

3. Privacy and Confidentiality

Non-Identification

  • Users will not use the SYSTACT CyTOF dataset, either alone or in combination with other data, to identify or contact individuals who participated in the data collection.
    If a user inadvertently obtains identifiable information or identifies a participant, they must promptly notify the SYSTACT CyTOF administrators and follow their written instructions, which may include returning or destroying the identifiable information.

4. Data Access and Disclosure

a. Permitted Use

The SYSTACT CyTOF dataset is to be used solely for research purposes as outlined in the study description. Any other use is prohibited unless explicitly authorized.

b. Prohibited Use

  • Users will not use or further disclose the SYSTACT CyTOF dataset beyond the permissions granted in this agreement.
  • Users will not create or disseminate derivative works or data that could be used to reconstruct identifiable information about participants.

c. Reporting Unauthorized Use

   Users must report any unauthorized use or disclosure of the SYSTACT CyTOF dataset promptly. The report should include:
    1. The nature of the unauthorized use or disclosure.
    2. The specific information that was used or disclosed.
    3. The identities of the individuals or entities responsible.
    4. Corrective actions taken to mitigate the impact.

d. Mitigation Efforts

Users must take all reasonable actions to mitigate any detrimental effects resulting from unauthorized use or disclosure.

5. Acknowledgment and Citation

a. Acknowledgment in Publications and Presentations

When publicly presenting results, algorithms, or findings derived from the SYSTACT CyTOF dataset, users must acknowledge the use of the SYSTACT CyTOF data as follows:
    
in the Acknowledgments section, please write:
    
    "Data were provided [in part] by the SYSTACT CyTOF dataset.”

b. In the References, the citation requirements:

Users must cite our original work that generated the SYSTACT CyTOF dataset appropriately in all publications and presentations. Please use the following citation format:
    
Reference Citation:

Dimitrii Pogorelov, Sebastian Felix Nepomuk Bode, Xin He, Javier Ramiro-Garcia, Fanny Hedin, Wim Ammerlaan, Maria Konstantinou, Christophe M. Capelle, Ni Zeng, Aurélie Poli, Olivia Domingues, Guillem Montamat, Oliver Hunewald, Séverine Ciré, Alexandre Baron, Joseph Longworth, Agnieszka Demczuk, Murilo Luiz Bazon, Ingrid Casper, Ludger Klimek, Lorie Neuberger-Castillo, Dominique Revets, Lea Guyonnet, Sylvie Delhalle, Jacques Zimmer, Vladimir Benes, Françoise Codreanu-Morel, Christiane Lehners-Weber, Ilse Weets, Pinar Alper, Dirk Brenner, Jan Gutermuth, Coralie Guerin, Martine Morisset, François Hentges, Reinhard Schneider, Mohamed H. Shamji, Fay Betsou, Paul  Wilmes, Enrico Glaab, Antonio Cosma, Jorge Goncalves, Feng Q. Hefeng, Markus Ollert, Multiomics approaches disclose very-early molecular and cellular switches during insect-venom allergen-specific immunotherapy: observational study, Nature Communications, 2024, In Press.

Of note: Please update and cite the above reference accordingly, after our work (Pogorelov et al, 2024) is officially published online in Nature Communications. Upon publication, the status and citation information of the corresponding preprint (https://www.researchsquare.com/article/rs-3917969/v1) will be updated.

6. User Obligations

a. Reporting Usage

Users agree to provide the SYSTACT CyTOF administrators with information regarding their use of the SYSTACT CyTOF dataset upon request. This includes details about the nature of the research, methodologies employed, and any publications resulting from the dataset.

b. Compliance

Failure to comply with the terms outlined in this Data Use Agreement may result in the termination of the user's access rights to the SYSTACT CyTOF dataset.

7. Termination

Violation of any terms of this agreement may result in the immediate termination of the user's rights to access and use the SYSTACT CyTOF dataset. In the event of termination, the user must destroy any copies of the dataset in their possession.

8. Agreement

By submitting a request to access the SYSTACT CyTOF dataset, you agree to abide by the terms and conditions of this Data Use Agreement.

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Contact Information:

For any questions or concerns regarding this Data Use Agreement, please contact:

Feng Hefeng (feng.hefeng@lih.lu) or Markus Ollert (Markus.Ollert@lih.lu)

Effective Date:

This agreement is effective as of 31/10/2024

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