About file location

As the EGA is co-managed by the EMBL-EBI and CRG, files could be located in the UK and/or Spain, as indicated by their respective flags.

Alternatively, files could be located in one of the international Federated EGA nodes, as indicated next to the node's flag.
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SUM-seq data for Primary T-cells differentiated to helper subtypes

Briefly, naive CD4+ T cells were isolated from PBMCs obtained from buffy coats from three healthy human donors, and differentiated into Th0, iTreg, Th2, Th1, Th17, and IFN-β-activated subsets. This allowed us to study the differentiation of naive CD4+ T cells into distinct helper subsets under the influence of a specific cytokine environment. Following 5 days of differentiation, T cells were left unstimulated or re-stimulated with phorbol 12-myristate 13-acetate (PMA) and ionomycin to assess their functional responses. Thus, this SUM-seq experiment consisted of 36 multiplexed conditions (3 donors x 6 stimulations x with/without re-stimulation). Single-cell chromatin accessibility and gene expression data is provided as demultiplexed fastq files.

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Data Access Agreement for Controlled Access of T-cell data from “Scalable ultra-high-throughput multiplexed single-cell chromatin and RNA profiling reveals gene regulatory dynamics during stimulation time courses and CRISPR perturbation screens” Data

Data Access Agreement for Controlled Access of T-cell data from “Scalable ultra-high-throughput multiplexed single-cell chromatin and RNA profiling reveals gene regulatory dynamics during stimulation time courses and CRISPR perturbation screens” Data Section I: Contact and Project Information A. Data Recipient (including contact details) Please ensure that a full postal address and a valid Institutional email address are included Name: Institution’s Legal Name: Institutional Postal Address: Institutional E-mail Address: Website of the Institution: B. Authorised Representative of the Data Recipient Name: Position: Affiliation: Institutional Postal Address: Institutional E-mail Address: C. Data Controller Institution’s Legal Name: European Molecular Biology Laboratory (EMBL) Institutional Postal Address: Meyerhofstraße 1, 69117 Heidelberg Institutional E-mail Address: info@embl.de Website of the Institution: https://www.embl.org/about/info/mmpu/ D. Authorised Representative of the Data Controller Name: Matti Tiirakari Position: Chief Operating Officer Affiliation: European Molecular Biology Laboratory (EMBL) Institutional Postal Address: Meyerhofstraße 1, 69117 Heidelberg Institutional E-mail Address: coo-office@embl.org E. Title of the Proposed Research Project F. Research Project (Scientific Abstract): Please provide a clear description of the Project, its stakeholders, its main question and its relevance to the research domain addressed, its specific aims, and duration. Note that any use of the Data, if approved, must fall under the framework of the described Project (300 words max): G. Research Credentials Please provide a list of three Publications, relevant to the Project description, of which the Data Recipient is author or co-author, and, also, attach their (Data Recipient’s) short CV. If the Data Recipient has not authored or co-authored three relevant Publications, please describe their relevant expertise or experience in no more than 150 words; also, notify how the research project will be carried out (e.g. available funding, infrastructure and so on). H. Authorised Personnel Please provide a list of all the individuals at the Data Recipient that will have access to the Data. Name e-mail Data Access/Transfer details Access method: The Data Recipient will access the Data through the European Genome Phenome Archive (refer to link above). Format: The data will be provided in FASTQ format, and accessed using EGA download client (https://github.com/EGA-archive/ega-download-client). Frequency: One off transfer.   Section II: Data Access Agreement (DAA) Definitions Authorised Personnel: The individual(s) at the Data Recipient requesting Access to the Data that are listed in Part H of Section I. Data: Refers to the controlled access data (the Data). Under this Agreement, the Data is pseudonymised. Data Access/Transfer: Refers to an Institution’s right to request access to the Data and retrieve them from the Data Controller upon approval of this DAA by the corresponding DAC within the Data Controller. Data Controller: Refers to the European Molecular Biology Laboratory, which is responsible for the generation of the Data and its pseudonymisation. Data Handling: Refers to an Institution’s ability to analyse and manipulate the Data within its own computer network. Data Protection Legislation: Refers, in respect of EMBL, to its Internal Policy No. 68 on General Data Protection, while, in respect of the Data Recipient to Regulation (EU) 2016/679 of the European Parliament and of the Council (GDPR) and/or any other applicable national data protection legislation. Data Recipient (‘You’): Refers to the Institution who requests Access to the Data through this Agreement. Data Subject: Refers to any individual who is the source of any Data covered by this Agreement. Publications: Refers, without limitation, to any and all articles published in print journals, electronic journals, reviews, books, posters, and other written and verbal presentations of Research that have been accepted by peer review. Research Project: The Project for which You have requested Access to the Data. Terms and Conditions In signing this Agreement: 1. You, the Data Recipient, agree to only use the Data for the Purpose of the Project. 2. You agree to preserve, at all times, the confidentiality of information and Data pertaining to Data Subjects. You undertake not to use or attempt to use the Data to compromise or otherwise infringe the confidentiality of information on Data Subjects and their right to privacy. 3. You agree that you will not use the Data, either alone or in concert with any other information, to make any effort to identify or contact the Data Subjects. Should You inadvertently receive any non-pseudonymised, identifiable information or otherwise identify a Data Subject, You shall promptly notify the Data Controller and follow any Data Controller’s reasonable written instructions, which may include return or destruction of the identifiable information. 4. You and Your Authorised Personnel agree to take into consideration any known usage restrictions (if any), stemming from consent, i.e. the appropriate lawful basis for processing the Data, as well as any usage restrictions stemming from any applicable internal policies of your Institution. You agree that in handling this Data You will follow an up-to-date information technology (IT) policy that must include, at a minimum, the following items: a. Logging and auditing of Access to the Data and to the computer network; b. Password protection to computer network and/or strong data encryption; c. Virus and malware protection to computers on the computer network; d. Secure backup procedure; The Data Controller reserves the right to request appropriate information or documentation in relation to Your compliance with this clause. 5. You acknowledge that Access to the Data is granted for the duration of the Project described in Section I, as well as any new Project under the same research field or area. Any use of the Data for a Project of another research field or area will need to be approved under a new Agreement. 6. You recognize that nothing in this Agreement shall operate to transfer to You any intellectual property rights to the Data. 7. You agree not to make intellectual property claims on the Data and not to use intellectual property protection in ways that would prevent or block access to, or use of, any element of the Data. 8. You can elect to perform further Research that would add intellectual and resource capital to the Data, and decide to obtain intellectual property rights on these downstream discoveries. In this case, You agree to implement licensing policies that will not obstruct further research. 9. You agree that the Data Controller 1) provides the data as is and makes no warranty, neither express nor implied, and assumes no legal responsibility for the accuracy, comprehensiveness, merchantability, or fitness for any particular purpose of the Data or that the use of the Data will not infringe any patent, copyright, trademark or other proprietary rights of third parties; 2) to the extent permitted by law, assumes no liability for any indirect, consequential, or incidental damages or losses arising from the acceptance, use, storage, disclosure or disposal of the Data; and 3) assumes no responsibility for Your further analysis or interpretation of the Data. 10. You agree to hold the Data Controller harmless and to defend and indemnify the Data Controller against all liabilities, demands, damages, expenses, and losses caused by You and/or Your use of the Data, except to the extent that such damage or liability is due to gross negligence or wilful misconduct of the Data Controller. 11. You assume all liability for damages that You may suffer arising from Your acceptance, use, handling, storage or disposal of the Data, and (ii) Your use of any results generated through the use of the Data, except to the extent such damages result directly from gross negligence or wilful misconduct of the Data Controller. 12. You agree to a moratorium on publishing global analyses of the dataset until the Data Controller has published its own global analysis or until twelve (12) months have passed from the time the Data were deposited by the Data Controller, whichever occurs first. You acknowledge that prompt publication or public disclosure of the results of the Research Project is encouraged. You also agree that by publishing Your analyses of the Data, you will not disclose any results generated from the Data. 13. You agree to acknowledge the contribution of the Data Controller in all oral and written presentations, disclosures, and Publications resulting from all analyses of the Data. 14. You agree to use the Data in Your Institution. Any Authorised Personnel shall work under Your direct supervision. You agree to distribute a copy of this Agreement to the Authorised Personnel. 15. You may not transfer the Data or any information included in the Data to anyone unless specifically designated in the Research Project, or by prior specific written authorisation of the Data Controller responsible for the generation of the original Data. 16. You may not transfer the Data itself to anyone outside Your Institution, unless the Data Controller has approved such transfer and its terms in writing. 17. Should You wish to share the Data with an external collaborator, the external collaborator must complete a separate Data Access Agreement. 18. You shall ensure that everyone who has Access to the Data, namely You and Your Authorised Personnel, will be listed out, and are made aware and be bound by the terms of this Agreement. You remain solely and fully responsible for Your Authorised Personnel’s non-compliance with the provision of this Agreement and/or applicable laws. 19. You must notify the Data Controller promptly and in any case within 24 hours of becoming aware of any accidental or unlawful and/or unauthorised disclosure of, or access to the Data. You are also responsible for complying with any obligations relating to data breaches under the applicable Data Protection Legislation to You. 20. In case of a ‘non-accidental or non-minor’ breach of this Agreement by You, You will further be required to destroy any Data held. 21. You accept that this Agreement will terminate immediately upon ‘any’ material breach by You, or upon the expiry of its term, as defined in Clause 6. 22. In the event of any dispute arising between the Parties concerning this Agreement, its enforceability or the interpretation thereof, the Parties shall endeavour to settle any such dispute amicably. If the Parties are unable to reach an agreement, through good faith negotiations within a reasonable period either Party shall be entitled to refer the dispute to arbitration in accordance with the following clause 23. If the Parties are unable to reach an agreement, through good faith negotiations within a reasonable period the dispute shall be referred to and finally determined by arbitration in accordance with the WIPO Expedited Arbitration Rules, without recourse to the ordinary courts of law, including for interim and/or injunctive relief. The award of the arbitration shall be final and binding upon the Parties concerned. The legal seat of the arbitration shall be Heidelberg (Germany). The language of the arbitration shall be English. 24. The provisions of this Agreement shall be interpreted in accordance with their true meaning and effect. Without prejudice to the Data Controller’s status as an intergovernmental institution, reference shall be made to German substantive law where: (a) a matter is not specifically covered by the agreement; or (b) a provision is ambiguous or unclear. Such reference shall be made exclusively for the matter or provision(s) concerned, and shall in no event apply to the other provisions of the Agreement. The rules of private international law and the United Nations Convention on Contracts for the International Sale of Goods shall not apply. 25. Nothing in this Agreement nor any document or activity under or in relation thereto shall be deemed or interpreted as a waiver, express or implied, of any privileges or immunities accorded to the Data Controller by its constituent documents or international law, or as the acceptance by the Data Controller of the jurisdiction of (i) the courts of any country, including in case of injunctive relief sought, or (ii) any national regulatory or supervisory authority. All references to specific regulations, including, but not limited to, national laws, policies, ordinances, statutes, guidelines, ethics rules and regulations, codes of conduct and other rules and regulations, should only be understood as a reference to these regulations, with regard to the Data Controller, to the extent that these regulations also apply to the Data Controller as an intergovernmental institution and, in cases where the Data Controller has issued its own rules, as a reference to those rules instead. Agreement I have read, understood and agree to abide by the terms and conditions stipulated in this Data Access Agreement. Authorised Representative of the Data Recipient: Name: Title and position (if applicable): Affiliation: Signature: _____________________________________Date: _____________________ Read and acknowledged by: Name: Title: Signature: _____________________________________Date: _____________________ Authorised Representative of the Data Controller: Name: Michael Milne Title and position: Chief Operating Officer European Molecular Biology Laboratory (EMBL) Signature: _____________________________________Date: _____________________

Studies are experimental investigations of a particular phenomenon, e.g., case-control studies on a particular trait or cancer research projects reporting matching cancer normal genomes from patients.

Study ID Study Title Study Type
EGAS50000000818 Gene Regulation Study
  • The sequencing platform was corrected.
  • Dataset Released

This table displays only public information pertaining to the files in the dataset. If you wish to access this dataset, please submit a request. If you already have access to these data files, please consult the download documentation.

ID File Type Size Quality Report
Located in
i
EGAF50000306012 fastq.gz 1.1 GB
EGAF50000306013 fastq.gz 3.3 GB
EGAF50000306014 fastq.gz 1.9 GB
EGAF50000306020 fastq.gz 490.2 MB
EGAF50000306021 fastq.gz 1.7 GB
EGAF50000306022 fastq.gz 748.6 MB
EGAF50000306023 fastq.gz 921.7 MB
EGAF50000306024 fastq.gz 1.4 GB
EGAF50000306028 fastq.gz 1.2 GB
EGAF50000306029 fastq.gz 528.8 MB
EGAF50000306030 fastq.gz 594.0 MB
EGAF50000306031 fastq.gz 327.1 MB
EGAF50000306032 fastq.gz 7.3 GB
EGAF50000306033 fastq.gz 2.4 GB
EGAF50000306034 fastq.gz 5.0 GB
EGAF50000306114 fastq.gz 1.1 GB
EGAF50000306122 fastq.gz 2.5 GB
EGAF50000306123 fastq.gz 4.9 GB
EGAF50000306124 fastq.gz 767.9 MB
EGAF50000306125 fastq.gz 1.9 GB
EGAF50000306126 fastq.gz 2.2 GB
EGAF50000306127 fastq.gz 2.3 GB
EGAF50000306128 fastq.gz 1.3 GB
EGAF50000306129 fastq.gz 4.3 GB
EGAF50000306130 fastq.gz 4.5 GB
EGAF50000306131 fastq.gz 587.1 MB
EGAF50000306132 fastq.gz 1.8 GB
EGAF50000306133 fastq.gz 2.3 GB
EGAF50000306134 fastq.gz 1.4 GB
EGAF50000306137 fastq.gz 1.3 GB
EGAF50000306138 fastq.gz 4.0 GB
EGAF50000306145 fastq.gz 1.3 GB
EGAF50000306146 fastq.gz 1.9 GB
EGAF50000306147 fastq.gz 830.0 MB
EGAF50000306156 fastq.gz 2.0 GB
EGAF50000306157 fastq.gz 2.4 GB
EGAF50000306158 fastq.gz 1.0 GB
EGAF50000306159 fastq.gz 2.2 GB
EGAF50000306160 fastq.gz 2.5 GB
EGAF50000306161 fastq.gz 3.4 GB
EGAF50000306162 fastq.gz 2.0 GB
EGAF50000306163 fastq.gz 6.1 GB
EGAF50000306164 fastq.gz 6.2 GB
EGAF50000306165 fastq.gz 238.4 MB
EGAF50000306166 fastq.gz 2.1 GB
EGAF50000306167 fastq.gz 664.3 MB
EGAF50000306168 fastq.gz 590.5 MB
EGAF50000306169 fastq.gz 1.8 GB
EGAF50000306170 fastq.gz 1.7 GB
EGAF50000306171 fastq.gz 5.5 GB
EGAF50000306172 fastq.gz 1.2 GB
EGAF50000306173 fastq.gz 704.8 MB
EGAF50000306174 fastq.gz 2.2 GB
EGAF50000306175 fastq.gz 2.2 GB
EGAF50000306263 fastq.gz 3.7 GB
EGAF50000306264 fastq.gz 2.0 GB
EGAF50000306265 fastq.gz 371.0 MB
EGAF50000306266 fastq.gz 158.2 MB
EGAF50000306267 fastq.gz 507.9 MB
EGAF50000306268 fastq.gz 3.1 GB
EGAF50000306269 fastq.gz 1.3 GB
EGAF50000306270 fastq.gz 4.0 GB
EGAF50000306271 fastq.gz 6.5 GB
EGAF50000306272 fastq.gz 6.7 GB
EGAF50000306273 fastq.gz 1.0 GB
EGAF50000306274 fastq.gz 3.3 GB
EGAF50000306275 fastq.gz 1.1 GB
EGAF50000306276 fastq.gz 3.2 GB
EGAF50000306277 fastq.gz 5.9 GB
EGAF50000306278 fastq.gz 6.0 GB
EGAF50000306279 fastq.gz 181.1 MB
EGAF50000306280 fastq.gz 551.4 MB
EGAF50000306281 fastq.gz 567.3 MB
EGAF50000306282 fastq.gz 3.5 GB
EGAF50000306283 fastq.gz 1.8 GB
EGAF50000306284 fastq.gz 1.7 GB
EGAF50000306285 fastq.gz 1.7 GB
EGAF50000306286 fastq.gz 3.5 GB
EGAF50000306295 fastq.gz 1.1 GB
EGAF50000306296 fastq.gz 590.8 MB
EGAF50000306297 fastq.gz 939.2 MB
EGAF50000306298 fastq.gz 787.2 MB
EGAF50000306299 fastq.gz 857.6 MB
EGAF50000306300 fastq.gz 864.3 MB
EGAF50000306301 fastq.gz 1.4 GB
EGAF50000306302 fastq.gz 7.1 GB
EGAF50000306303 fastq.gz 791.7 MB
EGAF50000306304 fastq.gz 249.8 MB
EGAF50000306305 fastq.gz 774.6 MB
EGAF50000306306 fastq.gz 800.6 MB
EGAF50000306307 fastq.gz 3.0 GB
EGAF50000306308 fastq.gz 295.2 MB
EGAF50000306309 fastq.gz 907.4 MB
EGAF50000306310 fastq.gz 946.4 MB
EGAF50000306311 fastq.gz 1.4 GB
EGAF50000306312 fastq.gz 785.5 MB
EGAF50000306313 fastq.gz 2.5 GB
EGAF50000306349 fastq.gz 1.9 GB
EGAF50000306351 fastq.gz 1.0 GB
EGAF50000306352 fastq.gz 793.1 MB
EGAF50000306353 fastq.gz 1.1 GB
EGAF50000306354 fastq.gz 455.0 MB
EGAF50000306355 fastq.gz 988.3 MB
EGAF50000306357 fastq.gz 867.7 MB
EGAF50000306358 fastq.gz 3.7 GB
EGAF50000306359 fastq.gz 1.7 GB
EGAF50000306360 fastq.gz 2.5 GB
EGAF50000306362 fastq.gz 6.6 GB
EGAF50000306365 fastq.gz 1.3 GB
EGAF50000306366 fastq.gz 530.3 MB
EGAF50000306367 fastq.gz 277.4 MB
EGAF50000306369 fastq.gz 2.4 GB
EGAF50000306370 fastq.gz 1.0 GB
EGAF50000306371 fastq.gz 397.0 MB
EGAF50000306373 fastq.gz 822.5 MB
EGAF50000306374 fastq.gz 1.2 GB
EGAF50000306375 fastq.gz 2.1 GB
EGAF50000306376 fastq.gz 3.5 GB
EGAF50000306377 fastq.gz 1.5 GB
EGAF50000306378 fastq.gz 1.8 GB
EGAF50000306380 fastq.gz 432.6 MB
EGAF50000306381 fastq.gz 1.2 GB
EGAF50000306382 fastq.gz 2.5 GB
EGAF50000306383 fastq.gz 2.5 GB
EGAF50000306384 fastq.gz 1.1 GB
EGAF50000306385 fastq.gz 1.9 GB
EGAF50000306386 fastq.gz 3.4 GB
EGAF50000306388 fastq.gz 564.6 MB
EGAF50000306389 fastq.gz 890.5 MB
EGAF50000306390 fastq.gz 2.1 GB
EGAF50000306391 fastq.gz 883.1 MB
EGAF50000306392 fastq.gz 933.1 MB
EGAF50000306393 fastq.gz 2.8 GB
EGAF50000306394 fastq.gz 1.2 GB
EGAF50000306395 fastq.gz 2.1 GB
EGAF50000306396 fastq.gz 901.5 MB
EGAF50000306397 fastq.gz 1.1 GB
EGAF50000306399 fastq.gz 5.2 GB
EGAF50000306400 fastq.gz 440.9 MB
EGAF50000306401 fastq.gz 1.4 GB
EGAF50000306402 fastq.gz 3.3 GB
EGAF50000306403 fastq.gz 2.1 GB
EGAF50000306404 fastq.gz 6.6 GB
EGAF50000306405 fastq.gz 6.8 GB
EGAF50000306406 fastq.gz 1.5 GB
EGAF50000306407 fastq.gz 4.6 GB
EGAF50000306408 fastq.gz 4.7 GB
EGAF50000306409 fastq.gz 2.0 GB
EGAF50000306410 fastq.gz 79.2 MB
EGAF50000306411 fastq.gz 6.7 GB
EGAF50000306412 fastq.gz 198.6 MB
EGAF50000306413 fastq.gz 647.5 MB
EGAF50000306414 fastq.gz 720.6 MB
EGAF50000306415 fastq.gz 4.0 GB
EGAF50000306416 fastq.gz 2.1 GB
EGAF50000306417 fastq.gz 3.2 GB
EGAF50000306418 fastq.gz 1.1 GB
EGAF50000306419 fastq.gz 3.8 GB
EGAF50000306420 fastq.gz 5.6 GB
EGAF50000306421 fastq.gz 5.7 GB
EGAF50000306422 fastq.gz 1.1 GB
EGAF50000306423 fastq.gz 3.5 GB
EGAF50000306424 fastq.gz 5.3 GB
EGAF50000306425 fastq.gz 3.8 GB
EGAF50000306426 fastq.gz 3.8 GB
EGAF50000306427 fastq.gz 3.5 GB
EGAF50000306428 fastq.gz 1.3 GB
EGAF50000306429 fastq.gz 4.1 GB
EGAF50000306471 fastq.gz 242.5 MB
EGAF50000306472 fastq.gz 1.6 GB
EGAF50000306478 fastq.gz 1.6 GB
EGAF50000306479 fastq.gz 2.3 GB
EGAF50000306480 fastq.gz 956.4 MB
EGAF50000306481 fastq.gz 404.0 MB
EGAF50000306482 fastq.gz 1.3 GB
EGAF50000306483 fastq.gz 3.2 GB
EGAF50000306484 fastq.gz 3.3 GB
EGAF50000306490 fastq.gz 543.9 MB
EGAF50000306499 fastq.gz 4.0 GB
EGAF50000306500 fastq.gz 4.3 GB
180 Files (393.2 GB)