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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Genotyping of targeted loci with single-cell chromatin accessibility

snATAC-seq (10x Genomics) with genotyping of CD34+ cells from patients treated with IFNa (n = 3 patients)

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nterferon-MPN study

Data Use Policy The DAC will email a Data Access Agreement to the requestor, for his or her institutional representative to sign. The body of the agreement is copied below and serves as the Data Use Policy. ======== Authorized Personnel: The individuals at User Institution to whom Cornell University grants access to the Data. This includes User, the individuals listed in Appendix II and any other individuals for whom User Institution subsequently requests access to the Data. Details of the initial Authorized Personnel are set out in Appendix II. Data: The managed access datasets to which User Institution has requested access. “Data” includes any dataset or database into which the Data, in whole or in part, has been aggregated, merged, or combined. Data Producers: Cornell University and the collaborators listed in Appendix I, who were responsible for the development, organization, and oversight of these Data. External Collaborator: A collaborator of User, working for an institution other than User Institution. Publications: Includes, without limitation, articles published in print journals, electronic journals, reviews, books, posters and other written and verbal presentations of research. Research Participant: An individual whose data form part of these Data. Research Purposes: Shall mean research that is seeking to advance the understanding of genetics and genomics, including the treatment of disorders, and work on statistical methods that may be applied to such research. “Research Purposes” specifically excludes: (a) licensing or sale of Data; (b) offering a service or other product using Data; (c) commercializing a machine learning model trained on the Data; and (d) using Data in regulatory filings. User: Principal Investigator at User Institution to whom Cornell University grants access to the Data. User Institution(s): The institution that has requested access to the Data. Cornell: Cornell University, through its Center for Technology Licensing, with offices at 395 Pine Tree Road, Suite 310, Ithaca, NY 14850 and at 1155 York Avenue, New York, NY 10065. Permanent email: mta-ctl@cornell.edu. Agreement 1. User Institution will use Data only for Research Purposes. 2. User Institution will destroy/discard Data held once it is no longer used by User, unless obliged to retain a copy of Data for archival purposes in conformity with audit or legal requirements. 3. Data security a. User Institution must follow, as a minimum standard, the NIH Best Practices for Controlled-Access Data Subject to the NIH Genomic Data Sharing Policy (for reference only: pdf, linked from this page). The use of cloud computing systems must meet the data use and security standards outlined in the NIH Position Statement on Use of Cloud Computing Services for Storage and Analysis of Controlled-Access Data Subject to the NIH Genomic Data Sharing Policy. (For reference only: https://osp.od.nih.gov/wp-content/uploads/2023/01/NIH_Position_Statement_on_Cloud_Computing.pdf) b. Data can be held in unencrypted files on an institutional computer system, with a role-based access system and protected behind a secure firewall. Data can be held in a cloud environment, on an encrypted filesystem, with role-based access controls and protected behind a secure firewall. Laptops holding these data should have encrypted hard drives, password protected logins and screenlocks. If held on USB keys or other portable hard drives, the data must be encrypted.User Institution will not use, or attempt to use, Data to compromise or otherwise infringe the confidentiality of information about Research Participants, and will limit the possibility of identification and in any research papers or publications. User Institution will not link or combine Data to other information or archived data available in a way that could re-identify the Research Participants, even if access to that data has been formally granted to User Institution or is freely available without restriction. 4. User Institution will preserve, at all times, the confidentiality of Data. Without prejudice to the generality of the foregoing, User Institution will use at least the measures set out in Paragraph 3 to protect Data. In particular, it will not use, or attempt to use, Data to compromise or otherwise infringe the confidentiality of information about Research Participants, and will limit the possibility of identification and in any research papers or publications. User Institution will not link or combine Data to other information or archived data available in a way that could re-identify the Research Participants or their family members, even if access to that data has been formally granted to User Institution or is freely available without restriction. 5. User Institution will only transfer or disclose Data, in whole or part, to the Authorized Personnel. User Institution will distribute a copy of these terms to the Authorized Personnel. User Institution will require that the Authorized Personnel comply with the terms of this agreement. Should User wish to share Data with any other laboratory at User Institution or with an External Collaborator, the other laboratory at User Institution or External Collaborator, as is relevant, must complete a separate application for access to Data at EGA. 6. The U.S. Department of Justice Final Rule entitled “Preventing Access to U.S. Sensitive Personal Data and Government- Related Data by Countries of Concern or Covered Persons,” as codified in the United States Code of Federal Regulations 28 CFR Part 202 (https://www.ecfr.gov/current/title-28/chapter-I/part-202), and any sub-regulatory guidance issued thereunder (the “DOJ Final Rule”) applies cumulatively to certain data transmitted by Cornell to a third party, and the following thresholds apply to types of Data that Cornell is providing to User Institution: Data Category Threshold for Bulk Data Human Genomic Data ≥ 100 U.S. Persons Other Human “-omic” Data (e.g., epigenomic, proteomic, transcriptomic) ≥ 1,000 U.S. Persons Personal Health Data ≥ 10,000 U.S. Persons The numbers of subjects whose data are in each dataset included in Data under this Agreement, are listed in Appendix A. With respect to data, including Data, provided by Cornell to User Institution in any given twelve-month period that exceeds the thresholds (“Protected Data”): a. User Institution represents that it is not a Covered Person (as that term is used in 28 CFR Part 202) and it will not engage, or attempt to engage, or knowingly permit others to engage or attempt to engage in any prohibited data brokerage transactions granting access to the Data or any part thereof to any Country of Concern or Covered Person as defined under 28 CFR Part 202. User Institution shall immediately notify Cornell if it knows or suspects that it or any of its employees, agents, or other parties, including third-party vendors and/or subcontractors, who receive access to the Data hereunder (i) is located in, organized or chartered under the laws of, has its principal place of business in, is ordinarily a resident in, or is 50% or more owned or controlled, directly or indirectly, by entities or persons located in, organized or chartered under the laws of, or having their principal place of business in, a “Country of Concern,” as such term is defined below, or (ii) is or otherwise becomes a Covered Person, including without limitation through designation as such by the U.S. Attorney General pursuant to the process set forth in 28 CFR Part 202. b. Upon receipt of such notification, Cornell may immediately terminate this Agreement if Cornell determines, in its sole discretion, that continuing performance of this Agreement would violate applicable law, including without limitation the DOJ Final Rule. Cornell shall further have the right to modify the volume of data transmitted hereunder if Cornell determines, in its sole discretion, that provision of the Data will violate the DOJ Final Rule or other applicable law. c. For purposes of this Agreement, the terms “Country of Concern” or “Countries of Concern” shall mean the People’s Republic of China (including Hong Kong and Macau), Cuba, Iran, North Korea, Russia, and Venezuela, including in each case any political subdivision, agency, or instrumentality thereof, and any other country designated as a “Country of Concern” pursuant to the process set forth in 28 CFR Part 202. d. Failure to comply with the above will constitute a breach of this Agreement and may constitute a violation of the DOJ Final Rule. 7. User Institution will notify Cornell as soon as it becomes aware of a breach of the terms or conditions of this agreement. 8. The Data Producers, and all other parties involved in the creation, funding or protection of Data: a) make no warranty or representation, express or implied as to the accuracy, quality or comprehensiveness of Data; b) shall have no liability for actions, claims, proceedings, demands, losses (including but not limited to loss of profit), costs, awards, damages and payments made by User Institution that may arise (whether directly or indirectly) in any way whatsoever from User Institution’s use of Data or from the unavailability of, or break in access to, Data for whatever reason and; c) bear no responsibility for the further analysis or interpretation of Data. 9. User Institution will acknowledge the Data Producers and will cite the paper cited in Appendix A, and will cite the EGA dataset number cited in Appendix A, in all reports or publications resulting from the use of Data, and will follow the Fort Lauderdale Guidelines (https://www.genome.gov/Pages/Research/WellcomeReport0303.pdf ) and the Toronto Statement (http://www.nature.com/nature/journal/v461/n7261/full/461168a.html). 10. Intellectual Property (a)User Institution will not make intellectual property claims on Data and will not use intellectual property protection in ways that would prevent or block access to, or use of, any element of Data, or conclusion drawn directly from Data. (b) Should User Institution elect to obtain intellectual property rights on downstream discoveries arising from its use of Data that comply with Paragraph 10(a), User Institution will implement licensing policies that will not obstruct further research and to follow the U.S. National Institutes of Health Best Practices for the Licensing of Genomic Inventions (2005) (https://www.ott.nih.gov/sites/default/files/documents/pdfs/70fr18413.pdf ) and the Organization for Economic Co-operation and Development Guidelines for the Licensing of the Genetic Inventions (2006) (https://legalinstruments.oecd.org/en/instruments/OECD-LEGAL-0342). 11. Cornell may terminate this agreement by written notice to User Institution. If this agreement terminates for any reason, User Institution will destroy any Data in its possession or control other than one copy Data retained solely for archival purpose in conformity with audit or legal requirements. 12. User Institution accepts that it may be necessary for the Data Producers to alter the terms of this agreement from time to time. In the event that changes are required, Cornell will contact User Institution to inform it of the changes and User Institution may elect to accept the changes or terminate the agreement. 13. If requested, User Institution will allow data security and management documentation to be inspected to verify that it is complying with the terms of this agreement, including the data security provisions of Paragraph 3. 14. This agreement (and any dispute, controversy, proceedings or claim of whatever nature arising out of this agreement or its formation) shall be construed, interpreted, and governed by the laws of the United States and shall be subject to the exclusive jurisdiction of the United States courts.

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
EGAS50000002009 Cancer Genomics

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
EGAF50000933113 fastq.gz 84.2 MB
EGAF50000933114 fastq.gz 111.6 MB
EGAF50000933115 fastq.gz 110.8 MB
EGAF50000933116 fastq.gz 113.4 MB
EGAF50000933117 fastq.gz 54.7 MB
EGAF50000933118 fastq.gz 84.0 MB
EGAF50000933119 fastq.gz 57.7 MB
EGAF50000933120 fastq.gz 207.0 kB
EGAF50000933121 fastq.gz 241.3 kB
EGAF50000933122 fastq.gz 4.6 MB
EGAF50000933123 fastq.gz 5.3 MB
EGAF50000933124 fastq.gz 146.3 MB
EGAF50000933125 fastq.gz 153.4 MB
EGAF50000933126 fastq.gz 140.2 MB
EGAF50000933127 fastq.gz 396.9 MB
EGAF50000933128 fastq.gz 145.7 MB
EGAF50000933129 fastq.gz 390.3 MB
EGAF50000933130 fastq.gz 997.3 MB
EGAF50000933131 fastq.gz 660.7 MB
EGAF50000933147 fastq.gz 226.1 MB
EGAF50000933148 fastq.gz 183.0 MB
EGAF50000933149 fastq.gz 220.5 MB
EGAF50000933150 fastq.gz 179.0 MB
EGAF50000933152 fastq.gz 233.2 MB
EGAF50000933153 fastq.gz 187.6 MB
EGAF50000933154 fastq.gz 227.3 MB
EGAF50000933155 fastq.gz 183.4 MB
EGAF50000933158 fastq.gz 210.0 MB
EGAF50000933160 fastq.gz 170.2 MB
EGAF50000933161 fastq.gz 204.1 MB
EGAF50000933162 fastq.gz 165.8 MB
EGAF50000933168 fastq.gz 195.9 MB
EGAF50000933169 fastq.gz 158.7 MB
EGAF50000933171 fastq.gz 192.3 MB
EGAF50000933172 fastq.gz 156.2 MB
EGAF50000933176 fastq.gz 1.3 GB
EGAF50000933177 fastq.gz 1.2 GB
EGAF50000933180 fastq.gz 1.2 GB
EGAF50000933181 fastq.gz 1.2 GB
EGAF50000933187 fastq.gz 1.1 GB
EGAF50000933194 fastq.gz 1.1 GB
EGAF50000933196 fastq.gz 1.1 GB
EGAF50000933198 fastq.gz 1.1 GB
EGAF50000933199 fastq.gz 97.8 MB
EGAF50000933200 fastq.gz 142.0 MB
EGAF50000933201 fastq.gz 139.0 MB
EGAF50000933202 fastq.gz 153.7 MB
EGAF50000933205 fastq.gz 183.3 MB
EGAF50000933206 fastq.gz 262.6 MB
EGAF50000933207 fastq.gz 177.3 MB
EGAF50000933208 fastq.gz 253.2 MB
EGAF50000933209 fastq.gz 246.8 MB
EGAF50000933210 fastq.gz 352.4 MB
EGAF50000933211 fastq.gz 241.2 MB
EGAF50000933212 fastq.gz 343.1 MB
EGAF50000933213 fastq.gz 767.9 MB
EGAF50000933214 fastq.gz 751.7 MB
EGAF50000933219 fastq.gz 1.1 GB
EGAF50000933223 fastq.gz 1.1 GB
EGAF50000933224 fastq.gz 74.0 MB
EGAF50000933225 fastq.gz 105.6 MB
EGAF50000933227 fastq.gz 72.3 MB
EGAF50000933228 fastq.gz 102.7 MB
EGAF50000933229 fastq.gz 312.6 MB
EGAF50000933230 fastq.gz 307.6 MB
EGAF50000933231 fastq.gz 873.4 MB
EGAF50000933233 fastq.gz 852.4 MB
EGAF50000933234 fastq.gz 202.4 MB
EGAF50000933235 fastq.gz 289.8 MB
EGAF50000933236 fastq.gz 197.4 MB
EGAF50000933237 fastq.gz 281.6 MB
EGAF50000933239 fastq.gz 653.0 MB
EGAF50000933240 fastq.gz 371.0 MB
EGAF50000933241 fastq.gz 366.1 MB
EGAF50000933243 fastq.gz 616.7 MB
EGAF50000933244 fastq.gz 610.3 MB
EGAF50000933245 fastq.gz 171.2 MB
EGAF50000933246 fastq.gz 170.4 MB
EGAF50000933247 fastq.gz 285.0 MB
EGAF50000933248 fastq.gz 284.3 MB
EGAF50000933249 fastq.gz 342.6 MB
EGAF50000933250 fastq.gz 337.4 MB
EGAF50000933252 fastq.gz 557.0 MB
EGAF50000933253 fastq.gz 551.7 MB
EGAF50000933254 fastq.gz 18.3 MB
EGAF50000933255 fastq.gz 21.0 MB
EGAF50000933256 fastq.gz 32.1 MB
EGAF50000933257 fastq.gz 36.4 MB
EGAF50000933258 fastq.gz 327.7 MB
EGAF50000933259 fastq.gz 322.5 MB
EGAF50000933260 fastq.gz 515.5 MB
EGAF50000933261 fastq.gz 508.2 MB
EGAF50000933262 fastq.gz 360.6 MB
EGAF50000933263 fastq.gz 353.3 MB
EGAF50000933265 fastq.gz 569.8 MB
EGAF50000933267 fastq.gz 559.1 MB
EGAF50000933270 fastq.gz 347.6 MB
EGAF50000933272 fastq.gz 338.8 MB
EGAF50000933273 fastq.gz 546.7 MB
EGAF50000933274 fastq.gz 533.5 MB
EGAF50000933305 fastq.gz 989.5 MB
EGAF50000933309 fastq.gz 1.0 GB
EGAF50000933311 fastq.gz 994.6 MB
EGAF50000933324 fastq.gz 1.2 GB
EGAF50000933333 fastq.gz 1.2 GB
EGAF50000933335 fastq.gz 1.2 GB
EGAF50000933336 fastq.gz 1.2 GB
EGAF50000933341 fastq.gz 1.2 GB
EGAF50000933343 fastq.gz 1.2 GB
EGAF50000933344 fastq.gz 1.2 GB
EGAF50000933347 fastq.gz 1.2 GB
EGAF50000933348 fastq.gz 1.3 GB
EGAF50000933352 fastq.gz 1.3 GB
EGAF50000933357 fastq.gz 1.3 GB
EGAF50000933360 fastq.gz 1.3 GB
EGAF50000933362 fastq.gz 123.8 MB
EGAF50000933363 fastq.gz 127.8 MB
EGAF50000933365 fastq.gz 118.4 MB
EGAF50000933367 fastq.gz 121.0 MB
EGAF50000933372 fastq.gz 877.5 MB
EGAF50000933374 fastq.gz 871.8 MB
EGAF50000933388 fastq.gz 881.4 MB
EGAF50000933390 fastq.gz 876.5 MB
EGAF50000933400 fastq.gz 986.3 MB
EGAF50000933410 fastq.gz 971.1 MB
EGAF50000933411 fastq.gz 1.0 GB
EGAF50000933413 fastq.gz 985.3 MB
EGAF50000933414 fastq.gz 816.1 MB
EGAF50000933416 fastq.gz 804.5 MB
EGAF50000933422 fastq.gz 824.1 MB
EGAF50000933442 fastq.gz 813.0 MB
EGAF50000933450 fastq.gz 906.8 MB
EGAF50000933451 fastq.gz 894.1 MB
EGAF50000933452 fastq.gz 5.0 GB
EGAF50000933453 fastq.gz 914.0 MB
EGAF50000933456 fastq.gz 901.6 MB
EGAF50000933457 fastq.gz 10.9 GB
EGAF50000933557 fastq.gz 396.8 MB
EGAF50000933558 fastq.gz 839.0 MB
139 Files (86.5 GB)