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scRNA-seq and scATAC-seq data of bone marrow

17 scRNA-seq and 16 scATAC-seq datasets on bone marrows derived from 16 patients. The sequencing dataset consists of 5 samples without bone marrow infiltration, defined as controls (C1, C2, C3, C4, and C5) and 11 neuroblastoma infiltrated bone marrow samples from patients with MYCN amplification (M1, M2, M3, M4), ATRX mutations (A1, A2), and cases lacking either alteration (S1, S2, S3, S4, S5).

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Data access policy for data describing single cell analyses of transcriptome and epigenome in neuroblastoma infiltrated bone marrow

DATA ACCESS AGREEMENT These terms and conditions govern access to the managed access datasets (details of which are set out in Appendix I) to which the User Institution has requested access. The User Institution agrees to be bound by these terms and conditions. Definitions Authorised Personnel: The individuals at the User Institution to whom The Data Accession Committee of this EGA dataset grants access to the Data. This includes the User, the individuals listed in Appendix II and any other individuals for whom the User Institution subsequently requests access to the Data. Details of the initial Authorised Personnel are set out in Appendix II. Data: The managed access datasets to which the User Institution has requested access. Data Producers: Dr. Sabine Taschner-Mandl, St. Anna Children’s Cancer Research Institute (CCRI) (see Appendix I) and the collaborators listed in Appendix I responsible for the development, organisation, and oversight of these Data. External Collaborator: A collaborator of the User, working for an institution other than the User Institution. Project: The project for which the User Institution has requested access to these Data. A description of the Project is set out in Appendix II. 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. User: The principal investigator for the Project. User Institution(s): The Institution that has requested access to the Data. Data Producer Institutions, DAC Data Accession Committee affiliated institution: St. Anna Children’s Cancer Research Institute (CCRI), Vienna, Austria; Terms 1. The User Institution agrees to only use these Data for the purpose of the Project (described in Appendix II) and only for Research Purposes. The User Institution further agrees that it will only use these Data for Research Purposes which are within the limitations (if any) set out in Appendix I. 2. The User Institution agrees to preserve, at all times, the confidentiality of these Data. In particular, it undertakes not to use, or attempt to use these Data to compromise or otherwise infringe the confidentiality of information on Research Participants. Without prejudice to the generality of the foregoing, the User Institution agrees to use at least the measures set out in Appendix I to protect these Data. 3. The User Institution agrees to protect the confidentiality of Research Participants in any research papers or publications that they prepare by taking all reasonable care to limit the possibility of identification. 4. The User Institution agrees not to link or combine these 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 the User Institution or is freely available without restriction. 5. The User Institution agrees only to transfer or disclose these Data, in whole or part, or any material derived from these Data, to the Authorised Personnel. Any person with whom the Data is shared with has to be listed in Appendix II (Authorised Personnel), or the person must complete a separate application for access to these Data. Should the User Institution wish to share these Data with an External Collaborator, the External Collaborator must complete a separate application for access to these Data. 6. The User Institution agrees that the Data Producers, and all other parties involved in the creation, funding or protection of these Data: a) make no warranty or representation, express or implied as to the accuracy, quality or comprehensiveness of these Data; b) exclude to the fullest extent permitted by law all liability for actions, claims, proceedings, demands, losses (including but not limited to loss of profit), costs, awards damages and payments made by the Recipient that may arise (whether directly or indirectly) in any way whatsoever from the Recipient’s use of these Data or from the unavailability of, or break in access to, these Data for whatever reason and; c) bear no responsibility for the further analysis or interpretation of these Data. 7. The User Institution agrees to follow the Fort Lauderdale Guidelines (http://www.wellcome.ac.uk/stellent/groups/corporatesite/@policy_communications/documents/web_document/wtd003207.pdf ) and the Toronto Statement (http://www.nature.com/nature/journal/v461/n7261/full/461168a.html). This includes but is not limited to recognising the contribution of the Data Producers and including a proper acknowledgement in all reports or publications resulting from the use of these Data. 8. The User Institution agrees to follow the Publication Policy in Appendix III. This includes respecting the moratorium period for the Data Producers to publish the first peer-reviewed report describing and analysing these Data. 9. The User Institution agrees not to make intellectual property claims on these Data and not to use intellectual property protection in ways that would prevent or block access to, or use of, any element of these Data, or conclusion drawn directly from these Data. 10. The User Institution can elect to perform further research that would add intellectual and resource capital to these data and decide to obtain intellectual property rights on these downstream discoveries. In this case, the User Institution agrees to 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.icgc.org/files/daco/NIH_BestPracticesLicensingGenomicInventions_2005_en.pdf ) in conformity with the Organisation for Economic Co-operation and Development Guidelines for the Licensing of the Genetic Inventions (2006) (http://www.oecd.org/science/biotech/36198812.pdf ). 11. The User Institution agrees to destroy/discard the Data held, once it is no longer used for the Project, unless obliged to retain the data for archival purposes in conformity with audit or legal requirements. 12. The User Institution will notify the DAC Data Accession Committee (see Appendix I) within 30 days after application, of any changes or departures of Authorised Personnel. 13. The User Institution will notify the DAC Data Accession Committee (see Appendix I) prior to any significant changes to the protocol for the Project. 14. The User Institution will notify the DAC Data Accession Committee (see Appendix I) as soon as it becomes aware of a breach of the terms or conditions of this agreement. 15. The DAC Data Accession Committee (see Appendix I) may terminate this agreement at any time by giving thirty (30) days written notice to the User Institution. The DAC Data Accession Committee may terminate this agreement in writing without notice for good cause. If this agreement terminates for any reason, the User Institution will be required to destroy any Data held, including copies and backup copies. This clause does not prevent the User Institution from retaining these data for archival purpose in conformity with audit or legal requirements. 16. The User Institution accepts that it may be necessary for the Data Producers to alter the terms of this agreement from time to time. As an example, this may include specific provisions relating to the Data required by Data Producers other than agreed on. In the event that changes are required, the Data Producers or their appointed agent will contact the User Institution to inform it of the changes and the User Institution may elect to accept the changes or terminate the agreement. 17. If requested, the User Institution will allow data security and management documentation to be inspected to verify that it is complying with the terms of this agreement. 18. The User Institution agrees to distribute a copy of these terms to the Authorised Personnel (as listed in Appendix II). The User Institution will procure that the Authorised Personnel comply with the terms of this agreement. 19. 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 Austria and shall be subject to the exclusive jurisdiction of the Austrian courts. APPENDIX I – DATASET DETAILS Dataset reference This EGA Study, which includes 17 scRNA-seq and 16 scATAC-seq datasets on bone marrows derived from 16 patients. The sequencing dataset consists of 5 samples without bone marrow infiltration, defined as controls (C1, C2, C3, C4, and C5) and 11 neuroblastoma infiltrated bone marrow samples from patients with MYCN amplification (M1, M2, M3, M4), ATRX mutations (A1, A2), and cases lacking either alteration (S1, S2, S3, S4, S5). Name of project that created the dataset Dissecting the cellular architecture of neuroblastoma bone marrow metastasis by single-cell transcriptomics and epigenomics Names of other data producers/collaborators DAC Data Accession Committee: Dr. Sabine Taschner-Mandl, Principal Investigator, St. Anna Children’s Cancer Research Institute (CCRI), Vienna, Austria Other data producers: BSF Biomedical Sequencing Facility, CeMM Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria Specific limitations on areas of research Biomedical Research Minimum protection measures required File access: Data can be held in unencrypted files on an institutional compute system, with Unix user group read/write access for one or more appropriate groups but not Unix world read/write access behind a secure firewall. Laptops holding these data should have password protected logins and screenlocks (set to lock after 5 min of inactivity). If held on USB keys or other portable hard drives, the data must be encrypted. APPENDIX II – PROJECT DETAILS (to be completed by the Requestor) - Details of dataset requested i.e., EGA Study and Dataset Accession Number - Brief abstract of the Project in which the Data will be used (500 words max, including a description of types of experiments/analyses to be performed on the dataset/parts of the dataset) - All Individuals who the User Institution to be named as registered users (name, email address, job title, supervisor) - All Individuals that should have an account created at the EGA (name, email, job title) APPENDIX III – PUBLICATION POLICY FOR DATA USERS The users intend to publish the results of their analysis of this dataset and do not consider its deposition into public databases to be the equivalent of such publications. The users anticipate that the dataset could be useful to other qualified researchers for a variety of purposes. However, some areas of work are subject to a publication moratorium. The publication moratorium covers any publications (including oral communications) that describe the use of the dataset. For research papers, submission for publication by the data users should not occur until 12 months after these data were first made available on the relevant hosting database, unless the DAC Data Accession Committee has provided written consent to earlier submission. This excludes publications of the Data provider / DAC member himself. In any publications based on these data, please describe how the data can be accessed, including the name of the hosting database (e.g., The European Genome-phenome Archive at the European Bioinformatics Institute) and its accession numbers (e.g., EGAS00001005675), and acknowledge its use in a form agreed by the User Institution with the DAC Data Accession Committee.

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
EGAS00001006106 Other

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 Located in
EGAF00006126980 fastq.gz 3.0 GB
EGAF00006126981 fastq.gz 2.7 GB
EGAF00006126982 fastq.gz 7.5 GB
EGAF00006126983 fastq.gz 2.9 GB
EGAF00006126984 fastq.gz 3.0 GB
EGAF00006126985 fastq.gz 2.4 GB
EGAF00006126986 fastq.gz 2.7 GB
EGAF00006126987 fastq.gz 3.1 GB
EGAF00006126988 fastq.gz 2.5 GB
EGAF00006126989 fastq.gz 2.4 GB
EGAF00006126990 fastq.gz 2.7 GB
EGAF00006126991 fastq.gz 2.4 GB
EGAF00006126992 fastq.gz 2.6 GB
EGAF00006126993 fastq.gz 2.4 GB
EGAF00006126994 fastq.gz 2.9 GB
EGAF00006126995 fastq.gz 2.4 GB
EGAF00006126996 fastq.gz 2.7 GB
EGAF00006126997 fastq.gz 2.4 GB
EGAF00006126998 fastq.gz 2.3 GB
EGAF00006126999 fastq.gz 7.7 GB
EGAF00006127000 fastq.gz 2.8 GB
EGAF00006127001 fastq.gz 2.8 GB
EGAF00006127002 fastq.gz 2.3 GB
EGAF00006127003 fastq.gz 3.2 GB
EGAF00006127004 fastq.gz 3.0 GB
EGAF00006127005 fastq.gz 3.1 GB
EGAF00006127006 fastq.gz 2.4 GB
EGAF00006127007 fastq.gz 2.4 GB
EGAF00006127008 fastq.gz 2.8 GB
EGAF00006127009 fastq.gz 4.9 GB
EGAF00006127010 fastq.gz 1.9 GB
EGAF00006127011 fastq.gz 4.4 GB
EGAF00006127012 fastq.gz 882.8 MB
EGAF00006127013 fastq.gz 671.6 MB
EGAF00006127014 fastq.gz 2.0 GB
EGAF00006127015 fastq.gz 4.6 GB
EGAF00006127016 fastq.gz 783.3 MB
EGAF00006127017 fastq.gz 587.4 MB
EGAF00006127018 fastq.gz 817.5 MB
EGAF00006127019 fastq.gz 614.5 MB
EGAF00006127020 fastq.gz 1.7 GB
EGAF00006127021 fastq.gz 4.0 GB
EGAF00006127022 fastq.gz 1.9 GB
EGAF00006127023 fastq.gz 4.5 GB
EGAF00006127024 fastq.gz 1.9 GB
EGAF00006127025 fastq.gz 4.6 GB
EGAF00006127026 fastq.gz 2.0 GB
EGAF00006127027 fastq.gz 4.6 GB
EGAF00006127028 fastq.gz 1.7 GB
EGAF00006127029 fastq.gz 3.9 GB
EGAF00006127030 fastq.gz 1.7 GB
EGAF00006127031 fastq.gz 4.0 GB
EGAF00006127032 fastq.gz 3.7 GB
EGAF00006127033 fastq.gz 6.3 GB
EGAF00006127034 fastq.gz 2.4 GB
EGAF00006127035 fastq.gz 8.4 GB
EGAF00006127036 fastq.gz 1.9 GB
EGAF00006127037 fastq.gz 4.5 GB
EGAF00006127038 fastq.gz 2.1 GB
EGAF00006127039 fastq.gz 5.0 GB
EGAF00006127040 fastq.gz 2.1 GB
EGAF00006127041 fastq.gz 4.9 GB
EGAF00006127042 fastq.gz 2.8 GB
EGAF00006127043 fastq.gz 4.8 GB
EGAF00006127044 fastq.gz 760.7 MB
EGAF00006127045 fastq.gz 566.9 MB
EGAF00006127046 fastq.gz 1.6 GB
EGAF00006127047 fastq.gz 3.8 GB
EGAF00006127048 fastq.gz 1.7 GB
EGAF00006127049 fastq.gz 5.7 GB
EGAF00006127050 fastq.gz 3.7 GB
EGAF00006127051 fastq.gz 6.8 GB
EGAF00006127052 fastq.gz 2.0 GB
EGAF00006127053 fastq.gz 4.8 GB
EGAF00006127054 fastq.gz 2.7 GB
EGAF00006127055 fastq.gz 4.6 GB
EGAF00006127056 fastq.gz 663.5 MB
EGAF00006127057 fastq.gz 497.8 MB
EGAF00006127058 fastq.gz 2.1 GB
EGAF00006127059 fastq.gz 4.9 GB
EGAF00006127060 fastq.gz 798.7 MB
EGAF00006127061 fastq.gz 593.6 MB
EGAF00006127062 fastq.gz 1.9 GB
EGAF00006127063 fastq.gz 4.4 GB
EGAF00006127064 fastq.gz 3.1 GB
EGAF00006127065 fastq.gz 5.6 GB
EGAF00006127066 fastq.gz 1.0 GB
EGAF00006127067 fastq.gz 760.1 MB
EGAF00006127068 fastq.gz 1.7 GB
EGAF00006127069 fastq.gz 4.0 GB
EGAF00006127070 fastq.gz 1.9 GB
EGAF00006127071 fastq.gz 4.5 GB
EGAF00006127072 fastq.gz 2.0 GB
EGAF00006127073 fastq.gz 4.6 GB
EGAF00006127074 fastq.gz 1.6 GB
EGAF00006127075 fastq.gz 3.9 GB
EGAF00006127076 fastq.gz 1.9 GB
EGAF00006127077 fastq.gz 4.5 GB
EGAF00006127078 fastq.gz 1.9 GB
EGAF00006127079 fastq.gz 4.6 GB
EGAF00006127080 fastq.gz 666.4 MB
EGAF00006127081 fastq.gz 498.5 MB
EGAF00006127082 fastq.gz 2.0 GB
EGAF00006127083 fastq.gz 4.7 GB
EGAF00006127084 fastq.gz 2.7 GB
EGAF00006127085 fastq.gz 1.4 GB
EGAF00006127086 fastq.gz 2.4 GB
EGAF00006127087 fastq.gz 1.2 GB
EGAF00006127088 fastq.gz 2.2 GB
EGAF00006127089 fastq.gz 1.3 GB
EGAF00006127090 fastq.gz 2.6 GB
EGAF00006127091 fastq.gz 1.4 GB
EGAF00006127092 fastq.gz 2.2 GB
EGAF00006127093 fastq.gz 1.2 GB
EGAF00006127094 fastq.gz 3.1 GB
EGAF00006127095 fastq.gz 1.7 GB
EGAF00006127096 fastq.gz 2.7 GB
EGAF00006127097 fastq.gz 1.4 GB
EGAF00006127098 fastq.gz 2.4 GB
EGAF00006127099 fastq.gz 1.3 GB
EGAF00006127100 fastq.gz 2.4 GB
EGAF00006127101 fastq.gz 1.3 GB
EGAF00006127102 fastq.gz 2.3 GB
EGAF00006127103 fastq.gz 1.2 GB
EGAF00006127104 fastq.gz 3.0 GB
EGAF00006127105 fastq.gz 1.6 GB
EGAF00006127106 fastq.gz 7.9 GB
EGAF00006127107 fastq.gz 4.1 GB
EGAF00006127108 fastq.gz 2.4 GB
EGAF00006127109 fastq.gz 1.3 GB
EGAF00006127110 fastq.gz 2.7 GB
EGAF00006127111 fastq.gz 1.4 GB
EGAF00006127112 fastq.gz 2.7 GB
EGAF00006127113 fastq.gz 1.5 GB
EGAF00006127114 fastq.gz 2.4 GB
EGAF00006127115 fastq.gz 1.3 GB
EGAF00006127116 fastq.gz 2.5 GB
EGAF00006127117 fastq.gz 1.3 GB
EGAF00006127118 fastq.gz 2.4 GB
EGAF00006127119 fastq.gz 1.4 GB
EGAF00006127120 fastq.gz 2.7 GB
EGAF00006127121 fastq.gz 1.4 GB
EGAF00006127122 fastq.gz 2.9 GB
EGAF00006127123 fastq.gz 1.5 GB
EGAF00006127124 fastq.gz 2.4 GB
EGAF00006127125 fastq.gz 1.3 GB
EGAF00006127126 fastq.gz 2.9 GB
EGAF00006127127 fastq.gz 1.5 GB
EGAF00006127128 fastq.gz 2.8 GB
EGAF00006127129 fastq.gz 1.5 GB
EGAF00006127130 fastq.gz 3.0 GB
EGAF00006127131 fastq.gz 1.6 GB
EGAF00006127132 fastq.gz 7.7 GB
EGAF00006127133 fastq.gz 3.9 GB
EGAF00006127134 fastq.gz 2.3 GB
EGAF00006127135 fastq.gz 1.2 GB
EGAF00006127136 fastq.gz 2.9 GB
EGAF00006127137 fastq.gz 1.6 GB
EGAF00006127138 fastq.gz 3.1 GB
EGAF00006127139 fastq.gz 1.6 GB
160 Files (432.9 GB)