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Glioblastoma stem cell lines RNA-seq (Guilhamon et al.)

RNA was extracted from GSCs using the Qiagen RNeasy Plus kit. RNA sample quality was measured by Qubit (Life Technologies) for concentration and by Agilent Bioanalyzer for RNA integrity. All samples had RIN above 9. Libraries were prepared using the TruSeq Stranded mRNA kit (Illumina). Two hundred nanograms from each sample were purified for polyA tail containing mRNA molecules using poly-T oligo attached magnetic beads, then fragmented post-purification. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. This is followed by second strand cDNA synthesis using RNase H and DNA Polymerase I. A single “A” base was added and adapter ligated followed by purification and enrichment with PCR to create cDNA libraries. Final cDNA libraries were verified by the Agilent Bioanalyzer for size and concentration quantified by qPCR. All libraries were pooled to a final concentration of 1.8nM, clustered and sequenced on the Illumina NextSeq500 as a pair-end 75 cycle sequencing run using v2 reagents to achieve a minimum of ~40 million reads per sample.

Request Access

Data access policy for the SU2C Brain Tumour Stem Cell datasets (Guilhamon et al.)

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 Authorized Personnel: The individuals at the User Institution to whom the SU2C Brain Tumour Stem Cell Group Data Access Committee (DAC) 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 Authorized Personnel are set out in Appendix II. Data: The managed access datasets to which the User Institution has requested access. Data Producers: Dr. Mathieu Lupien and Dr. Peter Dirks and the collaborators listed in Appendix I responsible for the development, organization, 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 molecular biology (genetics, genomics, transcriptomics, epigenetics, and epigenomics) 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. The Hospital for Sick Children and University Health Network: Institutions of data production and governance over data included here, by collaborating data producing institutions. 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 Authorized Personnel. 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 recognizing 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 analyzing 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 SU2C Brain Tumour Stem Cell Group DAC within 30 days of any changes or departures of Authorized Personnel. 13. The User Institution will notify SU2C Brain Tumour Stem Cell Group DAC prior to any significant changes to the protocol for the Project. 14. The User Institution will notify SU2C Brain Tumour Stem Cell Group DAC as soon as it becomes aware of a breach of the terms or conditions of this agreement. 15. SU2C Brain Tumour Stem Cell Group DAC may terminate this agreement by written notice to the User Institution. 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 Dr. Mathieu Lupien or Dr. Peter Dirks. 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 Authorized Personnel. The User Institution will procure that the Authorized 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 Ontario and PHIPA (Personal Health Information Protection Act) and shall be subject to the exclusive jurisdiction of the Canadian courts. Agreed for User Institution Signature: Name: Title: Date: Principal Investigator I confirm that I have read and understood this Agreement. Signature: Name: Title: Date: Agreed for SU2C Brain Tumour Stem Cell Group Signature: Name: Dr. Mathieu Lupien Title: Senior Scientist, University Health Network Date: APPENDIX I – DATASET DETAILS APPENDIX II ––PROJECT DETAILS APPENDIX III –– PUBLICATION POLICY APPENDIX I – DATASET DETAILS (to be completed by the data producer before passing to applicant) Dataset reference (EGA Study ID and Dataset Details) Study ID: ega-box-903 Dataset Details: RNA-seq of 27 Glioma Stem Cell populations. Name of project that created the dataset SU2C Canada Cancer Stem Cell Dream Team Names of other data producers/collaborators Paul Guilhamon, The Hospital for Sick Children (paul.guilhamon@sickkids.ca) Specific limitations on areas of research No limitations 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) All Individuals who the User Institution to be named as registered users Name of Registered User Email Job Title Supervisor* All Individuals that should have an account created at the EGA Name of Registered User Email Job Title APPENDIX III – PUBLICATION POLICY SU2C Brain Tumour Stem Cell Group 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. SU2C Brain Tumour Stem Cell Group 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 should not occur until 12 months after these data were first made available on the relevant hosting database, unless Dr. Peter Dirks, Dr. Mathieu Lupien or an authorized designate from SU2C Brain Tumour Stem Cell Group has provided written consent to earlier submission. 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., EGAS00000000029), and acknowledge its use in a form agreed by the User Institution with SU2C Brain Tumour Stem Cell Group.

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
EGAS00001003070 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
EGAF00002035483 fastq.gz 5.7 GB
EGAF00002035484 fastq.gz 5.9 GB
EGAF00002035485 fastq.gz 5.6 GB
EGAF00002035486 fastq.gz 5.9 GB
EGAF00002035487 fastq.gz 5.0 GB
EGAF00002035488 fastq.gz 5.0 GB
EGAF00002035489 fastq.gz 5.2 GB
EGAF00002035490 fastq.gz 5.5 GB
EGAF00002035491 fastq.gz 5.9 GB
EGAF00002035492 fastq.gz 6.1 GB
EGAF00002035493 fastq.gz 6.5 GB
EGAF00002035494 fastq.gz 6.8 GB
EGAF00002035495 fastq.gz 4.9 GB
EGAF00002035496 fastq.gz 5.1 GB
EGAF00002035497 fastq.gz 456.2 MB
EGAF00002035498 fastq.gz 463.7 MB
EGAF00002035499 fastq.gz 442.5 MB
EGAF00002035500 fastq.gz 452.0 MB
EGAF00002035501 fastq.gz 463.5 MB
EGAF00002035502 fastq.gz 468.0 MB
EGAF00002035503 fastq.gz 454.3 MB
EGAF00002035504 fastq.gz 464.1 MB
EGAF00002035505 fastq.gz 585.7 MB
EGAF00002035506 fastq.gz 599.6 MB
EGAF00002035507 fastq.gz 567.7 MB
EGAF00002035508 fastq.gz 584.9 MB
EGAF00002035509 fastq.gz 596.7 MB
EGAF00002035510 fastq.gz 606.7 MB
EGAF00002035511 fastq.gz 582.9 MB
EGAF00002035512 fastq.gz 601.5 MB
EGAF00002035513 fastq.gz 613.9 MB
EGAF00002035514 fastq.gz 623.4 MB
EGAF00002035515 fastq.gz 604.7 MB
EGAF00002035516 fastq.gz 616.0 MB
EGAF00002035517 fastq.gz 632.9 MB
EGAF00002035518 fastq.gz 641.5 MB
EGAF00002035519 fastq.gz 602.5 MB
EGAF00002035520 fastq.gz 610.7 MB
EGAF00002035521 fastq.gz 441.4 MB
EGAF00002035522 fastq.gz 447.0 MB
EGAF00002035523 fastq.gz 431.4 MB
EGAF00002035524 fastq.gz 439.2 MB
EGAF00002035525 fastq.gz 449.5 MB
EGAF00002035526 fastq.gz 452.4 MB
EGAF00002035527 fastq.gz 445.2 MB
EGAF00002035528 fastq.gz 453.3 MB
EGAF00002035529 fastq.gz 591.7 MB
EGAF00002035530 fastq.gz 601.6 MB
EGAF00002035531 fastq.gz 573.9 MB
EGAF00002035532 fastq.gz 586.6 MB
EGAF00002035533 fastq.gz 601.8 MB
EGAF00002035534 fastq.gz 607.7 MB
EGAF00002035535 fastq.gz 588.9 MB
EGAF00002035536 fastq.gz 602.1 MB
EGAF00002035537 fastq.gz 407.3 MB
EGAF00002035538 fastq.gz 413.5 MB
EGAF00002035539 fastq.gz 400.5 MB
EGAF00002035540 fastq.gz 407.8 MB
EGAF00002035541 fastq.gz 421.2 MB
EGAF00002035542 fastq.gz 426.7 MB
EGAF00002035543 fastq.gz 400.1 MB
EGAF00002035544 fastq.gz 405.4 MB
EGAF00002035545 fastq.gz 512.4 MB
EGAF00002035546 fastq.gz 531.0 MB
EGAF00002035547 fastq.gz 504.0 MB
EGAF00002035548 fastq.gz 522.1 MB
EGAF00002035549 fastq.gz 529.4 MB
EGAF00002035550 fastq.gz 547.1 MB
EGAF00002035551 fastq.gz 526.9 MB
EGAF00002035552 fastq.gz 545.1 MB
EGAF00002035553 fastq.gz 487.5 MB
EGAF00002035554 fastq.gz 504.4 MB
EGAF00002035555 fastq.gz 472.4 MB
EGAF00002035556 fastq.gz 490.9 MB
EGAF00002035557 fastq.gz 496.5 MB
EGAF00002035558 fastq.gz 509.8 MB
EGAF00002035559 fastq.gz 485.3 MB
EGAF00002035560 fastq.gz 505.8 MB
EGAF00002035561 fastq.gz 607.1 MB
EGAF00002035562 fastq.gz 613.9 MB
EGAF00002035563 fastq.gz 588.6 MB
EGAF00002035564 fastq.gz 598.3 MB
EGAF00002035565 fastq.gz 616.8 MB
EGAF00002035566 fastq.gz 619.7 MB
EGAF00002035567 fastq.gz 603.9 MB
EGAF00002035568 fastq.gz 614.1 MB
EGAF00002035569 fastq.gz 462.2 MB
EGAF00002035570 fastq.gz 473.3 MB
EGAF00002035571 fastq.gz 447.7 MB
EGAF00002035572 fastq.gz 460.6 MB
EGAF00002035573 fastq.gz 470.8 MB
EGAF00002035574 fastq.gz 478.8 MB
EGAF00002035575 fastq.gz 459.5 MB
EGAF00002035576 fastq.gz 473.9 MB
EGAF00002035577 fastq.gz 512.1 MB
EGAF00002035578 fastq.gz 525.6 MB
EGAF00002035579 fastq.gz 503.0 MB
EGAF00002035580 fastq.gz 516.2 MB
EGAF00002035581 fastq.gz 529.8 MB
EGAF00002035582 fastq.gz 543.0 MB
EGAF00002035583 fastq.gz 527.4 MB
EGAF00002035584 fastq.gz 540.4 MB
EGAF00002035585 fastq.gz 587.4 MB
EGAF00002035586 fastq.gz 604.1 MB
EGAF00002035587 fastq.gz 578.5 MB
EGAF00002035588 fastq.gz 594.9 MB
EGAF00002035589 fastq.gz 606.0 MB
EGAF00002035590 fastq.gz 622.6 MB
EGAF00002035591 fastq.gz 605.5 MB
EGAF00002035592 fastq.gz 621.8 MB
EGAF00002035593 fastq.gz 757.2 MB
EGAF00002035594 fastq.gz 765.2 MB
EGAF00002035595 fastq.gz 732.4 MB
EGAF00002035596 fastq.gz 744.5 MB
EGAF00002035597 fastq.gz 771.9 MB
EGAF00002035598 fastq.gz 775.4 MB
EGAF00002035599 fastq.gz 752.6 MB
EGAF00002035600 fastq.gz 765.4 MB
EGAF00002035601 fastq.gz 650.8 MB
EGAF00002035602 fastq.gz 666.9 MB
EGAF00002035603 fastq.gz 639.5 MB
EGAF00002035604 fastq.gz 655.2 MB
EGAF00002035605 fastq.gz 671.8 MB
EGAF00002035606 fastq.gz 687.7 MB
EGAF00002035607 fastq.gz 669.8 MB
EGAF00002035608 fastq.gz 685.3 MB
EGAF00002035609 fastq.gz 543.5 MB
EGAF00002035610 fastq.gz 550.1 MB
EGAF00002035611 fastq.gz 535.7 MB
EGAF00002035612 fastq.gz 543.2 MB
EGAF00002035613 fastq.gz 559.5 MB
EGAF00002035614 fastq.gz 565.1 MB
EGAF00002035615 fastq.gz 534.6 MB
EGAF00002035616 fastq.gz 539.6 MB
EGAF00002035617 fastq.gz 536.2 MB
EGAF00002035618 fastq.gz 548.6 MB
EGAF00002035619 fastq.gz 518.3 MB
EGAF00002035620 fastq.gz 533.6 MB
EGAF00002035621 fastq.gz 546.0 MB
EGAF00002035622 fastq.gz 554.6 MB
EGAF00002035623 fastq.gz 531.8 MB
EGAF00002035624 fastq.gz 548.6 MB
EGAF00002035625 fastq.gz 556.1 MB
EGAF00002035626 fastq.gz 572.6 MB
EGAF00002035627 fastq.gz 546.6 MB
EGAF00002035628 fastq.gz 562.7 MB
EGAF00002035629 fastq.gz 575.1 MB
EGAF00002035630 fastq.gz 591.1 MB
EGAF00002035631 fastq.gz 571.7 MB
EGAF00002035632 fastq.gz 587.6 MB
EGAF00002035633 fastq.gz 495.5 MB
EGAF00002035634 fastq.gz 503.3 MB
EGAF00002035635 fastq.gz 484.0 MB
EGAF00002035636 fastq.gz 494.7 MB
EGAF00002035637 fastq.gz 503.4 MB
EGAF00002035638 fastq.gz 507.7 MB
EGAF00002035639 fastq.gz 499.5 MB
EGAF00002035640 fastq.gz 510.5 MB
EGAF00002035641 fastq.gz 617.6 MB
EGAF00002035642 fastq.gz 626.8 MB
EGAF00002035643 fastq.gz 608.1 MB
EGAF00002035644 fastq.gz 618.7 MB
EGAF00002035645 fastq.gz 637.0 MB
EGAF00002035646 fastq.gz 645.0 MB
EGAF00002035647 fastq.gz 606.9 MB
EGAF00002035648 fastq.gz 614.4 MB
EGAF00002035649 fastq.gz 486.2 MB
EGAF00002035650 fastq.gz 496.7 MB
EGAF00002035651 fastq.gz 470.4 MB
EGAF00002035652 fastq.gz 483.3 MB
EGAF00002035653 fastq.gz 495.1 MB
EGAF00002035654 fastq.gz 502.4 MB
EGAF00002035655 fastq.gz 482.9 MB
EGAF00002035656 fastq.gz 496.7 MB
174 Files (167.4 GB)