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scRNA-seq of human follicular lymphoma and lymph node

Cryopreserved cells from human nodal follicular lymphoma and lymph node samples were thawed and processed for scRNA-seq analysis. CD3+ CD19− 7-AAD− live T cells (six FL samples from the Original cohort) or 7-AAD− whole live hematopoietic cells (five lymph node and nine FL samples from Validation cohort 1) were sorted using a FACS Aria II or III instrument (BD Biosciences). To generate single-cell emulsions, 6,000–10,000 live cells were loaded into the 10X Genomics Chromium Controller for single-cell partitioning, along with the reverse transcriptase reagent mixture and 3' or 5' gel beads. Sorted T or whole hematopoietic cells were converted to barcoded scRNA-seq libraries using 10X Genomics Chromium single cell 3' reagent kits (v3) for the Validation cohort 1, 5' reagent kits (v1) for the Original cohort, according to the manufacturer’s instructions. The libraries were sequenced on an Illumina HiSeq X Ten or NovaSeq X Plus system, mapped to the human genome (build GRCh38), and demultiplexed using CellRanger pipelines (v3.1.0, 10x Genomics).

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Data access policy

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 DAC for Department of Hematology, University of Tsukuba 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: DAC for Department of Hematology, University of Tsukuba 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 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. 1. The User Institution agrees to only use these Data for the purpose of the Project (described in Appendix II) and only for Non-Profit 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 Organization 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 DAC for Department of Hematology, University of Tsukuba within 30 days of any changes or departures of Authorized Personnel. 13. The User Institution will notify DAC for Department of Hematology, University of Tsukuba prior to any significant changes to the protocol for the Project. 14. The User Institution will notify DAC for Department of Hematology, University of Tsukuba as soon as it becomes aware of a breach of the terms or conditions of this agreement. 15. DAC for Department of Hematology, University of Tsukuba may terminate this agreement for any reason 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. 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. 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 England and Wales and shall be subject to the exclusive jurisdiction of the English 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
EGAS50000000778 Transcriptome Sequencing

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
EGAF50000276345 tsv.gz 35.0 kB
EGAF50000276346 tsv.gz 305.0 kB
EGAF50000276347 mtx.gz 52.4 MB
EGAF50000276348 tsv.gz 27.5 kB
EGAF50000276349 tsv.gz 305.0 kB
EGAF50000276350 mtx.gz 47.0 MB
EGAF50000276351 tsv.gz 35.6 kB
EGAF50000276352 tsv.gz 305.0 kB
EGAF50000276353 mtx.gz 51.1 MB
EGAF50000276354 tsv.gz 38.9 kB
EGAF50000276355 tsv.gz 305.0 kB
EGAF50000276356 mtx.gz 48.7 MB
EGAF50000276357 tsv.gz 34.9 kB
EGAF50000276358 csv 4.2 MB
EGAF50000276359 csv 3.3 MB
EGAF50000276360 tsv.gz 35.4 kB
EGAF50000276361 mtx.gz 32.4 MB
EGAF50000276362 tsv.gz 305.0 kB
EGAF50000276363 tsv.gz 305.0 kB
EGAF50000276364 mtx.gz 41.8 MB
EGAF50000276365 tsv.gz 37.2 kB
EGAF50000276366 tsv.gz 305.0 kB
EGAF50000276367 mtx.gz 44.9 MB
EGAF50000276368 tsv.gz 36.0 kB
EGAF50000276369 tsv.gz 305.0 kB
EGAF50000276370 tsv.gz 36.1 kB
EGAF50000276371 tsv.gz 305.0 kB
EGAF50000276372 tsv.gz 305.0 kB
EGAF50000276373 mtx.gz 27.5 MB
EGAF50000276374 tsv.gz 30.6 kB
EGAF50000276375 tsv.gz 305.0 kB
EGAF50000276376 mtx.gz 38.7 MB
EGAF50000276377 tsv.gz 32.3 kB
EGAF50000276378 tsv.gz 305.0 kB
EGAF50000276379 mtx.gz 38.2 MB
EGAF50000276380 mtx.gz 51.6 MB
EGAF50000276381 mtx.gz 51.5 MB
EGAF50000276382 tsv.gz 44.0 kB
EGAF50000276383 tsv.gz 305.0 kB
EGAF50000276384 mtx.gz 52.7 MB
EGAF50000276385 tsv.gz 44.6 kB
EGAF50000276386 tsv.gz 305.0 kB
EGAF50000276387 mtx.gz 50.0 MB
EGAF50000276388 tsv.gz 28.1 kB
EGAF50000276389 tsv.gz 36.3 kB
EGAF50000276390 tsv.gz 305.0 kB
EGAF50000276391 mtx.gz 48.3 MB
EGAF50000276392 tsv.gz 47.2 kB
EGAF50000276393 tsv.gz 305.0 kB
EGAF50000276394 mtx.gz 66.9 MB
EGAF50000276395 tsv.gz 33.6 kB
EGAF50000276396 tsv.gz 305.0 kB
EGAF50000276397 mtx.gz 51.0 MB
EGAF50000276398 tsv.gz 29.5 kB
EGAF50000276399 tsv.gz 305.0 kB
EGAF50000276400 mtx.gz 40.8 MB
EGAF50000276401 tsv.gz 38.1 kB
EGAF50000276402 tsv.gz 305.0 kB
EGAF50000276403 mtx.gz 54.9 MB
EGAF50000276404 tsv.gz 38.2 kB
EGAF50000276405 tsv.gz 305.0 kB
EGAF50000276406 mtx.gz 49.8 MB
62 Files (954.6 MB)