CRUK ACRCelerate CRC GEMM bulk RNAseq

Sansom group - CRUK Scotland (Beatson) Institute

doi:10.5281/zenodo.13827890

Published September 25, 2024 | Version V1

Dataset Open

CRUK ACRCelerate CRC GEMM bulk RNAseq

Sansom group - CRUK Scotland (Beatson) Institute

A comprehensive dataset comprising transcriptomic analysis of a world-leading collection of preclinical genetically engineered mouse models (GEMMs) of colorectal cancer (CRC). These patient-relevant models are driven by the mutation of key genes, or aberrant regulation of pathways central to human disease, including, but not limited to APC, TP53, KRAS, BRAF, TGFBR1 and NOTCH. Models within this cohort represent all stages of CRC, spanning from early lesion to late-stage metastatic disease; organoid, tumouroid, orthotopic engrafted disease and ultimately autochthonous primary and disseminated tumours. Moreover, models which discriminate key clinical features such as mismatch repair deficiency and proficiency (MMRd/MMRp), colitis association and anatomical location (right-sided/left-sided) are included.

A schematic of available models appears as Figure 1, with further details found in Table 1.

For access to the data set please contact: gemmdata@crukscotlandinstitute.ac.uk

Notes

The generation of this data was led by the Sansom lab and funded by the CRUK Scotland (Beatson) Institute, the CRUK Scotland Centre and the CRUK ACRCelerate International accelerator programme. The release of this data is aligned with the ethos of the FAIR principles (https://www.go-fair.org/fair-principles/) and our collective commitment to making data from these mouse models and our research team as widely and freely accessible as possible. This data is available from the point of access for academic researchers to perform their analyses across any of the available models/samples.

Publication of molecular subtyping and biological class discovery: The only time-limited embargo being that the data cannot be used for publication/pre-printing of any unsupervised classification/subtyping (or related AI/ML discovery) until after the publication of this approach by the data developers; once published, we will remove any academic publication embargo for unsupervised discovery. This unsupervised biological discovery is ongoing, and we propose to pre-print/publish the findings in the 12 months following this data release. If our unsupervised biological discovery pre-print/publication is not completed within our proposed timeline, aligned to our commitments of the FAIR principles, we will remove this academic restriction on 1st October 2025.

To reiterate, academic users can access and analyse these data immediately. The time-limited publication embargo solely relates to unsupervised biological class discovery to identify GEMM molecular subtypes in these samples. All other analyses can be published from these data immediately.

Citation and referencing of these data: If you use these data in a publication, users should include the following details in their pre-print/publication:

The Zenodo link in the Methods section, and DOI where relevant.
The following statement in the acknowledgements section:

The data were generated by the Sansom lab and funded by CRUK core funding to the CRUK Scotland (Beatson) Institute (A31287), the CRUK Scotland Centre (CTRQQR-2021\100006), and a CRUK Accelerator Award (ACRCelerate - A26825).

3. Citation of our initial pre-print/publication as the primary source of these data. Details will be updated here when available.

This dataset is available through Zenodo for academic non-commercial use only. To request access, you must use your work/university email address and submit the following details in the ‘Request Message’ box below:

─ Your Full Name, Role and Affiliated Institution

─ An overview of your intended use of the dataset – 1 or 2 paragraphs

─ Acknowledgement of the restrictions for academic non-commercial use only.

o Request Messages will be reviewed by the Data Access Committee and only those with sufficient detail that are bona-fide academic, non-commercial institutions will be granted access via Zenodo.

o The dataset can only be used by the named applicant and for the intended use specified in the request. Copying or redistribution of this dataset is strictly prohibited.

o If you are a commercial entity wishing to access the dataset please email gemmdata@crukscotlandinstitute.ac.uk and include in the subject heading ‘Zenodo Data Access Request – CRUK ACRCelerate CRC GEMM bulk RNASeq'.

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CRUK_Scotland_Institute_GEMM_RNAseq_metadata_complete.xlsx md5:6f6f632e6ad18b5a5aed2601bfe01a09	71.6 kB	Download
Figure 1.docx md5:b11ab4709f977d013d9628317c1f4d65	163.8 kB	Download
Table 1.docx md5:80f216bf094682441559f1107e4acdc5	238.3 kB	Download

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License: TERMS AND CONDITIONS FOR USE OF THE CRUK ACRCelerate CRC GEMM bulk RNASeq DATASET

PLEASE READ CAREFULLY BEFORE MAKING APPLICATION TO USE THE DATASET. 1. Status of this document 1.1. This is an end-user licence agreement in respect of the Dataset (as defined below) (“Agreement”). 1.2. This Agreement is made between Cancer Research Technology Limited trading as Cancer Research Horizons, of 2 Redman Place, Stratford, London, E20 1JQ (“CRH”) and you (“You” and “Your”). For clarity, in respect of each application for access to the Dataset (“application”), ‘You’ is intended to refer to the person who has been authorised by CRH in response to the application. 1.3. If the application as approved by CRH was made by an organisation as opposed to an individual, then the Licence (as defined below) is limited to the individual or individuals listed in the application that has been approved by CRH and not the organisation generally, or others in the organisation. 1.4. If the application was made by an organisation as opposed to an individual, then the organisation takes responsibility for ensuring that only the individuals mentioned in its application (as approved by CRH) access and use the Dataset. 1.5. This Agreement is personal to You. You may not transfer or assign, sub-licence, delegate, or otherwise allow a third party to benefit under this Agreement, including individuals working in Your organisation who have not been listed and approved in the application. 1.6. The Interpretation Act 1978 applies to this Agreement. 2. Subject matter of this Licence Agreement 2.1. This Agreement relates to the digitised dataset known as (CRUK ACRCelerate CRC GEMM bulk RNASeq “Dataset”), including any updates and revisions that CRH may in its discretion make and issue from time to time. 3. Acceptance of this Licence Agreement 3.1. As part of Your application, You were informed of and accepted this Agreement. 3.2. By submitting your application and subsequently, if approved, downloading the Dataset from this repository You are confirming Your acceptance of this Agreement without amendment and to the exclusion of all other terms including any terms that You may have included in the application that are inconsistent or conflict with this Agreement. 4. Licence 4.1. Subject to the above clauses and the other provisions of this Agreement, and noting that CRH relies on the information that You provided in the application, if your application is approved, CRH hereby licences You to download and use the Dataset (“Licence”). 4.2. The Licence granted to You under clause 4.1 is: 4.2.1. free of charge; 4.2.2. non-exclusive; 4.2.3. may be used only for the Academic Purpose (as defined below) 4.2.4. time limited (see clause 12 below); and 4.2.5. excludes any right to sub-license or permit others to access and use the Dataset. 4.2.6. “Academic Purpose” means, together: 4.2.6.1. research, teaching or other scholarly use which is undertaken for the charitable purposes of education and research; and 4.2.6.2. within the limitations described in clause 4.2.6.1 above, the purpose stated in Your application as may be approved by CRH. 4.3. You agree to make a fresh submission to CRH if You wish to use the Dataset for a purpose other than the Academic Purpose and not use the Dataset for that further or other purpose unless CRH gives You written authorisation for such use. 4.4. You agree to comply with the process for downloading the Dataset that You are given notice of and not disclose to any third party any passwords associated with the process. 5. Restrictions regarding use of Dataset You agree: 5.1. not to, or permit or assist a third party to, disassemble, decompile, reverse-engineer or create derivative works based on the whole or any part of the Dataset; 5.2. not to create any copies of the downloaded Dataset beyond what is required to perform the Academic Purpose; 5.3. to keep the Dataset secure and not to permit third parties who have not been authorised by CRH and notified to You by CRH to access the Dataset; 5.4. not to remove or interfere with any copyright or other legal notices that have been placed on the Dataset; and 5.5. not to use the Dataset for the creation or supply of any service or product or for any commercial purpose whatsoever. 6. Acknowledgements 6.1. CRH hereby acknowledges that the Dataset was designed and developed by the Sansom lab and funded by CRUK core funding to the CRUK Scotland (Beatson) Institute (A31287), the CRUK Scotland Centre (CTRQQR-2021\100006) and a CRUK Accelerator Award (ACRCelerate - A26825) (together “the Collaborators”). 7. Intellectual Property 7.1. You agree that: 7.1.1. the copyright, database rights and all other IPRs in respect of the Dataset solely belong to CRH or its licensors; 7.1.2. You have no right, title or interest in respect of the Dataset save under the Licence as set out in this Agreement and no rights benefitting You in respect of the Dataset shall survive the termination of this Agreement howsoever that may happen; 7.1.3. any results, feedback, suggestions for improvements of the Dataset or any other information that You may provide to CRH in connection with the Dataset may be copied and used by CRH free of charge, irrevocably and in perpetuity, worldwide in any manner as CRH may in its discretion decide for the research, development and exploitation of the Dataset. 8. Publishing of Results 8.1. Upon request by CRH You agree to make available copies of the results or other output from Your use of the Dataset in a prompt, fair and transparent manner to ensure compliance with this agreement. 8.2. Every publication by You of the results or other output from Your use of the Dataset must contain the following acknowledgment: ‘this publication uses the CRUK ACRCelerate CRC GEMM bulk RNASeq data set generated by the Sansom lab and funded by CRUK core funding to the CRUK Scotland (Beatson) Institute (A31287), the CRUK Scotland Centre (CTRQQR-2021\100006) and a CRUK Accelerator Award (ACRCelerate - A26825)). 9. Data Protection and Privacy 9.1. The Dataset does not contain personal data as defined by applicable data protection laws. You undertake not to derive or attempt to derive any personal data from the Dataset. 9.2. Any personal data submitted by You in connection with Your application will be held and managed by us in accordance with CRH’s Privacy policy, which can be found here: https://www.cancerresearchhorizons.com/our-privacy-policy 10. Warranties 10.1. CRH hereby warrants to You that CRH is entitled to licence the use of the Dataset in accordance with this Agreement but we do not warrant that: 10.1.1. Your use of the Dataset will not infringe the rights of any third party (not being either of the Collaborators (as defined above)); 10.1.2. the Dataset is free of errors or defects or is complete and accurate; or 10.1.3. the Dataset is of any particular quality or that it meets any general or specific quality requirements including any requirements that You may have specified in the application. 10.2. CRH does not represent or warrant that the Dataset will be available to download or use at any particular times or at all. 10.3. To the maximum extent allowed by applicable law, all express and implied warranties in respect of the Dataset are hereby excluded. 11. Liability 11.1. The Dataset is used by You at Your own risk. It is Your responsibility to ensure that the Dataset meets Your requirements. 11.2. The maximum aggregate liability of CRH together with the Collaborators under or in connection with this Agreement whether in contract, tort (including negligence) or otherwise, shall in all circumstances be limited to £50. This limitation does not apply to any type of loss or damage that cannot be limited or excluded by English law. 11.3. CRH and the Collaborators shall not be liable for any loss of profit or for any indirect or consequential loss or damage whatsoever and howsoever arising in connection with Your possession or use of the Dataset. 12. Duration and termination 12.1. The Licence shall commence on the date that CRH in writing notifies You that Your application is approved and shall continue until the earlier of: 12.1.1. thirty days from the date that You are notified by CRH that You are approved to download the Dataset if You and have not downloaded the Dataset within the thirty days’ time period or any extension to that time period that CRH may agree; 12.1.2. Your completion of the Academic Purpose; or 12.1.3. the second anniversary of the commencement date of the Licence; or 12.1.4. termination by us giving You not less than ten days written notice that expires at any time. 13. Effect of termination 13.1. Upon termination of the Licence, You must immediately permanently: delete all copies of the Dataset that You hold and cease using the Dataset. Upon request by us You will arrange for a senior officer of Yours to sign and issue a certificate to CRH that confirm You have complied with the requirements of this clause. 13.2. The following clauses of the Agreement shall survive termination: 1, 5, 7, 8, 9, 11, 13, 14.2-14.8 14. General 14.1. You agree to use the Dataset in accordance with all applicable laws and regulations, including but not limited to applicable data protection laws. 14.2. If CRH fails to enforce or delays in enforcing Your obligations under this Agreement that will not mean that we have waived our rights against You and will not mean that You do not have to comply with those obligations. If we do waive a default by You, we will only do so in writing, and that will not mean that we will automatically waive any later default by You. 14.3. This Agreement, together with Your application and our approval of Your application represent the entire understanding between us relating to the subject matter of this Agreement. You have not relied on any statement that is not expressly set out in any of those documents. 14.4. Any variation of this Agreement must be in writing and signed by authorised signatories for both parties. For the avoidance of doubt, the parties to this Agreement may rescind or vary this agreement without the consent of either Collaborator. 14.5. The parties to this Agreement intend that by virtue of the Contracts (Rights of Third Parties) Act 1999 the Collaborators will be able to enforce clauses 10.3 and 11 of this Agreement as if they were party to this Agreement. 14.6. This Agreement including its formation and subject matter are governed by English Law. 14.7. You and CRH both agree that the courts of England and Wales will have exclusive jurisdiction in respect of any claim or dispute arising out of this Agreement or in connection with its subject matter (“Claims”). 14.8. All Claims will be settled by arbitration under the rules of the London Court of International Arbitration (“LCIA”) by a single arbitrator in London who shall be appointed jointly by the parties or failing that by the President of the LCIA upon the application to him by either party. The arbitration shall be conducted in the English language. The costs shall be shared equally by the parties unless the arbitrator in his discretion determines that a party has behaved manifestly unreasonably and should therefore bear a higher or all of the proportion of the costs of the arbitration provided always that each party shall bear its own costs of legal representation regarding the arbitration.

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Created: September 25, 2024
Modified: September 25, 2024

CRUK ACRCelerate CRC GEMM bulk RNAseq

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