DOI: 10.5281/zenodo.13827890
title: CRUK ACRCelerate CRC GEMM bulk RNAseq

description: 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

 

 

 

 
description: 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'.