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Spatial CosMx Human 6K

we profiled the cellular composition and TME spatial organization in 4 ICB-resistant HCC patients using single-cell spatial transcriptomics (CosMx Human 6K Discovery Panel). We identified 397 fields-of-view (0.51 mm by 0.51 mm) of hematoxylin and eosin (H&E)-defined tumor and stromal regions followed by cell segmentation using a nuclear stain plus 4 protein markers, yielding 485,209 high-confidence single-cell profiles that were subsequently categorized into distinct cell types based on marker gene annotation.

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Single cell RNA-seq Result for a phase II clinical trail on HCC (NCT03419481)

Thank you for your interest in accessing the EGAC50000000565. This dataset is available under controlled access. All requests will be reviewed by the Data Access Committee (DAC) to ensure that the proposed use of the data is consistent with the informed consent provided by the research participants, applicable ethical requirements, and the terms of this Data Access Policy. Application procedure To apply for access, applicants should submit a written application by email to: alfredcheng@cuhk.edu.hk The email subject should state: Data Access Request – [Dataset Name or EGA Dataset Accession Number] The application must include the following information. 1. Applicant information The applicant’s full name, position, institutional affiliation, institutional address, email address and contact details must be provided. All individuals who will access or analyse the data should be listed. PhD student applicants must include their supervisors as co-applicants and provide their supervisors’ full contact details, including name, position, institution, institutional email address and telephone number. 2. Project description Applicants must provide a clear description of the proposed research project and its specific aims. The application should explain: Why the dataset is required; What analyses will be performed; How the data will be used; The expected research outputs; Relevant key references supporting the proposed research. Ethical approval and data security Where applicable, applicants should provide evidence of approval or exemption from their institutional ethics committee or other relevant regulatory authority. Applicants must also briefly describe how the data will be securely stored, processed and protected at their institution. Conditions of access and use By requesting and accessing the data, approved applicants and their institutions agree: 1. To use the data solely for the research project and specific aims approved by the DAC. 2. Not to use the data for any new, expanded or substantially modified project without obtaining prior written approval from the DAC. 3. Not to attempt to identify or contact any research participant represented in the dataset. 4. Not to disclose, transfer, distribute or otherwise make the data available to any individual or institution that has not been approved by the DAC. 5. To ensure that access is limited to the authorised individuals named in the application. 6. To maintain appropriate administrative, physical and technical safeguards to protect the confidentiality and security of the data. 7. To notify the DAC promptly of any actual or suspected data breach, unauthorised access or other failure to comply with the access conditions. 8. To notify the DAC of any changes in the authorised personnel, institutional affiliation, project aims or data-analysis plan. 9. To comply with all applicable institutional, ethical, legal and regulatory requirements governing the use of human genetic, genomic, phenotypic and clinical data. 10. To acknowledge the original data producers and cite the following publication in all publications, presentations and other research outputs arising from the use of the data: Liang Z, et al. Tumor cells metabolically resist immune-checkpoint therapy by macrophage efferocytosis-mediated fatty acid recycling. Cancer Cell. 2026;44(6):1235–1254.e11. doi: 10.1016/j.ccell.2026.05.005 . PMID: 42259249. The relevant EGA study and dataset accession numbers must also be included where appropriate. 11. To provide the DAC with details of publications or other significant research outputs resulting from the use of the dataset. 12. To securely delete or destroy all copies of the controlled-access data when the approved project is completed, the access period expires or access is withdrawn, unless retention is required by applicable law or institutional policy. Before access is granted, the principal investigator, relevant data users and, where required, an authorised representative of the applicant’s institution may be asked to sign a Data Access Agreement. Approval of an application does not transfer ownership of the data and does not grant permission for unrestricted reuse, redistribution or commercial use. The DAC reserves the right to reject an application, impose additional conditions, establish an access-expiration date or withdraw access if the conditions of this policy or the associated Data Access Agreement are not followed. Changes to This Policy We may update this Privacy Policy occasionally. We will notify you of any changes by posting the new policy on this page. If you have any questions about this Privacy Policy, please contact us at alfredcheng@cuhk.edu.hk

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
EGAS50000001416 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 Quality Report
Located in
EGAF50000499893 rds 10.4 MB
EGAF50000499894 rds 361.1 MB
2 Files (371.5 MB)