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Capture-based Methods for Transcriptomic Profiling of FFPE material

This dataset includes all FASTQ files for 11 samples where different capture-based methods for transcriptome profiling have been tested. Specifically, we have the 'traditional' RNA-seq experiment with fresh frozen (FF) material, and 3 different capture methods for the matching formalin-fixed paraffin-embedded samples: Agilent (AGI), IDT, and Twist Biosciences (TBS). In total, there are 43 samples with paired-end FASTQ files (1 sample did not have sufficient material to test all methods). Samples are identified by the R01-R11 IDs with a suffix that indicates the capture method used (or FF for fresh frozen).

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Password protection to computer network and/or strong data encryption; c. Virus and malware protection to computers on the computer network; d. Secure backup procedure; 6. You acknowledge that Access to the Data is granted for the duration of the Project described in Section I, as well as any new Project under the same research field or area. Any use of the Data for a Project of another research field or area will need to be approved under a new Agreement. 7. You recognize that nothing in this Agreement shall operate to transfer to You any intellectual property rights to the Data. 8. You agree not to make intellectual property claims on the Data and not to use intellectual property protection in ways that would prevent or block Access to, or use of, any element of the Data. 9. You can elect to perform further Research that would add intellectual and resource capital to the Data, and decide to obtain intellectual property rights on these downstream discoveries. In this case, You agree to implement licensing policies that will not obstruct further Research, following the Organisation for Economic Co-operation and Development Guidelines. 10. You agree that the Research Project 1) bears no legal responsibility for the accuracy or comprehensiveness of the Data; 2) accepts no liability for indirect, consequential, or incidental damages or losses arising from use of the Data; and 3) bears no responsibility for the further analysis or interpretation of these Data over and above that published by the Controller(s). 11. You agree to hold the Data Subject(s) and Data Controller(s) harmless and to defend and indemnify all these parties against all liabilities, demands, damages, expenses, and losses arising out of Your use for any Purpose of the Data. 12. You agree to a moratorium on publishing global analyses of the dataset until the Data Controller(s) have published their own global analysis or twelve (12) months, the maximum, have passed from the time the Data were deposited, whichever occurs first. You acknowledge that prompt publication or public disclosure of the results of the Research Project is encouraged. You also agree that by publishing Your global analyses of the Data, you will not disclose any results generated from the Data. 13. You agree to acknowledge the contribution of the Data Controller(s) in all oral and written presentations, disclosures, and Publications resulting from all analyses of the Data. 14. You agree to use the Data in Your laboratory. Any Authorised Personnel shall work under Your direct supervision. You agree to distribute a copy of these terms to the Authorised Personnel. 15. You may not transfer any information included in the Data to anyone unless specifically designated in the Research Project, or by prior specific or general written authorisation of the Data Controller(s) responsible for the generation of the original Data in each case. 16. You may not transfer the Data itself to anyone outside the Institution, unless the Controller(s) has (have) approved such transfer and its terms in writing. 17. Should You wish to share the Data with an external collaborator, the external collaborator must complete a separate Data Access Agreement. 18. You shall ensure that ‘all’ who have Access to the Data, namely You and Your Authorised Personnel, will be listed out, and are made aware and be bound by the terms of this Agreement. You remain solely and fully responsible for Your Authorised Personnel’s non-compliance with the provision of the Agreement and/or applicable laws. 19. In case of a breach of security resulting from ‘accidental’ use of Data by You and Your Authorised Personnel, which leads to disclosure of Data, then You must report this to Data Controller(s) within 72 hours maximum, and follow any relevant rule as provided by the GDPR. 20. In case of a ‘non-accidental or minor’ breach of hDAA by You, You will further be required to destroy any Data held. 21. You accept that this Agreement will terminate immediately upon ‘any’ breach by You, or its termination (see Section I). 22. You endeavour to settle any dispute with the Data Controller(s) amicably. If you are unable to reach an Agreement, you will meet and negotiate in good faith in an effort to resolve the issue. If the issue has not been resolved within a reasonable period (e.g. 30 calendar days), you are both entitled to submit it for resolution by an arbitrator. 23. Further, the language of the proceedings will be ‘English’ if not otherwise agreed. 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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
EGAS00001005255 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
EGAF00005279593 fastq.gz 2.0 GB
EGAF00005279594 fastq.gz 2.0 GB
EGAF00005279595 fastq.gz 2.4 GB
EGAF00005279596 fastq.gz 2.4 GB
EGAF00005279597 fastq.gz 4.0 GB
EGAF00005279598 fastq.gz 4.0 GB
EGAF00005279599 fastq.gz 3.5 GB
EGAF00005279600 fastq.gz 3.5 GB
EGAF00005279601 fastq.gz 2.1 GB
EGAF00005279602 fastq.gz 2.1 GB
EGAF00005279603 fastq.gz 2.8 GB
EGAF00005279604 fastq.gz 2.8 GB
EGAF00005279605 fastq.gz 2.1 GB
EGAF00005279606 fastq.gz 2.2 GB
EGAF00005279607 fastq.gz 1.8 GB
EGAF00005279608 fastq.gz 1.8 GB
EGAF00005279609 fastq.gz 2.2 GB
EGAF00005279610 fastq.gz 2.2 GB
EGAF00005279611 fastq.gz 3.7 GB
EGAF00005279612 fastq.gz 3.8 GB
EGAF00005279613 fastq.gz 1.9 GB
EGAF00005279614 fastq.gz 2.0 GB
EGAF00005279615 fastq.gz 1.6 GB
EGAF00005279616 fastq.gz 1.7 GB
EGAF00005279617 fastq.gz 2.0 GB
EGAF00005279618 fastq.gz 2.2 GB
EGAF00005279619 fastq.gz 2.3 GB
EGAF00005279620 fastq.gz 2.3 GB
EGAF00005279621 fastq.gz 2.4 GB
EGAF00005279622 fastq.gz 2.3 GB
EGAF00005279623 fastq.gz 2.4 GB
EGAF00005279624 fastq.gz 2.5 GB
EGAF00005279625 fastq.gz 3.1 GB
EGAF00005279626 fastq.gz 3.0 GB
EGAF00005279627 fastq.gz 2.5 GB
EGAF00005279628 fastq.gz 2.5 GB
EGAF00005279629 fastq.gz 2.8 GB
EGAF00005279630 fastq.gz 3.0 GB
EGAF00005279631 fastq.gz 2.6 GB
EGAF00005279632 fastq.gz 2.7 GB
EGAF00005279633 fastq.gz 2.4 GB
EGAF00005279634 fastq.gz 2.3 GB
EGAF00005279635 fastq.gz 3.7 GB
EGAF00005279636 fastq.gz 3.8 GB
EGAF00005279637 fastq.gz 2.0 GB
EGAF00005279638 fastq.gz 2.1 GB
EGAF00005279639 fastq.gz 1.7 GB
EGAF00005279640 fastq.gz 1.7 GB
EGAF00005279641 fastq.gz 1.7 GB
EGAF00005279642 fastq.gz 1.6 GB
EGAF00005279643 fastq.gz 2.1 GB
EGAF00005279644 fastq.gz 2.2 GB
EGAF00005279645 fastq.gz 2.7 GB
EGAF00005279646 fastq.gz 2.6 GB
EGAF00005279647 fastq.gz 1.8 GB
EGAF00005279648 fastq.gz 1.8 GB
EGAF00005279649 fastq.gz 679.5 MB
EGAF00005279650 fastq.gz 674.7 MB
EGAF00005279651 fastq.gz 2.6 GB
EGAF00005279652 fastq.gz 2.7 GB
EGAF00005279653 fastq.gz 2.3 GB
EGAF00005279654 fastq.gz 2.3 GB
EGAF00005279655 fastq.gz 3.3 GB
EGAF00005279656 fastq.gz 3.3 GB
EGAF00005279657 fastq.gz 2.2 GB
EGAF00005279658 fastq.gz 2.2 GB
EGAF00005279659 fastq.gz 2.0 GB
EGAF00005279660 fastq.gz 2.0 GB
EGAF00005279661 fastq.gz 2.4 GB
EGAF00005279662 fastq.gz 2.4 GB
EGAF00005279663 fastq.gz 3.3 GB
EGAF00005279664 fastq.gz 3.3 GB
EGAF00005279665 fastq.gz 3.1 GB
EGAF00005279666 fastq.gz 3.1 GB
EGAF00005279667 fastq.gz 1.9 GB
EGAF00005279668 fastq.gz 2.0 GB
EGAF00005279669 fastq.gz 3.4 GB
EGAF00005279670 fastq.gz 3.7 GB
EGAF00005279671 fastq.gz 1.6 GB
EGAF00005279672 fastq.gz 1.6 GB
EGAF00005279673 fastq.gz 1.5 GB
EGAF00005279674 fastq.gz 1.5 GB
EGAF00005279675 fastq.gz 3.1 GB
EGAF00005279676 fastq.gz 3.1 GB
EGAF00005279677 fastq.gz 2.7 GB
EGAF00005279678 fastq.gz 2.9 GB
86 Files (210.3 GB)