Paired-end RNA-Seq Dataset of 72 Brain Organoid Samples: Sequencing and Gene Expression Analysis
72 fastq sequencing files of 72 brain-organoid paired-end sequenced samples (R1/R2). RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina following the manufacturer’s instructions (New England Biolabs, USA). mRNAs were first enriched with Oligo(dT) beads. The samples were sequenced using a 2x150 Pair-End configuration (ver. 1.5) on an Illumina NovaSeq 6000 The raw sequence reads were aligned to the human reference genome GRCh38 using the STAR aligner (Dobin et al., 2013). Gene expression levels were quantified using the FeatureCounts tool (Liao et al., 2014) (file: "All_Counts_final.xlsx") For more information, see "Study Description"
- 07/11/2024
- 72 samples
- DAC: EGAC50000000380
- Technology: Illumina NovaSeq 6000
Organoid sequencing data access policy
The basis of this data access policy is the compliance to the Regulation (EU) 2016/679 of the European Parliament and of the Council, the General Data Protection Regulation (‘GDPR’). 1. You, the Data Recipient, agree to only use the Data for the Purpose of the Project. 2. You agree to preserve, at all times, the confidentiality of information and Data pertaining to Data Subjects. You undertake not to use or attempt to use the Data to compromise or otherwise infringe the confidentiality of information on Data Subjects and their right to privacy. 3. You agree not to attempt to identify Data Subjects. 4. You and your Authorised Personnel agree to take into consideration any usage restrictions (if any), stemming from consent, i.e. the appropriate lawful basis for processing the Data, as well as any usage restrictions stemming from any applicable internal policies of your Institution. 5. You agree that in handling this Data You will follow an up-to-date information technology (IT) policy that must include, at a minimum, the following items: a. Logging and auditing of Access to the Data and to the computer network; b. 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. The award of the arbitration will be final and binding upon the parties concerned. 24. This Agreement (and any dispute, controversy, proceedings, or claim of whatever nature arising out of it or its formation) shall be interpreted, governed by and construed in accordance with the Laws of Germany, and shall be subject to the exclusive jurisdiction of German 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 |
|---|---|---|
| EGAS50000000659 | RNASeq |
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 | |
|---|---|---|---|---|
| EGAF50000219439 | fastq.gz | 1.6 GB | ||
| EGAF50000219440 | fastq.gz | 1.7 GB | ||
| EGAF50000219441 | fastq.gz | 2.0 GB | ||
| EGAF50000219442 | fastq.gz | 1.5 GB | ||
| EGAF50000219443 | fastq.gz | 1.8 GB | ||
| EGAF50000219444 | fastq.gz | 1.7 GB | ||
| EGAF50000219445 | fastq.gz | 1.8 GB | ||
| EGAF50000219446 | fastq.gz | 1.7 GB | ||
| EGAF50000219447 | fastq.gz | 1.5 GB | ||
| EGAF50000219448 | fastq.gz | 1.6 GB | ||
| EGAF50000219449 | fastq.gz | 2.0 GB | ||
| EGAF50000219450 | fastq.gz | 2.1 GB | ||
| EGAF50000219451 | fastq.gz | 2.6 GB | ||
| EGAF50000219452 | fastq.gz | 2.4 GB | ||
| EGAF50000219453 | fastq.gz | 2.7 GB | ||
| EGAF50000219454 | fastq.gz | 2.8 GB | ||
| EGAF50000219455 | fastq.gz | 1.7 GB | ||
| EGAF50000219456 | fastq.gz | 1.6 GB | ||
| EGAF50000219457 | fastq.gz | 2.5 GB | ||
| EGAF50000219458 | fastq.gz | 2.6 GB | ||
| EGAF50000219459 | fastq.gz | 2.3 GB | ||
| EGAF50000219460 | fastq.gz | 2.1 GB | ||
| EGAF50000219461 | fastq.gz | 2.1 GB | ||
| EGAF50000219462 | fastq.gz | 2.2 GB | ||
| EGAF50000219463 | fastq.gz | 2.3 GB | ||
| EGAF50000219464 | fastq.gz | 2.2 GB | ||
| EGAF50000219465 | fastq.gz | 2.4 GB | ||
| EGAF50000219466 | fastq.gz | 2.3 GB | ||
| EGAF50000219467 | fastq.gz | 1.9 GB | ||
| EGAF50000219468 | fastq.gz | 1.8 GB | ||
| EGAF50000219469 | fastq.gz | 2.3 GB | ||
| EGAF50000219470 | fastq.gz | 2.1 GB | ||
| EGAF50000219471 | fastq.gz | 1.8 GB | ||
| EGAF50000219472 | fastq.gz | 1.7 GB | ||
| EGAF50000219473 | fastq.gz | 1.9 GB | ||
| EGAF50000219474 | fastq.gz | 1.8 GB | ||
| EGAF50000219475 | fastq.gz | 2.3 GB | ||
| EGAF50000219476 | fastq.gz | 2.4 GB | ||
| EGAF50000219477 | fastq.gz | 2.2 GB | ||
| EGAF50000219478 | fastq.gz | 2.1 GB | ||
| EGAF50000219479 | fastq.gz | 1.9 GB | ||
| EGAF50000219480 | fastq.gz | 1.8 GB | ||
| EGAF50000219481 | fastq.gz | 2.1 GB | ||
| EGAF50000219482 | fastq.gz | 2.0 GB | ||
| EGAF50000219483 | fastq.gz | 1.7 GB | ||
| EGAF50000219484 | fastq.gz | 1.6 GB | ||
| EGAF50000219485 | fastq.gz | 2.5 GB | ||
| EGAF50000219486 | fastq.gz | 2.4 GB | ||
| EGAF50000219487 | fastq.gz | 1.6 GB | ||
| EGAF50000219488 | fastq.gz | 1.7 GB | ||
| EGAF50000219489 | fastq.gz | 2.6 GB | ||
| EGAF50000219490 | fastq.gz | 2.5 GB | ||
| EGAF50000219491 | fastq.gz | 2.3 GB | ||
| EGAF50000219492 | fastq.gz | 2.1 GB | ||
| EGAF50000219493 | fastq.gz | 2.0 GB | ||
| EGAF50000219494 | fastq.gz | 1.9 GB | ||
| EGAF50000219495 | fastq.gz | 2.2 GB | ||
| EGAF50000219496 | fastq.gz | 2.1 GB | ||
| EGAF50000219497 | fastq.gz | 1.7 GB | ||
| EGAF50000219498 | fastq.gz | 1.6 GB | ||
| EGAF50000219499 | fastq.gz | 5.9 GB | ||
| EGAF50000219500 | fastq.gz | 5.6 GB | ||
| EGAF50000219501 | fastq.gz | 2.1 GB | ||
| EGAF50000219502 | fastq.gz | 2.0 GB | ||
| EGAF50000219503 | fastq.gz | 2.4 GB | ||
| EGAF50000219504 | fastq.gz | 2.3 GB | ||
| EGAF50000219505 | fastq.gz | 2.1 GB | ||
| EGAF50000219506 | fastq.gz | 2.3 GB | ||
| EGAF50000219507 | fastq.gz | 2.1 GB | ||
| EGAF50000219508 | fastq.gz | 2.0 GB | ||
| EGAF50000219509 | fastq.gz | 2.9 GB | ||
| EGAF50000219510 | fastq.gz | 2.7 GB | ||
| EGAF50000219511 | fastq.gz | 1.9 GB | ||
| EGAF50000219512 | fastq.gz | 1.8 GB | ||
| EGAF50000219513 | fastq.gz | 2.3 GB | ||
| EGAF50000219514 | fastq.gz | 2.4 GB | ||
| EGAF50000219515 | fastq.gz | 1.6 GB | ||
| EGAF50000219516 | fastq.gz | 1.7 GB | ||
| EGAF50000219517 | fastq.gz | 1.9 GB | ||
| EGAF50000219518 | fastq.gz | 1.8 GB | ||
| EGAF50000219519 | fastq.gz | 2.3 GB | ||
| EGAF50000219520 | fastq.gz | 2.1 GB | ||
| EGAF50000219521 | fastq.gz | 2.3 GB | ||
| EGAF50000219522 | fastq.gz | 2.2 GB | ||
| EGAF50000219523 | fastq.gz | 2.2 GB | ||
| EGAF50000219524 | fastq.gz | 2.3 GB | ||
| EGAF50000219525 | fastq.gz | 1.8 GB | ||
| EGAF50000219526 | fastq.gz | 1.8 GB | ||
| EGAF50000219527 | fastq.gz | 1.8 GB | ||
| EGAF50000219528 | fastq.gz | 1.7 GB | ||
| EGAF50000219529 | fastq.gz | 1.8 GB | ||
| EGAF50000219530 | fastq.gz | 1.9 GB | ||
| EGAF50000219531 | fastq.gz | 2.9 GB | ||
| EGAF50000219532 | fastq.gz | 3.0 GB | ||
| EGAF50000219533 | fastq.gz | 1.7 GB | ||
| EGAF50000219534 | fastq.gz | 1.6 GB | ||
| EGAF50000219535 | fastq.gz | 1.9 GB | ||
| EGAF50000219536 | fastq.gz | 1.8 GB | ||
| EGAF50000219537 | fastq.gz | 1.6 GB | ||
| EGAF50000219538 | fastq.gz | 1.7 GB | ||
| EGAF50000219539 | fastq.gz | 2.0 GB | ||
| EGAF50000219540 | fastq.gz | 2.1 GB | ||
| EGAF50000219541 | fastq.gz | 2.0 GB | ||
| EGAF50000219542 | fastq.gz | 1.9 GB | ||
| EGAF50000219543 | fastq.gz | 2.4 GB | ||
| EGAF50000219544 | fastq.gz | 2.5 GB | ||
| EGAF50000219545 | fastq.gz | 2.2 GB | ||
| EGAF50000219546 | fastq.gz | 2.3 GB | ||
| EGAF50000219547 | fastq.gz | 2.4 GB | ||
| EGAF50000219548 | fastq.gz | 2.6 GB | ||
| EGAF50000219549 | fastq.gz | 2.4 GB | ||
| EGAF50000219550 | fastq.gz | 2.5 GB | ||
| EGAF50000219551 | fastq.gz | 2.0 GB | ||
| EGAF50000219552 | fastq.gz | 2.2 GB | ||
| EGAF50000219553 | fastq.gz | 2.2 GB | ||
| EGAF50000219554 | fastq.gz | 2.0 GB | ||
| EGAF50000219555 | fastq.gz | 2.2 GB | ||
| EGAF50000219556 | fastq.gz | 2.2 GB | ||
| EGAF50000219557 | fastq.gz | 2.3 GB | ||
| EGAF50000219558 | fastq.gz | 2.1 GB | ||
| EGAF50000219559 | fastq.gz | 2.0 GB | ||
| EGAF50000219560 | fastq.gz | 1.9 GB | ||
| EGAF50000219561 | fastq.gz | 2.5 GB | ||
| EGAF50000219562 | fastq.gz | 2.4 GB | ||
| EGAF50000219563 | fastq.gz | 2.0 GB | ||
| EGAF50000219564 | fastq.gz | 2.1 GB | ||
| EGAF50000219565 | fastq.gz | 1.8 GB | ||
| EGAF50000219566 | fastq.gz | 1.7 GB | ||
| EGAF50000219567 | fastq.gz | 1.9 GB | ||
| EGAF50000219568 | fastq.gz | 2.0 GB | ||
| EGAF50000219569 | fastq.gz | 2.7 GB | ||
| EGAF50000219570 | fastq.gz | 2.9 GB | ||
| EGAF50000219571 | fastq.gz | 2.7 GB | ||
| EGAF50000219572 | fastq.gz | 2.5 GB | ||
| EGAF50000219573 | fastq.gz | 2.3 GB | ||
| EGAF50000219574 | fastq.gz | 2.5 GB | ||
| EGAF50000219575 | fastq.gz | 2.8 GB | ||
| EGAF50000219576 | fastq.gz | 2.6 GB | ||
| EGAF50000219577 | fastq.gz | 2.3 GB | ||
| EGAF50000219578 | fastq.gz | 2.2 GB | ||
| EGAF50000219579 | fastq.gz | 2.8 GB | ||
| EGAF50000219580 | fastq.gz | 2.7 GB | ||
| EGAF50000219581 | fastq.gz | 3.0 GB | ||
| EGAF50000219582 | fastq.gz | 2.8 GB | ||
| EGAF50000219583 | xlsx | 19.0 MB | ||
| 145 Files (314.4 GB) | ||||