scRNA-seq of HSPC treated with gemcitabine and carboplatin
4 samples of 2000000 HSPCs in 2 ml media each were then prepared and treated for 24 hours: carboplatin-high: 150 µg/ml carboplatin carboplatin-low: 18.75 µg/ml carboplatin gemcitabine: 25 ng/ml gemcitabine control: no drug Single-cells were subsequently extracted using the ddSEQ™ Single-Cell Isolator (Bio-Rad) and later sequenced using the SureCell™ Whole Transcriptome Analysis 3' Library Prep Kit (Illumina) on the NextSeq 500 System (Illumina) using the NextSeq 500/550 High Output Kit v2.5 150 Cycles (Illumina) all following the manufacturer's instructions. The raw FASTQ-files are available as read 1 and read 2 files from 4 lanes for each sample giving a total of 16 FASTQ-files. The FASTQ-files were also processed following the ddSeeker (Romagnoli, D., et al., BMC Genomics 2018, doi:10.1186/s12864-018-5249-x) and Drop-seq (Macosko, E.Z., et al., Cell 2015, doi:10.1016/j.cell.2015.05.002) protocols for processing scRNA-seq data to yield the final digital gene expression (dge) for each cell of each sample. This has resulted in one dge text file and one dge summary text file per sample. These 8 text-files with dge data are found in the zip-compressed analysis data-file.
- 4 samples
- DAC: EGAC00001001559
- Technology: NextSeq 500
- HMB DUO:0000006 (version: 2019-01-07)health or medical or biomedical researchThis data use permission indicates that use is allowed for health/medical/biomedical purposes; does not include the study of population origins or ancestry.
- RU DUO:0000014 (version: 2019-01-07)research use onlyThis data use limitation indicates that use is limited to research purposes (e.g., does not include its use in clinical care).
- COL DUO:0000020 (version: 2019-01-07)collaboration requiredThis data use modifier indicates that the requestor must agree to collaboration with the primary study investigator(s).
data access policy for the data associated to scRNA-seq of HSPC treated with gemcitabine and carbplatin
###################################################### The data access policy and data access agreement for the associated data is restricted by the following data use ontology codes. DUO:0000006 - health/medical/biomedical research and clinical care. This consent code indicates that use of this data is allowed for health/medical/biomedical purposes, but does not include the study of population origins or ancestry. DUO:0000014 - research use only. This consent code indicates that the use of this data is limited to research purposes. DUO:0000020 - collaboration required. This consent code indicates a requirement that the requestor must agree to collaboration with the primary study investigator(s). The data available is limited to the raw sequencing data (FASTQ-files) of the 4 samples together with the associated processed digital gene expression files. ###################################################### Terms and Conditions of this Data Access Agreement: 1. You agree to use the Data only for the advancement of medical research, according to the data use ontology codes DUO:0000006, DUO:0000014, and DUO:0000020. 2. You agree to the required collaboration with the original primary study principal investigator and that the study will fall in line with the original consent obtained from sample donors. 3. You agree not to use the data or any part thereof for the creation of products for sale or for any commercial purpose. 4. You agree to preserve, at all times, the confidentiality of information and Data pertaining to Data Subjects. In particular, 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. 5. You agree not to attempt to link the data provided under this agreement to other information or archive data available for the data sets provided, even if access to that data has been formally granted to you, or it is freely available without restriction, without specific permission being sought from the relevant access committees. 6. You agree not to transfer or disclose the Data, in whole or part, or any identifiable material derived from the Data to others, except as necessary for data/safety monitoring or programme management. Should You wish to share the Data with a collaborator outwith the same Institution, a revised application to include the collaborator must be submitted and the third party must sign the Data Access Agreement. 7. You agree to use the data for the approved purpose and project described in your application; use of the data for a new purpose or project will require a new application and approval. 8. You accept that Data will be reissued from time to time, with suitable versioning. If the reissue is at the request of sample donors and/or another ethical scrutiny, You will destroy earlier versions of the Data. 9. You agree to acknowledge in any work based in whole or part on the Data, the original published paper from which the Data derives. 10. You accept that the data access committee, the original data creators, depositors or copyright holders, or the funders of the Data or any part of the Data supplied: a) bear no legal responsibility for the accuracy or comprehensiveness of the Data, and b) accept no liability for indirect, consequential, or incidental, damages or losses arising from use of the Data, or from the unavailability of, or break in access to, the Data for whatever reason. 11. You understand and acknowledge that the Data is protected by copyright and other intellectual property rights, and that duplication, except as reasonably required to carry out Your research with the Data, or sale of all or part of the Data on any media is not permitted. 12. You recognise that nothing in this agreement shall operate to transfer to the User Institution any intellectual property rights relating to the Data. The User Institution has the right to develop an intellectual property based on comparisons with their own data. 13. You accept that this agreement will terminate immediately upon any breach of this agreement by You and You will be required to destroy any Data held. 14. You accept that it may be necessary for the data access committee, or their appointed agents to alter the terms of this agreement from time to time in order to address new concerns. In this event, You will be contacted and informed of any changes and Your continued use of the Data shall be dependent on all parties entering into a new version of the Agreement. 15. You agree that you will submit a report to the data access committee, if requested, on completion of the agreed purpose. The data access committee agrees to treat the report and all information, data, results, and conclusions contained within such report as confidential information belonging to the User Institution. 16. You accept that the Data is protected by and subject to international laws, including but not limited to GDPR, and that You are responsible for ensuring compliance with any such applicable law. The data access committee reserves the right to request and inspect data security and management documentation to ensure the adequacy of data protection measures in countries that have no national laws comparable to that which pertain in the EAA. 17. This agreement shall be interpreted and construed in accordance with the laws of the country of the defending party, original study, Linköping University, and Region Östergötland. Unless specified otherwise, reference in this agreement to a statute refers to that statute as it may be amended, or to any restated or successor legislation of comparable effect. Agreement I have read and agree to abide by the terms and conditions outlined in the Data Access Agreement and Data Access Policy Name: Institution: Signature : ######################################################
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 |
|---|---|---|
| EGAS00001004381 | 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 | |
|---|---|---|---|---|
| EGAF00003614182 | fastq.gz | 161.3 MB | ||
| EGAF00003614183 | fastq.gz | 353.2 MB | ||
| EGAF00003614184 | fastq.gz | 178.1 MB | ||
| EGAF00003614185 | fastq.gz | 387.9 MB | ||
| EGAF00003614186 | fastq.gz | 183.3 MB | ||
| EGAF00003614187 | fastq.gz | 397.7 MB | ||
| EGAF00003614188 | fastq.gz | 486.2 MB | ||
| EGAF00003614189 | fastq.gz | 1.0 GB | ||
| EGAF00003614190 | fastq.gz | 489.4 MB | ||
| EGAF00003614191 | fastq.gz | 1.0 GB | ||
| EGAF00003614192 | fastq.gz | 507.6 MB | ||
| EGAF00003614193 | fastq.gz | 1.1 GB | ||
| EGAF00003614194 | fastq.gz | 520.1 MB | ||
| EGAF00003614195 | fastq.gz | 1.1 GB | ||
| EGAF00003614196 | fastq.gz | 159.5 MB | ||
| EGAF00003614197 | fastq.gz | 349.4 MB | ||
| EGAF00003614198 | fastq.gz | 237.2 MB | ||
| EGAF00003614199 | fastq.gz | 517.5 MB | ||
| EGAF00003614200 | fastq.gz | 240.4 MB | ||
| EGAF00003614201 | fastq.gz | 525.1 MB | ||
| EGAF00003614202 | fastq.gz | 257.2 MB | ||
| EGAF00003614203 | fastq.gz | 558.6 MB | ||
| EGAF00003614204 | fastq.gz | 264.3 MB | ||
| EGAF00003614205 | fastq.gz | 571.9 MB | ||
| EGAF00003614206 | fastq.gz | 400.9 MB | ||
| EGAF00003614207 | fastq.gz | 886.3 MB | ||
| EGAF00003614208 | fastq.gz | 404.3 MB | ||
| EGAF00003614209 | fastq.gz | 894.1 MB | ||
| EGAF00003614210 | fastq.gz | 437.5 MB | ||
| EGAF00003614211 | fastq.gz | 961.4 MB | ||
| EGAF00003614212 | fastq.gz | 449.5 MB | ||
| EGAF00003614213 | fastq.gz | 983.9 MB | ||
| EGAF00003614214 | 7z | 3.0 MB | ||
| 33 Files (17.0 GB) | ||||