AML Proteogenomic Landscape Whole-transcriptome RNA-Sequencing
Whole transcriptome RNA-sequencing of purified bone marrow blasts of 136 de novo, treatment naive AML patients. For further details, we refer to the manuscript "The Proteogenomic Landscape of AML" by Jayavelu, Wolf, Buettner et al. mRNA extraction and whole transcriptome sequencing For transcriptome analysis the TruSeq Total Stranded RNA kit was used, starting with 250ng of total RNA, to generate RNA libraries following the manufacturer’s recommendations (Illumina, San Diego, CA, USA). 100bp paired-end reads were sequenced on the NovaSeq 6000 (Illumina) with a median of 57 mio. reads per sample. RNA Data Analysis Data quality control was performed with FastQC v0.11.9. Reads were aligned to the human reference genome (Ensembl GRCh38 release 82) using STAR v2.6.1. Gene count tables were generated while mapping, using Gencode v31 annotations. All downstream analyses were carried out using R v4.0 and BioConductor v3.12 (Huber et al., 2015; R Core Team, 2020). Size-factor based normalization was performed using DESeq2 v1.28.1(Love et al., 2014).
- 177 samples
- DAC: EGAC00001002483
- Technology: Illumina NovaSeq 6000
DAP for genomic sequencing data generated as part of the "AML proteogenomic landscape" paper.
In requesting access to and retrieving data from this repository: 1. You agree to use the Data only for the advancement of medical research, according to the consent obtained from sample donors. 2. You agree not to use the data or any part thereof for the creation of products for sale or for any commercial purpose. 3. 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. 4. 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 relevent access committees. 5. 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, the third party must make a separate application for access to the Data. 6. 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. 7. 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 other 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 published paper from which the Data derives, the version of the data, and the role of the authors and the relevant primary collectors and their funders. Suitable wording is provided upon request. 10. You accept that the authors, represented by the data accessing 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 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 authors, represented by the data accessing committee, or its appointed agent to alter the terms of this agreement from time to time in order to address new concerns. In this event, the authors, represented by the data accessing committee, or its appointed agent will contact You to inform You of any changes and You agree that Your continued use of the Data shall be dependent on the 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 the “Gendiagnostikgesetzt”, the EU General Data Protection Regulation (GDPR), and that You are responsible for ensuring compliance with any such applicable law. The Consortium 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 EU. 17. This agreement shall be construed, interpreted and governed by the laws of the Federal Republic of Germany and the European Union and shall be subject to the non-exclusive jurisdiction of the german and european 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 |
|---|---|---|
| EGAS00001005950 | 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 | |
|---|---|---|---|---|
| EGAF00005776072 | fastq.gz | 3.5 GB | ||
| EGAF00005776073 | fastq.gz | 3.5 GB | ||
| EGAF00005776074 | fastq.gz | 2.8 GB | ||
| EGAF00005776075 | fastq.gz | 2.9 GB | ||
| EGAF00005776076 | fastq.gz | 3.7 GB | ||
| EGAF00005776077 | fastq.gz | 3.9 GB | ||
| EGAF00005776078 | fastq.gz | 2.9 GB | ||
| EGAF00005776079 | fastq.gz | 3.1 GB | ||
| EGAF00005776080 | fastq.gz | 1.8 GB | ||
| EGAF00005776081 | fastq.gz | 1.9 GB | ||
| EGAF00005776082 | fastq.gz | 4.0 GB | ||
| EGAF00005776083 | fastq.gz | 4.2 GB | ||
| EGAF00005776084 | fastq.gz | 3.0 GB | ||
| EGAF00005776085 | fastq.gz | 3.1 GB | ||
| EGAF00005776086 | fastq.gz | 2.7 GB | ||
| EGAF00005776087 | fastq.gz | 2.9 GB | ||
| EGAF00005776088 | fastq.gz | 4.5 GB | ||
| EGAF00005776089 | fastq.gz | 4.7 GB | ||
| EGAF00005776090 | fastq.gz | 3.1 GB | ||
| EGAF00005776091 | fastq.gz | 3.3 GB | ||
| EGAF00005776092 | fastq.gz | 2.6 GB | ||
| EGAF00005776093 | fastq.gz | 2.6 GB | ||
| EGAF00005776094 | fastq.gz | 3.4 GB | ||
| EGAF00005776095 | fastq.gz | 3.5 GB | ||
| EGAF00005776096 | fastq.gz | 2.6 GB | ||
| EGAF00005776097 | fastq.gz | 2.7 GB | ||
| EGAF00005776098 | fastq.gz | 2.5 GB | ||
| EGAF00005776099 | fastq.gz | 2.6 GB | ||
| EGAF00005776100 | fastq.gz | 3.1 GB | ||
| EGAF00005776101 | fastq.gz | 3.2 GB | ||
| EGAF00005776102 | fastq.gz | 2.6 GB | ||
| EGAF00005776103 | fastq.gz | 2.7 GB | ||
| EGAF00005776104 | fastq.gz | 2.3 GB | ||
| EGAF00005776105 | fastq.gz | 2.4 GB | ||
| EGAF00005776106 | fastq.gz | 3.2 GB | ||
| EGAF00005776107 | fastq.gz | 3.3 GB | ||
| EGAF00005776108 | fastq.gz | 3.9 GB | ||
| EGAF00005776109 | fastq.gz | 4.2 GB | ||
| EGAF00005776110 | fastq.gz | 1.9 GB | ||
| EGAF00005776111 | fastq.gz | 2.0 GB | ||
| EGAF00005776112 | fastq.gz | 3.1 GB | ||
| EGAF00005776113 | fastq.gz | 3.3 GB | ||
| EGAF00005776114 | fastq.gz | 2.3 GB | ||
| EGAF00005776115 | fastq.gz | 2.4 GB | ||
| EGAF00005776116 | fastq.gz | 2.4 GB | ||
| EGAF00005776117 | fastq.gz | 2.5 GB | ||
| EGAF00005776118 | fastq.gz | 2.2 GB | ||
| EGAF00005776119 | fastq.gz | 2.3 GB | ||
| EGAF00005776120 | fastq.gz | 3.1 GB | ||
| EGAF00005776121 | fastq.gz | 3.3 GB | ||
| EGAF00005776122 | fastq.gz | 2.8 GB | ||
| EGAF00005776123 | fastq.gz | 2.9 GB | ||
| EGAF00005776124 | fastq.gz | 3.1 GB | ||
| EGAF00005776125 | fastq.gz | 3.2 GB | ||
| EGAF00005776126 | fastq.gz | 2.8 GB | ||
| EGAF00005776127 | fastq.gz | 2.9 GB | ||
| EGAF00005776128 | fastq.gz | 3.5 GB | ||
| EGAF00005776129 | fastq.gz | 3.7 GB | ||
| EGAF00005776130 | fastq.gz | 2.1 GB | ||
| EGAF00005776131 | fastq.gz | 2.2 GB | ||
| EGAF00005776132 | fastq.gz | 2.4 GB | ||
| EGAF00005776133 | fastq.gz | 2.5 GB | ||
| EGAF00005776134 | fastq.gz | 2.6 GB | ||
| EGAF00005776135 | fastq.gz | 2.7 GB | ||
| EGAF00005776136 | fastq.gz | 3.5 GB | ||
| EGAF00005776137 | fastq.gz | 3.6 GB | ||
| EGAF00005776138 | fastq.gz | 3.8 GB | ||
| EGAF00005776139 | fastq.gz | 4.0 GB | ||
| EGAF00005776140 | fastq.gz | 2.4 GB | ||
| EGAF00005776141 | fastq.gz | 2.5 GB | ||
| EGAF00005776142 | fastq.gz | 2.9 GB | ||
| EGAF00005776143 | fastq.gz | 3.0 GB | ||
| EGAF00005776144 | fastq.gz | 3.0 GB | ||
| EGAF00005776145 | fastq.gz | 3.1 GB | ||
| EGAF00005776146 | fastq.gz | 3.7 GB | ||
| EGAF00005776147 | fastq.gz | 3.9 GB | ||
| EGAF00005776148 | fastq.gz | 2.7 GB | ||
| EGAF00005776149 | fastq.gz | 2.9 GB | ||
| EGAF00005776150 | fastq.gz | 4.4 GB | ||
| EGAF00005776151 | fastq.gz | 4.6 GB | ||
| EGAF00005776152 | fastq.gz | 3.1 GB | ||
| EGAF00005776153 | fastq.gz | 3.3 GB | ||
| EGAF00005776154 | fastq.gz | 2.9 GB | ||
| EGAF00005776155 | fastq.gz | 3.1 GB | ||
| EGAF00005776156 | fastq.gz | 2.1 GB | ||
| EGAF00005776157 | fastq.gz | 2.3 GB | ||
| EGAF00005776158 | fastq.gz | 2.3 GB | ||
| EGAF00005776159 | fastq.gz | 2.4 GB | ||
| EGAF00005776160 | fastq.gz | 3.4 GB | ||
| EGAF00005776161 | fastq.gz | 3.5 GB | ||
| EGAF00005776162 | fastq.gz | 2.9 GB | ||
| EGAF00005776163 | fastq.gz | 3.0 GB | ||
| EGAF00005776164 | fastq.gz | 2.7 GB | ||
| EGAF00005776165 | fastq.gz | 2.8 GB | ||
| EGAF00005776166 | fastq.gz | 2.9 GB | ||
| EGAF00005776167 | fastq.gz | 3.0 GB | ||
| EGAF00005776168 | fastq.gz | 2.5 GB | ||
| EGAF00005776169 | fastq.gz | 2.6 GB | ||
| EGAF00005776170 | fastq.gz | 3.6 GB | ||
| EGAF00005776171 | fastq.gz | 3.7 GB | ||
| EGAF00005776172 | fastq.gz | 4.0 GB | ||
| EGAF00005776173 | fastq.gz | 4.2 GB | ||
| EGAF00005776174 | fastq.gz | 4.4 GB | ||
| EGAF00005776175 | fastq.gz | 4.6 GB | ||
| EGAF00005776176 | fastq.gz | 2.3 GB | ||
| EGAF00005776177 | fastq.gz | 2.4 GB | ||
| EGAF00005776178 | fastq.gz | 3.2 GB | ||
| EGAF00005776179 | fastq.gz | 3.4 GB | ||
| EGAF00005776180 | fastq.gz | 3.0 GB | ||
| EGAF00005776181 | fastq.gz | 3.1 GB | ||
| EGAF00005776182 | fastq.gz | 3.3 GB | ||
| EGAF00005776183 | fastq.gz | 3.4 GB | ||
| EGAF00005776184 | fastq.gz | 3.6 GB | ||
| EGAF00005776185 | fastq.gz | 3.7 GB | ||
| EGAF00005776186 | fastq.gz | 2.5 GB | ||
| EGAF00005776187 | fastq.gz | 2.6 GB | ||
| EGAF00005776188 | fastq.gz | 3.1 GB | ||
| EGAF00005776189 | fastq.gz | 3.2 GB | ||
| EGAF00005776190 | fastq.gz | 3.2 GB | ||
| EGAF00005776191 | fastq.gz | 3.4 GB | ||
| EGAF00005776192 | fastq.gz | 3.5 GB | ||
| EGAF00005776193 | fastq.gz | 3.7 GB | ||
| EGAF00005776194 | fastq.gz | 3.3 GB | ||
| EGAF00005776195 | fastq.gz | 3.4 GB | ||
| EGAF00005776196 | fastq.gz | 2.9 GB | ||
| EGAF00005776197 | fastq.gz | 3.0 GB | ||
| EGAF00005776198 | fastq.gz | 3.9 GB | ||
| EGAF00005776199 | fastq.gz | 4.0 GB | ||
| EGAF00005776200 | fastq.gz | 2.1 GB | ||
| EGAF00005776201 | fastq.gz | 2.2 GB | ||
| EGAF00005776202 | fastq.gz | 2.7 GB | ||
| EGAF00005776203 | fastq.gz | 2.9 GB | ||
| EGAF00005776204 | fastq.gz | 2.7 GB | ||
| EGAF00005776205 | fastq.gz | 2.9 GB | ||
| EGAF00005776206 | fastq.gz | 3.4 GB | ||
| EGAF00005776207 | fastq.gz | 3.5 GB | ||
| EGAF00005776208 | fastq.gz | 3.7 GB | ||
| EGAF00005776209 | fastq.gz | 3.8 GB | ||
| EGAF00005776210 | fastq.gz | 4.0 GB | ||
| EGAF00005776211 | fastq.gz | 4.0 GB | ||
| EGAF00005776212 | fastq.gz | 2.8 GB | ||
| EGAF00005776213 | fastq.gz | 3.0 GB | ||
| EGAF00005776214 | fastq.gz | 3.2 GB | ||
| EGAF00005776215 | fastq.gz | 3.3 GB | ||
| EGAF00005776216 | fastq.gz | 2.8 GB | ||
| EGAF00005776217 | fastq.gz | 3.0 GB | ||
| EGAF00005776218 | fastq.gz | 2.5 GB | ||
| EGAF00005776219 | fastq.gz | 2.6 GB | ||
| EGAF00005776220 | fastq.gz | 3.9 GB | ||
| EGAF00005776221 | fastq.gz | 4.1 GB | ||
| EGAF00005776222 | fastq.gz | 2.7 GB | ||
| EGAF00005776223 | fastq.gz | 2.8 GB | ||
| EGAF00005776224 | fastq.gz | 2.2 GB | ||
| EGAF00005776225 | fastq.gz | 2.3 GB | ||
| EGAF00005776226 | fastq.gz | 1.8 GB | ||
| EGAF00005776227 | fastq.gz | 1.9 GB | ||
| EGAF00005776228 | fastq.gz | 1.9 GB | ||
| EGAF00005776229 | fastq.gz | 2.0 GB | ||
| EGAF00005776230 | fastq.gz | 2.9 GB | ||
| EGAF00005776231 | fastq.gz | 3.0 GB | ||
| EGAF00005776232 | fastq.gz | 2.3 GB | ||
| EGAF00005776233 | fastq.gz | 2.4 GB | ||
| EGAF00005776234 | fastq.gz | 2.6 GB | ||
| EGAF00005776235 | fastq.gz | 2.8 GB | ||
| EGAF00005776236 | fastq.gz | 4.2 GB | ||
| EGAF00005776237 | fastq.gz | 4.4 GB | ||
| EGAF00005776238 | fastq.gz | 3.4 GB | ||
| EGAF00005776239 | fastq.gz | 3.5 GB | ||
| EGAF00005776240 | fastq.gz | 3.2 GB | ||
| EGAF00005776241 | fastq.gz | 3.4 GB | ||
| EGAF00005776242 | fastq.gz | 3.9 GB | ||
| EGAF00005776243 | fastq.gz | 4.1 GB | ||
| EGAF00005776244 | fastq.gz | 2.8 GB | ||
| EGAF00005776245 | fastq.gz | 3.0 GB | ||
| EGAF00005776246 | fastq.gz | 3.6 GB | ||
| EGAF00005776247 | fastq.gz | 3.8 GB | ||
| EGAF00005776248 | fastq.gz | 3.2 GB | ||
| EGAF00005776249 | fastq.gz | 3.3 GB | ||
| EGAF00005776250 | fastq.gz | 1.9 GB | ||
| EGAF00005776251 | fastq.gz | 2.0 GB | ||
| EGAF00005776252 | fastq.gz | 3.0 GB | ||
| EGAF00005776253 | fastq.gz | 3.1 GB | ||
| EGAF00005776254 | fastq.gz | 3.0 GB | ||
| EGAF00005776255 | fastq.gz | 3.2 GB | ||
| EGAF00005776256 | fastq.gz | 3.3 GB | ||
| EGAF00005776257 | fastq.gz | 3.5 GB | ||
| EGAF00005776258 | fastq.gz | 2.1 GB | ||
| EGAF00005776259 | fastq.gz | 2.2 GB | ||
| EGAF00005776260 | fastq.gz | 3.2 GB | ||
| EGAF00005776261 | fastq.gz | 3.4 GB | ||
| EGAF00005776262 | fastq.gz | 2.9 GB | ||
| EGAF00005776263 | fastq.gz | 3.1 GB | ||
| EGAF00005776264 | fastq.gz | 3.4 GB | ||
| EGAF00005776265 | fastq.gz | 3.7 GB | ||
| EGAF00005776266 | fastq.gz | 2.4 GB | ||
| EGAF00005776267 | fastq.gz | 2.5 GB | ||
| EGAF00005776268 | fastq.gz | 3.5 GB | ||
| EGAF00005776269 | fastq.gz | 3.7 GB | ||
| EGAF00005776270 | fastq.gz | 2.5 GB | ||
| EGAF00005776271 | fastq.gz | 2.6 GB | ||
| EGAF00005776272 | fastq.gz | 2.5 GB | ||
| EGAF00005776273 | fastq.gz | 2.6 GB | ||
| EGAF00005776274 | fastq.gz | 2.9 GB | ||
| EGAF00005776275 | fastq.gz | 3.1 GB | ||
| EGAF00005776276 | fastq.gz | 3.1 GB | ||
| EGAF00005776277 | fastq.gz | 3.2 GB | ||
| EGAF00005776278 | fastq.gz | 3.8 GB | ||
| EGAF00005776279 | fastq.gz | 3.9 GB | ||
| EGAF00005776280 | fastq.gz | 2.9 GB | ||
| EGAF00005776281 | fastq.gz | 3.0 GB | ||
| EGAF00005776282 | fastq.gz | 3.8 GB | ||
| EGAF00005776283 | fastq.gz | 3.9 GB | ||
| EGAF00005776284 | fastq.gz | 2.7 GB | ||
| EGAF00005776285 | fastq.gz | 2.8 GB | ||
| EGAF00005776286 | fastq.gz | 2.7 GB | ||
| EGAF00005776287 | fastq.gz | 2.8 GB | ||
| EGAF00005776288 | fastq.gz | 3.9 GB | ||
| EGAF00005776289 | fastq.gz | 4.1 GB | ||
| EGAF00005776290 | fastq.gz | 3.6 GB | ||
| EGAF00005776291 | fastq.gz | 3.6 GB | ||
| EGAF00005776292 | fastq.gz | 3.0 GB | ||
| EGAF00005776293 | fastq.gz | 3.2 GB | ||
| EGAF00005776294 | fastq.gz | 2.6 GB | ||
| EGAF00005776295 | fastq.gz | 2.7 GB | ||
| EGAF00005776296 | fastq.gz | 2.9 GB | ||
| EGAF00005776297 | fastq.gz | 3.1 GB | ||
| EGAF00005776298 | fastq.gz | 2.6 GB | ||
| EGAF00005776299 | fastq.gz | 2.8 GB | ||
| EGAF00005776300 | fastq.gz | 3.4 GB | ||
| EGAF00005776301 | fastq.gz | 3.6 GB | ||
| EGAF00005776302 | fastq.gz | 2.6 GB | ||
| EGAF00005776303 | fastq.gz | 2.8 GB | ||
| EGAF00005776304 | fastq.gz | 3.2 GB | ||
| EGAF00005776305 | fastq.gz | 3.4 GB | ||
| EGAF00005776306 | fastq.gz | 3.0 GB | ||
| EGAF00005776307 | fastq.gz | 3.2 GB | ||
| EGAF00005776308 | fastq.gz | 3.6 GB | ||
| EGAF00005776309 | fastq.gz | 3.8 GB | ||
| EGAF00005776310 | fastq.gz | 3.7 GB | ||
| EGAF00005776311 | fastq.gz | 3.7 GB | ||
| EGAF00005776312 | fastq.gz | 3.9 GB | ||
| EGAF00005776313 | fastq.gz | 4.1 GB | ||
| EGAF00005776314 | fastq.gz | 2.8 GB | ||
| EGAF00005776315 | fastq.gz | 3.0 GB | ||
| EGAF00005776316 | fastq.gz | 2.7 GB | ||
| EGAF00005776317 | fastq.gz | 2.9 GB | ||
| EGAF00005776318 | fastq.gz | 2.0 GB | ||
| EGAF00005776319 | fastq.gz | 2.1 GB | ||
| EGAF00005776320 | fastq.gz | 2.3 GB | ||
| EGAF00005776321 | fastq.gz | 2.4 GB | ||
| EGAF00005776322 | fastq.gz | 2.9 GB | ||
| EGAF00005776323 | fastq.gz | 3.0 GB | ||
| EGAF00005776324 | fastq.gz | 3.3 GB | ||
| EGAF00005776325 | fastq.gz | 3.5 GB | ||
| EGAF00005776326 | fastq.gz | 3.3 GB | ||
| EGAF00005776327 | fastq.gz | 3.5 GB | ||
| EGAF00005776328 | fastq.gz | 2.5 GB | ||
| EGAF00005776329 | fastq.gz | 2.6 GB | ||
| EGAF00005776330 | fastq.gz | 4.0 GB | ||
| EGAF00005776331 | fastq.gz | 4.2 GB | ||
| EGAF00005776332 | fastq.gz | 3.4 GB | ||
| EGAF00005776333 | fastq.gz | 3.5 GB | ||
| EGAF00005776334 | fastq.gz | 2.5 GB | ||
| EGAF00005776335 | fastq.gz | 2.7 GB | ||
| EGAF00005776336 | fastq.gz | 3.5 GB | ||
| EGAF00005776337 | fastq.gz | 3.7 GB | ||
| EGAF00005776338 | fastq.gz | 5.0 GB | ||
| EGAF00005776339 | fastq.gz | 5.2 GB | ||
| EGAF00005776340 | fastq.gz | 2.8 GB | ||
| EGAF00005776341 | fastq.gz | 2.9 GB | ||
| EGAF00005776342 | fastq.gz | 3.0 GB | ||
| EGAF00005776343 | fastq.gz | 3.2 GB | ||
| EGAF00005776662 | txt | 68.9 MB | ||
| 273 Files (843.0 GB) | ||||