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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).

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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
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 1642527000389 3.5 GB
EGAF00005776073 1642538342193 3.5 GB
EGAF00005776074 1642580640469 2.8 GB
EGAF00005776075 1642540209148 2.9 GB
EGAF00005776076 1642522682394 3.7 GB
EGAF00005776077 1642567862323 3.9 GB
EGAF00005776078 1642538646650 2.9 GB
EGAF00005776079 1642580701739 3.1 GB
EGAF00005776080 1642555020910 1.8 GB
EGAF00005776081 1642580044233 1.9 GB
EGAF00005776082 1642541460516 4.0 GB
EGAF00005776083 1642553402812 4.2 GB
EGAF00005776084 1642581480274 3.0 GB
EGAF00005776085 1642580185645 3.1 GB
EGAF00005776086 1642581074209 2.7 GB
EGAF00005776087 1642524660452 2.9 GB
EGAF00005776088 1642580522827 4.5 GB
EGAF00005776089 1642541340345 4.7 GB
EGAF00005776090 1642554292591 3.1 GB
EGAF00005776091 1642538285918 3.3 GB
EGAF00005776092 1642517340351 2.6 GB
EGAF00005776093 1642554292591 2.6 GB
EGAF00005776094 1642581600196 3.4 GB
EGAF00005776095 1642529640257 3.5 GB
EGAF00005776096 1642552802088 2.6 GB
EGAF00005776097 1642527061397 2.7 GB
EGAF00005776098 1642566423102 2.5 GB
EGAF00005776099 1642552440294 2.6 GB
EGAF00005776100 1642517400510 3.1 GB
EGAF00005776101 1642580762339 3.2 GB
EGAF00005776102 1642524060228 2.6 GB
EGAF00005776103 1642538160597 2.7 GB
EGAF00005776104 1642580460424 2.3 GB
EGAF00005776105 1642581074209 2.4 GB
EGAF00005776106 1642555500508 3.2 GB
EGAF00005776107 1642518082489 3.3 GB
EGAF00005776108 1642520341134 3.9 GB
EGAF00005776109 1642552802088 4.2 GB
EGAF00005776110 1642566362742 1.9 GB
EGAF00005776111 1642538764954 2.0 GB
EGAF00005776112 1642555500508 3.1 GB
EGAF00005776113 1642517460117 3.3 GB
EGAF00005776114 1642540562833 2.3 GB
EGAF00005776115 1642554840173 2.4 GB
EGAF00005776116 1642517520366 2.4 GB
EGAF00005776117 1642552920226 2.5 GB
EGAF00005776118 1642520761024 2.2 GB
EGAF00005776119 1642554292591 2.3 GB
EGAF00005776120 1642552200284 3.1 GB
EGAF00005776121 1642566423102 3.3 GB
EGAF00005776122 1642519202081 2.8 GB
EGAF00005776123 1642580943855 2.9 GB
EGAF00005776124 1642554292591 3.1 GB
EGAF00005776125 1642580100955 3.2 GB
EGAF00005776126 1642539802531 2.8 GB
EGAF00005776127 1642518720228 2.9 GB
EGAF00005776128 1642554723264 3.5 GB
EGAF00005776129 1642553162952 3.7 GB
EGAF00005776130 1642580400346 2.1 GB
EGAF00005776131 1642580044233 2.2 GB
EGAF00005776132 1642580589547 2.4 GB
EGAF00005776133 1642551540707 2.5 GB
EGAF00005776134 1642529110114 2.6 GB
EGAF00005776135 1642554360347 2.7 GB
EGAF00005776136 1642519141479 3.5 GB
EGAF00005776137 1642580882398 3.6 GB
EGAF00005776138 1642553466231 3.8 GB
EGAF00005776139 1642522741194 4.0 GB
EGAF00005776140 1642525571874 2.4 GB
EGAF00005776141 1642540620468 2.5 GB
EGAF00005776142 1642580762339 2.9 GB
EGAF00005776143 1642552560373 3.0 GB
EGAF00005776144 1642555500508 3.0 GB
EGAF00005776145 1642524660452 3.1 GB
EGAF00005776146 1642540381794 3.7 GB
EGAF00005776147 1642553521108 3.9 GB
EGAF00005776148 1642521480295 2.7 GB
EGAF00005776149 1642553588067 2.9 GB
EGAF00005776150 1642525687212 4.4 GB
EGAF00005776151 1642517760166 4.6 GB
EGAF00005776152 1642581007186 3.1 GB
EGAF00005776153 1642547109238 3.3 GB
EGAF00005776154 1642555140082 2.9 GB
EGAF00005776155 1642523642506 3.1 GB
EGAF00005776156 1642554292591 2.1 GB
EGAF00005776157 1642580640469 2.3 GB
EGAF00005776158 1642554543447 2.3 GB
EGAF00005776159 1642554292591 2.4 GB
EGAF00005776160 1642554360347 3.4 GB
EGAF00005776161 1642581192567 3.5 GB
EGAF00005776162 1642554723264 2.9 GB
EGAF00005776163 1642553521108 3.0 GB
EGAF00005776164 1642528021533 2.7 GB
EGAF00005776165 1642525571874 2.8 GB
EGAF00005776166 1642555380157 2.9 GB
EGAF00005776167 1642553162952 3.0 GB
EGAF00005776168 1642580943855 2.5 GB
EGAF00005776169 1642552920226 2.6 GB
EGAF00005776170 1642555380157 3.6 GB
EGAF00005776171 1642520580267 3.7 GB
EGAF00005776172 1642581074209 4.0 GB
EGAF00005776173 1642527840585 4.2 GB
EGAF00005776174 1642581074209 4.4 GB
EGAF00005776175 1642522321598 4.6 GB
EGAF00005776176 1642552861649 2.3 GB
EGAF00005776177 1642552560373 2.4 GB
EGAF00005776178 1642519740200 3.2 GB
EGAF00005776179 1642580282865 3.4 GB
EGAF00005776180 1642566067300 3.0 GB
EGAF00005776181 1642581127846 3.1 GB
EGAF00005776182 1642580882398 3.3 GB
EGAF00005776183 1642529110114 3.4 GB
EGAF00005776184 1642581664042 3.6 GB
EGAF00005776185 1642538580579 3.7 GB
EGAF00005776186 1642553340433 2.5 GB
EGAF00005776187 1642518541854 2.6 GB
EGAF00005776188 1642554543447 3.1 GB
EGAF00005776189 1642540209148 3.2 GB
EGAF00005776190 1642519502583 3.2 GB
EGAF00005776191 1642525571874 3.4 GB
EGAF00005776192 1642526101481 3.5 GB
EGAF00005776193 1642538285918 3.7 GB
EGAF00005776194 1642552382482 3.3 GB
EGAF00005776195 1642544043709 3.4 GB
EGAF00005776196 1642522202392 2.9 GB
EGAF00005776197 1642581367702 3.0 GB
EGAF00005776198 1642527600331 3.9 GB
EGAF00005776199 1642539180214 4.0 GB
EGAF00005776200 1642581007186 2.1 GB
EGAF00005776201 1642525861914 2.2 GB
EGAF00005776202 1642518480323 2.7 GB
EGAF00005776203 1642541822756 2.9 GB
EGAF00005776204 1642540686375 2.7 GB
EGAF00005776205 1642543672051 2.9 GB
EGAF00005776206 1642581425039 3.4 GB
EGAF00005776207 1642539613064 3.5 GB
EGAF00005776208 1642526582370 3.7 GB
EGAF00005776209 1642554723264 3.8 GB
EGAF00005776210 1642541700437 4.0 GB
EGAF00005776211 1642518960281 4.0 GB
EGAF00005776212 1642518300323 2.8 GB
EGAF00005776213 1642566120492 3.0 GB
EGAF00005776214 1642538101000 3.2 GB
EGAF00005776215 1642515600297 3.3 GB
EGAF00005776216 1642552140570 2.8 GB
EGAF00005776217 1642524960270 3.0 GB
EGAF00005776218 1642518082489 2.5 GB
EGAF00005776219 1642516500397 2.6 GB
EGAF00005776220 1642581783968 3.9 GB
EGAF00005776221 1642518600382 4.1 GB
EGAF00005776222 1642517520366 2.7 GB
EGAF00005776223 1642539300330 2.8 GB
EGAF00005776224 1642551964601 2.2 GB
EGAF00005776225 1642580100955 2.3 GB
EGAF00005776226 1642551840471 1.8 GB
EGAF00005776227 1642517100272 1.9 GB
EGAF00005776228 1642538580579 1.9 GB
EGAF00005776229 1642529400649 2.0 GB
EGAF00005776230 1642517460117 2.9 GB
EGAF00005776231 1642521480295 3.0 GB
EGAF00005776232 1642541640278 2.3 GB
EGAF00005776233 1642516620107 2.4 GB
EGAF00005776234 1642519260241 2.6 GB
EGAF00005776235 1642554480229 2.8 GB
EGAF00005776236 1642516020301 4.2 GB
EGAF00005776237 1642685340028 4.4 GB
EGAF00005776238 1642542480181 3.4 GB
EGAF00005776239 1642526050205 3.5 GB
EGAF00005776240 1642521960247 3.2 GB
EGAF00005776241 1642518960281 3.4 GB
EGAF00005776242 1642528680794 3.9 GB
EGAF00005776243 1642539480669 4.1 GB
EGAF00005776244 1642517585997 2.8 GB
EGAF00005776245 1642521780970 3.0 GB
EGAF00005776246 1642518720228 3.6 GB
EGAF00005776247 1642518120321 3.8 GB
EGAF00005776248 1642519560435 3.2 GB
EGAF00005776249 1642541223091 3.3 GB
EGAF00005776250 1642580701739 1.9 GB
EGAF00005776251 1642580701739 2.0 GB
EGAF00005776252 1642552140570 3.0 GB
EGAF00005776253 1642518120321 3.1 GB
EGAF00005776254 1642541880266 3.0 GB
EGAF00005776255 1642519381809 3.2 GB
EGAF00005776256 1642581367703 3.3 GB
EGAF00005776257 1642547160089 3.5 GB
EGAF00005776258 1642537981370 2.1 GB
EGAF00005776259 1642525802909 2.2 GB
EGAF00005776260 1642518082489 3.2 GB
EGAF00005776261 1642521000333 3.4 GB
EGAF00005776262 1642518480323 2.9 GB
EGAF00005776263 1642580589548 3.1 GB
EGAF00005776264 1642540860122 3.4 GB
EGAF00005776265 1642540686375 3.7 GB
EGAF00005776266 1642516800297 2.4 GB
EGAF00005776267 1642580762339 2.5 GB
EGAF00005776268 1642580822341 3.5 GB
EGAF00005776269 1642523702450 3.7 GB
EGAF00005776270 1642540686375 2.5 GB
EGAF00005776271 1642580640469 2.6 GB
EGAF00005776272 1642580100955 2.5 GB
EGAF00005776273 1642518842012 2.6 GB
EGAF00005776274 1642518420257 2.9 GB
EGAF00005776275 1642518541854 3.1 GB
EGAF00005776276 1642566904140 3.1 GB
EGAF00005776277 1642567202838 3.2 GB
EGAF00005776278 1642554292591 3.8 GB
EGAF00005776279 1642517700319 3.9 GB
EGAF00005776280 1642553402812 2.9 GB
EGAF00005776281 1642553281710 3.0 GB
EGAF00005776282 1642554480229 3.8 GB
EGAF00005776283 1642552382482 3.9 GB
EGAF00005776284 1642520341134 2.7 GB
EGAF00005776285 1642580100955 2.8 GB
EGAF00005776286 1642553402812 2.7 GB
EGAF00005776287 1642554900299 2.8 GB
EGAF00005776288 1642519560435 3.9 GB
EGAF00005776289 1642523880719 4.1 GB
EGAF00005776290 1642517160235 3.6 GB
EGAF00005776291 1642519680484 3.6 GB
EGAF00005776292 1642524360410 3.0 GB
EGAF00005776293 1642529703206 3.2 GB
EGAF00005776294 1642518541854 2.6 GB
EGAF00005776295 1642537745550 2.7 GB
EGAF00005776296 1642530000901 2.9 GB
EGAF00005776297 1642518842012 3.1 GB
EGAF00005776298 1642519560435 2.6 GB
EGAF00005776299 1642580460424 2.8 GB
EGAF00005776300 1642581367702 3.4 GB
EGAF00005776301 1642524660452 3.6 GB
EGAF00005776302 1642519440191 2.6 GB
EGAF00005776303 1642554292591 2.8 GB
EGAF00005776304 1642554606698 3.2 GB
EGAF00005776305 1642530482843 3.4 GB
EGAF00005776306 1642521420246 3.0 GB
EGAF00005776307 1642519620325 3.2 GB
EGAF00005776308 1642519502583 3.6 GB
EGAF00005776309 1642522572483 3.8 GB
EGAF00005776310 1642526222258 3.7 GB
EGAF00005776311 1642520341134 3.7 GB
EGAF00005776312 1642525571874 3.9 GB
EGAF00005776313 1642519260241 4.1 GB
EGAF00005776314 1642520940291 2.8 GB
EGAF00005776315 1642552500679 3.0 GB
EGAF00005776316 1642539541277 2.7 GB
EGAF00005776317 1642519502583 2.9 GB
EGAF00005776318 1642520160320 2.0 GB
EGAF00005776319 1642517220402 2.1 GB
EGAF00005776320 1642580589548 2.3 GB
EGAF00005776321 1642518082489 2.4 GB
EGAF00005776322 1642517400510 2.9 GB
EGAF00005776323 1642552320345 3.0 GB
EGAF00005776324 1642580943855 3.3 GB
EGAF00005776325 1642581425039 3.5 GB
EGAF00005776326 1642516200315 3.3 GB
EGAF00005776327 1642540686375 3.5 GB
EGAF00005776328 1642516560497 2.5 GB
EGAF00005776329 1642524360410 2.6 GB
EGAF00005776330 1642523880719 4.0 GB
EGAF00005776331 1642541460516 4.2 GB
EGAF00005776332 1642581367702 3.4 GB
EGAF00005776333 1642521900328 3.5 GB
EGAF00005776334 1642521240439 2.5 GB
EGAF00005776335 1642519502583 2.7 GB
EGAF00005776336 1642538285918 3.5 GB
EGAF00005776337 1642516200315 3.7 GB
EGAF00005776338 1642521678407 5.0 GB
EGAF00005776339 1642517820241 5.2 GB
EGAF00005776340 1642517340351 2.8 GB
EGAF00005776341 1642525571874 2.9 GB
EGAF00005776342 1642543860310 3.0 GB
EGAF00005776343 1642525571874 3.2 GB
EGAF00005776662 1642618980226 68.9 MB
273 Files (843.0 GB)