About file location

As the EGA is co-managed by the EMBL-EBI and CRG, files could be located in the UK and/or Spain, as indicated by their respective flags.

Alternatively, files could be located in one of the international Federated EGA nodes, as indicated next to the node's flag.
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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).

Request Access

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 Quality Report
Located in
i
EGAF00005776072 fastq.gz 3.5 GB Report
EGAF00005776073 fastq.gz 3.5 GB Report
EGAF00005776074 fastq.gz 2.8 GB Report
EGAF00005776075 fastq.gz 2.9 GB Report
EGAF00005776076 fastq.gz 3.7 GB Report
EGAF00005776077 fastq.gz 3.9 GB Report
EGAF00005776078 fastq.gz 2.9 GB Report
EGAF00005776079 fastq.gz 3.1 GB Report
EGAF00005776080 fastq.gz 1.8 GB Report
EGAF00005776081 fastq.gz 1.9 GB Report
EGAF00005776082 fastq.gz 4.0 GB Report
EGAF00005776083 fastq.gz 4.2 GB Report
EGAF00005776084 fastq.gz 3.0 GB Report
EGAF00005776085 fastq.gz 3.1 GB Report
EGAF00005776086 fastq.gz 2.7 GB Report
EGAF00005776087 fastq.gz 2.9 GB Report
EGAF00005776088 fastq.gz 4.5 GB Report
EGAF00005776089 fastq.gz 4.7 GB Report
EGAF00005776090 fastq.gz 3.1 GB Report
EGAF00005776091 fastq.gz 3.3 GB Report
EGAF00005776092 fastq.gz 2.6 GB Report
EGAF00005776093 fastq.gz 2.6 GB Report
EGAF00005776094 fastq.gz 3.4 GB Report
EGAF00005776095 fastq.gz 3.5 GB Report
EGAF00005776096 fastq.gz 2.6 GB Report
EGAF00005776097 fastq.gz 2.7 GB Report
EGAF00005776098 fastq.gz 2.5 GB Report
EGAF00005776099 fastq.gz 2.6 GB Report
EGAF00005776100 fastq.gz 3.1 GB Report
EGAF00005776101 fastq.gz 3.2 GB Report
EGAF00005776102 fastq.gz 2.6 GB Report
EGAF00005776103 fastq.gz 2.7 GB Report
EGAF00005776104 fastq.gz 2.3 GB Report
EGAF00005776105 fastq.gz 2.4 GB Report
EGAF00005776106 fastq.gz 3.2 GB Report
EGAF00005776107 fastq.gz 3.3 GB Report
EGAF00005776108 fastq.gz 3.9 GB Report
EGAF00005776109 fastq.gz 4.2 GB Report
EGAF00005776110 fastq.gz 1.9 GB Report
EGAF00005776111 fastq.gz 2.0 GB Report
EGAF00005776112 fastq.gz 3.1 GB Report
EGAF00005776113 fastq.gz 3.3 GB Report
EGAF00005776114 fastq.gz 2.3 GB Report
EGAF00005776115 fastq.gz 2.4 GB Report
EGAF00005776116 fastq.gz 2.4 GB Report
EGAF00005776117 fastq.gz 2.5 GB Report
EGAF00005776118 fastq.gz 2.2 GB Report
EGAF00005776119 fastq.gz 2.3 GB Report
EGAF00005776120 fastq.gz 3.1 GB Report
EGAF00005776121 fastq.gz 3.3 GB Report
EGAF00005776122 fastq.gz 2.8 GB Report
EGAF00005776123 fastq.gz 2.9 GB Report
EGAF00005776124 fastq.gz 3.1 GB Report
EGAF00005776125 fastq.gz 3.2 GB Report
EGAF00005776126 fastq.gz 2.8 GB Report
EGAF00005776127 fastq.gz 2.9 GB Report
EGAF00005776128 fastq.gz 3.5 GB Report
EGAF00005776129 fastq.gz 3.7 GB Report
EGAF00005776130 fastq.gz 2.1 GB Report
EGAF00005776131 fastq.gz 2.2 GB Report
EGAF00005776132 fastq.gz 2.4 GB Report
EGAF00005776133 fastq.gz 2.5 GB Report
EGAF00005776134 fastq.gz 2.6 GB Report
EGAF00005776135 fastq.gz 2.7 GB Report
EGAF00005776136 fastq.gz 3.5 GB Report
EGAF00005776137 fastq.gz 3.6 GB Report
EGAF00005776138 fastq.gz 3.8 GB Report
EGAF00005776139 fastq.gz 4.0 GB Report
EGAF00005776140 fastq.gz 2.4 GB Report
EGAF00005776141 fastq.gz 2.5 GB Report
EGAF00005776142 fastq.gz 2.9 GB Report
EGAF00005776143 fastq.gz 3.0 GB Report
EGAF00005776144 fastq.gz 3.0 GB Report
EGAF00005776145 fastq.gz 3.1 GB Report
EGAF00005776146 fastq.gz 3.7 GB Report
EGAF00005776147 fastq.gz 3.9 GB Report
EGAF00005776148 fastq.gz 2.7 GB Report
EGAF00005776149 fastq.gz 2.9 GB Report
EGAF00005776150 fastq.gz 4.4 GB Report
EGAF00005776151 fastq.gz 4.6 GB Report
EGAF00005776152 fastq.gz 3.1 GB Report
EGAF00005776153 fastq.gz 3.3 GB Report
EGAF00005776154 fastq.gz 2.9 GB Report
EGAF00005776155 fastq.gz 3.1 GB Report
EGAF00005776156 fastq.gz 2.1 GB Report
EGAF00005776157 fastq.gz 2.3 GB Report
EGAF00005776158 fastq.gz 2.3 GB Report
EGAF00005776159 fastq.gz 2.4 GB Report
EGAF00005776160 fastq.gz 3.4 GB Report
EGAF00005776161 fastq.gz 3.5 GB Report
EGAF00005776162 fastq.gz 2.9 GB Report
EGAF00005776163 fastq.gz 3.0 GB Report
EGAF00005776164 fastq.gz 2.7 GB Report
EGAF00005776165 fastq.gz 2.8 GB Report
EGAF00005776166 fastq.gz 2.9 GB Report
EGAF00005776167 fastq.gz 3.0 GB Report
EGAF00005776168 fastq.gz 2.5 GB Report
EGAF00005776169 fastq.gz 2.6 GB Report
EGAF00005776170 fastq.gz 3.6 GB Report
EGAF00005776171 fastq.gz 3.7 GB Report
EGAF00005776172 fastq.gz 4.0 GB Report
EGAF00005776173 fastq.gz 4.2 GB Report
EGAF00005776174 fastq.gz 4.4 GB Report
EGAF00005776175 fastq.gz 4.6 GB Report
EGAF00005776176 fastq.gz 2.3 GB Report
EGAF00005776177 fastq.gz 2.4 GB Report
EGAF00005776178 fastq.gz 3.2 GB Report
EGAF00005776179 fastq.gz 3.4 GB Report
EGAF00005776180 fastq.gz 3.0 GB Report
EGAF00005776181 fastq.gz 3.1 GB Report
EGAF00005776182 fastq.gz 3.3 GB Report
EGAF00005776183 fastq.gz 3.4 GB Report
EGAF00005776184 fastq.gz 3.6 GB Report
EGAF00005776185 fastq.gz 3.7 GB Report
EGAF00005776186 fastq.gz 2.5 GB Report
EGAF00005776187 fastq.gz 2.6 GB Report
EGAF00005776188 fastq.gz 3.1 GB Report
EGAF00005776189 fastq.gz 3.2 GB Report
EGAF00005776190 fastq.gz 3.2 GB Report
EGAF00005776191 fastq.gz 3.4 GB Report
EGAF00005776192 fastq.gz 3.5 GB Report
EGAF00005776193 fastq.gz 3.7 GB Report
EGAF00005776194 fastq.gz 3.3 GB Report
EGAF00005776195 fastq.gz 3.4 GB Report
EGAF00005776196 fastq.gz 2.9 GB Report
EGAF00005776197 fastq.gz 3.0 GB Report
EGAF00005776198 fastq.gz 3.9 GB Report
EGAF00005776199 fastq.gz 4.0 GB Report
EGAF00005776200 fastq.gz 2.1 GB Report
EGAF00005776201 fastq.gz 2.2 GB Report
EGAF00005776202 fastq.gz 2.7 GB Report
EGAF00005776203 fastq.gz 2.9 GB Report
EGAF00005776204 fastq.gz 2.7 GB Report
EGAF00005776205 fastq.gz 2.9 GB Report
EGAF00005776206 fastq.gz 3.4 GB Report
EGAF00005776207 fastq.gz 3.5 GB Report
EGAF00005776208 fastq.gz 3.7 GB Report
EGAF00005776209 fastq.gz 3.8 GB Report
EGAF00005776210 fastq.gz 4.0 GB Report
EGAF00005776211 fastq.gz 4.0 GB Report
EGAF00005776212 fastq.gz 2.8 GB Report
EGAF00005776213 fastq.gz 3.0 GB Report
EGAF00005776214 fastq.gz 3.2 GB Report
EGAF00005776215 fastq.gz 3.3 GB Report
EGAF00005776216 fastq.gz 2.8 GB Report
EGAF00005776217 fastq.gz 3.0 GB Report
EGAF00005776218 fastq.gz 2.5 GB Report
EGAF00005776219 fastq.gz 2.6 GB Report
EGAF00005776220 fastq.gz 3.9 GB Report
EGAF00005776221 fastq.gz 4.1 GB Report
EGAF00005776222 fastq.gz 2.7 GB Report
EGAF00005776223 fastq.gz 2.8 GB Report
EGAF00005776224 fastq.gz 2.2 GB Report
EGAF00005776225 fastq.gz 2.3 GB Report
EGAF00005776226 fastq.gz 1.8 GB Report
EGAF00005776227 fastq.gz 1.9 GB Report
EGAF00005776228 fastq.gz 1.9 GB Report
EGAF00005776229 fastq.gz 2.0 GB Report
EGAF00005776230 fastq.gz 2.9 GB Report
EGAF00005776231 fastq.gz 3.0 GB Report
EGAF00005776232 fastq.gz 2.3 GB Report
EGAF00005776233 fastq.gz 2.4 GB Report
EGAF00005776234 fastq.gz 2.6 GB Report
EGAF00005776235 fastq.gz 2.8 GB Report
EGAF00005776236 fastq.gz 4.2 GB Report
EGAF00005776237 fastq.gz 4.4 GB Report
EGAF00005776238 fastq.gz 3.4 GB Report
EGAF00005776239 fastq.gz 3.5 GB Report
EGAF00005776240 fastq.gz 3.2 GB Report
EGAF00005776241 fastq.gz 3.4 GB Report
EGAF00005776242 fastq.gz 3.9 GB Report
EGAF00005776243 fastq.gz 4.1 GB Report
EGAF00005776244 fastq.gz 2.8 GB Report
EGAF00005776245 fastq.gz 3.0 GB Report
EGAF00005776246 fastq.gz 3.6 GB Report
EGAF00005776247 fastq.gz 3.8 GB Report
EGAF00005776248 fastq.gz 3.2 GB Report
EGAF00005776249 fastq.gz 3.3 GB Report
EGAF00005776250 fastq.gz 1.9 GB Report
EGAF00005776251 fastq.gz 2.0 GB Report
EGAF00005776252 fastq.gz 3.0 GB Report
EGAF00005776253 fastq.gz 3.1 GB Report
EGAF00005776254 fastq.gz 3.0 GB Report
EGAF00005776255 fastq.gz 3.2 GB Report
EGAF00005776256 fastq.gz 3.3 GB Report
EGAF00005776257 fastq.gz 3.5 GB Report
EGAF00005776258 fastq.gz 2.1 GB Report
EGAF00005776259 fastq.gz 2.2 GB Report
EGAF00005776260 fastq.gz 3.2 GB Report
EGAF00005776261 fastq.gz 3.4 GB Report
EGAF00005776262 fastq.gz 2.9 GB Report
EGAF00005776263 fastq.gz 3.1 GB Report
EGAF00005776264 fastq.gz 3.4 GB Report
EGAF00005776265 fastq.gz 3.7 GB Report
EGAF00005776266 fastq.gz 2.4 GB Report
EGAF00005776267 fastq.gz 2.5 GB Report
EGAF00005776268 fastq.gz 3.5 GB Report
EGAF00005776269 fastq.gz 3.7 GB Report
EGAF00005776270 fastq.gz 2.5 GB Report
EGAF00005776271 fastq.gz 2.6 GB Report
EGAF00005776272 fastq.gz 2.5 GB Report
EGAF00005776273 fastq.gz 2.6 GB Report
EGAF00005776274 fastq.gz 2.9 GB Report
EGAF00005776275 fastq.gz 3.1 GB Report
EGAF00005776276 fastq.gz 3.1 GB Report
EGAF00005776277 fastq.gz 3.2 GB Report
EGAF00005776278 fastq.gz 3.8 GB Report
EGAF00005776279 fastq.gz 3.9 GB Report
EGAF00005776280 fastq.gz 2.9 GB Report
EGAF00005776281 fastq.gz 3.0 GB Report
EGAF00005776282 fastq.gz 3.8 GB Report
EGAF00005776283 fastq.gz 3.9 GB Report
EGAF00005776284 fastq.gz 2.7 GB Report
EGAF00005776285 fastq.gz 2.8 GB Report
EGAF00005776286 fastq.gz 2.7 GB Report
EGAF00005776287 fastq.gz 2.8 GB Report
EGAF00005776288 fastq.gz 3.9 GB Report
EGAF00005776289 fastq.gz 4.1 GB Report
EGAF00005776290 fastq.gz 3.6 GB Report
EGAF00005776291 fastq.gz 3.6 GB Report
EGAF00005776292 fastq.gz 3.0 GB Report
EGAF00005776293 fastq.gz 3.2 GB Report
EGAF00005776294 fastq.gz 2.6 GB Report
EGAF00005776295 fastq.gz 2.7 GB Report
EGAF00005776296 fastq.gz 2.9 GB Report
EGAF00005776297 fastq.gz 3.1 GB Report
EGAF00005776298 fastq.gz 2.6 GB Report
EGAF00005776299 fastq.gz 2.8 GB Report
EGAF00005776300 fastq.gz 3.4 GB Report
EGAF00005776301 fastq.gz 3.6 GB Report
EGAF00005776302 fastq.gz 2.6 GB Report
EGAF00005776303 fastq.gz 2.8 GB Report
EGAF00005776304 fastq.gz 3.2 GB Report
EGAF00005776305 fastq.gz 3.4 GB Report
EGAF00005776306 fastq.gz 3.0 GB Report
EGAF00005776307 fastq.gz 3.2 GB Report
EGAF00005776308 fastq.gz 3.6 GB Report
EGAF00005776309 fastq.gz 3.8 GB Report
EGAF00005776310 fastq.gz 3.7 GB Report
EGAF00005776311 fastq.gz 3.7 GB Report
EGAF00005776312 fastq.gz 3.9 GB Report
EGAF00005776313 fastq.gz 4.1 GB Report
EGAF00005776314 fastq.gz 2.8 GB Report
EGAF00005776315 fastq.gz 3.0 GB Report
EGAF00005776316 fastq.gz 2.7 GB Report
EGAF00005776317 fastq.gz 2.9 GB Report
EGAF00005776318 fastq.gz 2.0 GB Report
EGAF00005776319 fastq.gz 2.1 GB Report
EGAF00005776320 fastq.gz 2.3 GB Report
EGAF00005776321 fastq.gz 2.4 GB Report
EGAF00005776322 fastq.gz 2.9 GB Report
EGAF00005776323 fastq.gz 3.0 GB Report
EGAF00005776324 fastq.gz 3.3 GB Report
EGAF00005776325 fastq.gz 3.5 GB Report
EGAF00005776326 fastq.gz 3.3 GB Report
EGAF00005776327 fastq.gz 3.5 GB Report
EGAF00005776328 fastq.gz 2.5 GB Report
EGAF00005776329 fastq.gz 2.6 GB Report
EGAF00005776330 fastq.gz 4.0 GB Report
EGAF00005776331 fastq.gz 4.2 GB Report
EGAF00005776332 fastq.gz 3.4 GB Report
EGAF00005776333 fastq.gz 3.5 GB Report
EGAF00005776334 fastq.gz 2.5 GB Report
EGAF00005776335 fastq.gz 2.7 GB Report
EGAF00005776336 fastq.gz 3.5 GB Report
EGAF00005776337 fastq.gz 3.7 GB Report
EGAF00005776338 fastq.gz 5.0 GB Report
EGAF00005776339 fastq.gz 5.2 GB Report
EGAF00005776340 fastq.gz 2.8 GB Report
EGAF00005776341 fastq.gz 2.9 GB Report
EGAF00005776342 fastq.gz 3.0 GB Report
EGAF00005776343 fastq.gz 3.2 GB Report
EGAF00005776662 txt 68.9 MB
273 Files (843.0 GB)