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Whole exome and Transcriptome sequencing of treatment-naïve esophageal adenocarcinoma biopsies and matched peripheral blood mononuclear cells

Exome sequencing was performed on n=28 treatment-naïve esophageal adenocarcinoma (EACs). Three to four biopsies sampling different areas of each tumor were pooled before nucleic acid extractions to mitigate the elevated heterogeneity described for EAC. WES was performed on EAC biopsies at 120X average coverage, with autologous PBMCs used as germline controls at 80X average coverage. Libraries were prepared from 30 ng of input DNA using the SureSelect QXT Human All Exon V7 kit (Agilent Technologies) and sequenced on the NextSeq 550 (Illumina), 2x150 bp. BCL files were demultiplexed to FastQ files using bcl2fastq2 software (Illumina). Three paired end sequencing batches were analyzed independently (Batch1: samples 8, 10, 11, 12, 15, 17, 18; Batch2: samples 20, 24, 25, 26, 27, 29, 30, 31, 33, 34 ; Batch3: samples 35, 37, 39, 40, 41, 43, 45, 48, 54, 55, 57). RNA sequencing was performed on n=26 treatment-naïve esophageal adenocarcinoma (EACs). Three to four biopsies sampling different areas of each tumor were pooled before nucleic acid extractions to mitigate the elevated heterogeneity described for EAC. RNAseq libraries were prepared on 50 ng of total RNA (with RNA integrity index RIN >=7) with the TruSeq Stranded mRNA library preparation kit (Illumina) in accordance with low-throughput protocol. After PCR enrichment (15 cycles) and purification of adapter-ligated fragments, the concentration and length of DNA fragments were measured using D1000 Screen Tape System (Agilent), obtaining a median insert size of 311 nucleotides. Then, RNAseq libraries were sequenced using the Illumina NovaSeq platform, 1x100 bp, obtaining on average 100 million single reads per sample.

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ESO-CA001 DAC

Any access to the data must be approved by the Data Access Commitee and a Data Access Agreement between data owner IRCCS Ospedale San Raffaele and the institution requiring access to the data must be signed before accessing the data.

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
EGAS00001007245 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
EGAF00008071137 fastq.gz 5.1 GB
EGAF00008071138 fastq.gz 5.2 GB
EGAF00008071139 fastq.gz 2.3 GB
EGAF00008071140 fastq.gz 2.3 GB
EGAF00008071141 fastq.gz 4.7 GB
EGAF00008071142 fastq.gz 5.1 GB
EGAF00008071143 fastq.gz 2.5 GB
EGAF00008071144 fastq.gz 2.5 GB
EGAF00008071145 fastq.gz 4.0 GB
EGAF00008071146 fastq.gz 4.1 GB
EGAF00008071147 fastq.gz 2.6 GB
EGAF00008071148 fastq.gz 2.7 GB
EGAF00008071149 fastq.gz 5.3 GB
EGAF00008071150 fastq.gz 5.4 GB
EGAF00008071151 fastq.gz 2.1 GB
EGAF00008071152 fastq.gz 2.1 GB
EGAF00008071153 fastq.gz 4.3 GB
EGAF00008071154 fastq.gz 4.3 GB
EGAF00008071155 fastq.gz 2.6 GB
EGAF00008071156 fastq.gz 2.6 GB
EGAF00008071157 fastq.gz 5.6 GB
EGAF00008071158 fastq.gz 5.7 GB
EGAF00008071159 fastq.gz 2.2 GB
EGAF00008071160 fastq.gz 2.3 GB
EGAF00008071161 fastq.gz 4.3 GB
EGAF00008071162 fastq.gz 4.4 GB
EGAF00008071163 fastq.gz 2.7 GB
EGAF00008071164 fastq.gz 2.7 GB
EGAF00008071165 fastq.gz 2.0 GB
EGAF00008071166 fastq.gz 2.0 GB
EGAF00008071167 fastq.gz 4.8 GB
EGAF00008071168 fastq.gz 4.9 GB
EGAF00008071169 fastq.gz 2.4 GB
EGAF00008071170 fastq.gz 2.5 GB
EGAF00008071171 fastq.gz 2.6 GB
EGAF00008071172 fastq.gz 2.6 GB
EGAF00008071173 fastq.gz 2.1 GB
EGAF00008071174 fastq.gz 2.1 GB
EGAF00008071175 fastq.gz 2.8 GB
EGAF00008071176 fastq.gz 2.9 GB
EGAF00008071177 fastq.gz 1.3 GB
EGAF00008071178 fastq.gz 1.4 GB
EGAF00008071179 fastq.gz 2.3 GB
EGAF00008071180 fastq.gz 2.3 GB
EGAF00008071181 fastq.gz 2.0 GB
EGAF00008071182 fastq.gz 2.0 GB
EGAF00008071183 fastq.gz 2.9 GB
EGAF00008071184 fastq.gz 2.9 GB
EGAF00008071185 fastq.gz 1.7 GB
EGAF00008071186 fastq.gz 1.8 GB
EGAF00008071187 fastq.gz 2.4 GB
EGAF00008071188 fastq.gz 2.5 GB
EGAF00008071189 fastq.gz 2.9 GB
EGAF00008071190 fastq.gz 2.9 GB
EGAF00008071191 fastq.gz 3.0 GB
EGAF00008071192 fastq.gz 3.0 GB
EGAF00008071193 fastq.gz 4.2 GB
EGAF00008071194 fastq.gz 4.3 GB
EGAF00008071195 fastq.gz 2.8 GB
EGAF00008071196 fastq.gz 2.8 GB
EGAF00008071197 fastq.gz 3.3 GB
EGAF00008071198 fastq.gz 3.4 GB
EGAF00008071199 fastq.gz 3.1 GB
EGAF00008071200 fastq.gz 3.1 GB
EGAF00008071201 fastq.gz 3.5 GB
EGAF00008071202 fastq.gz 3.6 GB
EGAF00008071203 fastq.gz 3.2 GB
EGAF00008071204 fastq.gz 3.2 GB
EGAF00008071205 fastq.gz 3.3 GB
EGAF00008071206 fastq.gz 3.4 GB
EGAF00008071207 fastq.gz 3.2 GB
EGAF00008071208 fastq.gz 3.3 GB
EGAF00008071209 fastq.gz 3.5 GB
EGAF00008071210 fastq.gz 3.5 GB
EGAF00008071211 fastq.gz 3.1 GB
EGAF00008071212 fastq.gz 3.2 GB
EGAF00008071213 fastq.gz 3.5 GB
EGAF00008071214 fastq.gz 3.6 GB
EGAF00008071215 fastq.gz 4.0 GB
EGAF00008071216 fastq.gz 4.0 GB
EGAF00008071217 fastq.gz 3.2 GB
EGAF00008071218 fastq.gz 3.3 GB
EGAF00008071219 fastq.gz 5.4 GB
EGAF00008071220 fastq.gz 5.4 GB
EGAF00008071221 fastq.gz 3.7 GB
EGAF00008071222 fastq.gz 3.8 GB
EGAF00008071223 fastq.gz 3.2 GB
EGAF00008071224 fastq.gz 3.4 GB
EGAF00008071225 fastq.gz 2.7 GB
EGAF00008071226 fastq.gz 2.7 GB
EGAF00008071227 fastq.gz 3.0 GB
EGAF00008071228 fastq.gz 3.0 GB
EGAF00008071229 fastq.gz 4.7 GB
EGAF00008071230 fastq.gz 4.8 GB
EGAF00008071231 fastq.gz 2.8 GB
EGAF00008071232 fastq.gz 2.8 GB
EGAF00008071233 fastq.gz 3.1 GB
EGAF00008071234 fastq.gz 3.2 GB
EGAF00008071235 fastq.gz 4.1 GB
EGAF00008071236 fastq.gz 4.4 GB
EGAF00008071237 fastq.gz 5.3 GB
EGAF00008071238 fastq.gz 4.4 GB
EGAF00008071239 fastq.gz 4.8 GB
EGAF00008071240 fastq.gz 4.0 GB
EGAF00008071241 fastq.gz 3.4 GB
EGAF00008071242 fastq.gz 2.8 GB
EGAF00008071243 fastq.gz 4.8 GB
EGAF00008071244 fastq.gz 4.0 GB
EGAF00008071245 fastq.gz 3.9 GB
EGAF00008071246 fastq.gz 3.3 GB
EGAF00008071247 fastq.gz 2.9 GB
EGAF00008071248 fastq.gz 2.4 GB
EGAF00008071249 fastq.gz 1.3 GB
EGAF00008071250 fastq.gz 1.1 GB
EGAF00008071251 fastq.gz 3.4 GB
EGAF00008071252 fastq.gz 2.9 GB
EGAF00008071253 fastq.gz 6.1 GB
EGAF00008071254 fastq.gz 5.1 GB
EGAF00008071255 fastq.gz 5.7 GB
EGAF00008071256 fastq.gz 4.8 GB
EGAF00008071257 fastq.gz 2.7 GB
EGAF00008071258 fastq.gz 2.4 GB
EGAF00008071259 fastq.gz 3.8 GB
EGAF00008071260 fastq.gz 3.9 GB
EGAF00008071261 fastq.gz 972.1 MB
EGAF00008071262 fastq.gz 976.5 MB
EGAF00008071263 fastq.gz 2.8 GB
EGAF00008071264 fastq.gz 2.9 GB
EGAF00008071265 fastq.gz 4.4 GB
EGAF00008071266 fastq.gz 4.6 GB
EGAF00008071267 fastq.gz 3.3 GB
EGAF00008071268 fastq.gz 3.4 GB
EGAF00008071269 fastq.gz 6.0 GB
EGAF00008071270 fastq.gz 6.3 GB
EGAF00008071271 fastq.gz 3.2 GB
EGAF00008071272 fastq.gz 3.3 GB
EGAF00008071273 fastq.gz 5.5 GB
EGAF00008071274 fastq.gz 5.6 GB
EGAF00008071275 fastq.gz 3.2 GB
EGAF00008071276 fastq.gz 3.3 GB
EGAF00008071277 fastq.gz 5.2 GB
EGAF00008071278 fastq.gz 5.3 GB
EGAF00008071279 fastq.gz 2.6 GB
EGAF00008071280 fastq.gz 2.7 GB
EGAF00008071281 fastq.gz 6.2 GB
EGAF00008071282 fastq.gz 6.4 GB
EGAF00008071283 fastq.gz 2.3 GB
EGAF00008071284 fastq.gz 2.4 GB
EGAF00008071285 fastq.gz 4.7 GB
EGAF00008071286 fastq.gz 4.8 GB
EGAF00008071287 fastq.gz 2.9 GB
EGAF00008071288 fastq.gz 2.9 GB
EGAF00008071289 fastq.gz 6.4 GB
EGAF00008071290 fastq.gz 6.5 GB
EGAF00008071291 fastq.gz 3.2 GB
EGAF00008071292 fastq.gz 3.4 GB
EGAF00008071293 fastq.gz 4.9 GB
EGAF00008071294 fastq.gz 5.1 GB
EGAF00008071295 fastq.gz 3.1 GB
EGAF00008071296 fastq.gz 3.2 GB
EGAF00008071297 fastq.gz 5.1 GB
EGAF00008071298 fastq.gz 5.3 GB
EGAF00008071299 fastq.gz 2.6 GB
EGAF00008071300 fastq.gz 2.7 GB
EGAF00008071301 fastq.gz 5.8 GB
EGAF00008071302 fastq.gz 6.0 GB
EGAF00008071303 fastq.gz 3.0 GB
EGAF00008071304 fastq.gz 3.2 GB
EGAF00008071305 fastq.gz 6.3 GB
EGAF00008071306 fastq.gz 6.5 GB
EGAF00008071307 fastq.gz 3.7 GB
EGAF00008071308 fastq.gz 3.9 GB
EGAF00008071309 fastq.gz 5.2 GB
EGAF00008071310 fastq.gz 5.4 GB
EGAF00008071311 fastq.gz 2.5 GB
EGAF00008071312 fastq.gz 2.6 GB
EGAF00008071313 fastq.gz 5.7 GB
EGAF00008071314 fastq.gz 5.9 GB
EGAF00008071315 fastq.gz 2.2 GB
EGAF00008071316 fastq.gz 2.3 GB
EGAF00008071317 fastq.gz 5.2 GB
EGAF00008071318 fastq.gz 5.4 GB
EGAF00008071319 fastq.gz 1.7 GB
EGAF00008071320 fastq.gz 1.6 GB
EGAF00008071321 fastq.gz 1.5 GB
EGAF00008071322 fastq.gz 1.4 GB
EGAF00008071323 fastq.gz 2.7 GB
EGAF00008071324 fastq.gz 2.5 GB
EGAF00008071325 fastq.gz 1.6 GB
EGAF00008071326 fastq.gz 1.5 GB
EGAF00008071327 fastq.gz 1.6 GB
EGAF00008071328 fastq.gz 1.5 GB
EGAF00008071329 fastq.gz 1.7 GB
EGAF00008071330 fastq.gz 1.5 GB
EGAF00008071331 fastq.gz 1.3 GB
EGAF00008071332 fastq.gz 1.2 GB
EGAF00008071333 fastq.gz 2.4 GB
EGAF00008071334 fastq.gz 1.8 GB
EGAF00008071335 fastq.gz 1.8 GB
EGAF00008071336 fastq.gz 1.9 GB
EGAF00008071337 fastq.gz 789.7 MB
EGAF00008071338 fastq.gz 362.8 MB
EGAF00008071339 fastq.gz 2.4 GB
EGAF00008071340 fastq.gz 2.1 GB
EGAF00008071341 fastq.gz 2.4 GB
EGAF00008071342 fastq.gz 1.8 GB
EGAF00008071343 fastq.gz 2.0 GB
EGAF00008071344 fastq.gz 2.0 GB
EGAF00008071345 fastq.gz 1.4 GB
EGAF00008071346 fastq.gz 2.0 GB
EGAF00008071347 fastq.gz 2.0 GB
EGAF00008071348 fastq.gz 2.7 GB
EGAF00008071349 fastq.gz 1.4 GB
EGAF00008071350 fastq.gz 2.0 GB
EGAF00008071351 fastq.gz 998.6 MB
EGAF00008071352 fastq.gz 1.4 GB
EGAF00008071353 fastq.gz 1.0 GB
EGAF00008071354 fastq.gz 1.4 GB
EGAF00008071355 fastq.gz 3.0 GB
EGAF00008071356 fastq.gz 4.0 GB
EGAF00008071357 fastq.gz 2.6 GB
EGAF00008071358 fastq.gz 3.5 GB
EGAF00008071359 fastq.gz 1.6 GB
EGAF00008071360 fastq.gz 2.3 GB
EGAF00008071361 fastq.gz 1.8 GB
EGAF00008071362 fastq.gz 1.8 GB
EGAF00008071363 fastq.gz 1.5 GB
EGAF00008071364 fastq.gz 1.5 GB
EGAF00008071365 fastq.gz 1.9 GB
EGAF00008071366 fastq.gz 2.0 GB
EGAF00008071367 fastq.gz 2.7 GB
EGAF00008071368 fastq.gz 2.7 GB
EGAF00008071369 fastq.gz 1.4 GB
EGAF00008071370 fastq.gz 1.4 GB
EGAF00008071371 fastq.gz 1.6 GB
EGAF00008071372 fastq.gz 1.6 GB
EGAF00008071373 fastq.gz 1.5 GB
EGAF00008071374 fastq.gz 1.5 GB
EGAF00008071375 fastq.gz 1.3 GB
EGAF00008071376 fastq.gz 1.4 GB
EGAF00008071377 fastq.gz 1.3 GB
EGAF00008071378 fastq.gz 1.3 GB
EGAF00008071379 fastq.gz 1.7 GB
EGAF00008071380 fastq.gz 1.7 GB
EGAF00008071381 fastq.gz 1.5 GB
EGAF00008071382 fastq.gz 1.5 GB
EGAF00008071383 fastq.gz 1.4 GB
EGAF00008071384 fastq.gz 1.4 GB
EGAF00008071385 fastq.gz 1.4 GB
EGAF00008071386 fastq.gz 1.4 GB
EGAF00008071387 fastq.gz 1.2 GB
EGAF00008071388 fastq.gz 1.2 GB
EGAF00008071389 fastq.gz 597.3 MB
EGAF00008071390 fastq.gz 615.7 MB
EGAF00008071391 fastq.gz 6.3 GB
EGAF00008071392 fastq.gz 1.8 GB
EGAF00008071393 fastq.gz 7.8 GB
257 Files (796.7 GB)