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.
- 166 samples
- DAC: EGAC00001003245
- Technologies: Illumina NovaSeq 6000, NextSeq 550
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 | 4.1 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 | 3.1 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 | 3.3 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 | 971.7 MB | ||
| EGAF00008071262 | fastq.gz | 976.0 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 | 6.1 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 | 789.3 MB | ||
| EGAF00008071338 | fastq.gz | 362.7 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 | 998.1 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 | 597.0 MB | ||
| EGAF00008071390 | fastq.gz | 615.4 MB | ||
| EGAF00008071391 | fastq.gz | 6.3 GB | ||
| EGAF00008071392 | fastq.gz | 1.8 GB | ||
| EGAF00008071393 | fastq.gz | 7.8 GB | ||
| 257 Files (796.4 GB) | ||||