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.
- 19/05/2023
- 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 | Quality Report |
Located in
i
|
|---|---|---|---|---|
| EGAF00008071137 | fastq.gz | 5.1 GB | Report |
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| EGAF00008071138 | fastq.gz | 5.2 GB | Report |
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| EGAF00008071139 | fastq.gz | 2.3 GB | Report |
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| EGAF00008071140 | fastq.gz | 2.3 GB | Report |
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| EGAF00008071141 | fastq.gz | 4.7 GB | Report |
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| EGAF00008071142 | fastq.gz | 5.1 GB | Report |
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| EGAF00008071143 | fastq.gz | 2.5 GB | Report |
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| EGAF00008071144 | fastq.gz | 2.5 GB | Report |
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| EGAF00008071145 | fastq.gz | 4.0 GB | Report |
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| EGAF00008071146 | fastq.gz | 4.1 GB | Report |
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| EGAF00008071147 | fastq.gz | 2.6 GB | Report |
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| EGAF00008071148 | fastq.gz | 2.7 GB | Report |
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| EGAF00008071149 | fastq.gz | 5.3 GB | Report |
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| EGAF00008071150 | fastq.gz | 5.4 GB | Report |
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| EGAF00008071151 | fastq.gz | 2.1 GB | Report |
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| EGAF00008071152 | fastq.gz | 2.1 GB | Report |
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| EGAF00008071153 | fastq.gz | 4.3 GB | Report |
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| EGAF00008071154 | fastq.gz | 4.3 GB | Report |
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| EGAF00008071155 | fastq.gz | 2.6 GB | Report |
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| EGAF00008071156 | fastq.gz | 2.6 GB | Report |
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| EGAF00008071157 | fastq.gz | 5.6 GB | Report |
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| EGAF00008071158 | fastq.gz | 5.7 GB | Report |
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| EGAF00008071159 | fastq.gz | 2.2 GB | Report |
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| EGAF00008071160 | fastq.gz | 2.3 GB | Report |
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| EGAF00008071161 | fastq.gz | 4.3 GB | Report |
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| EGAF00008071162 | fastq.gz | 4.4 GB | Report |
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| EGAF00008071163 | fastq.gz | 2.7 GB | Report |
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| EGAF00008071164 | fastq.gz | 2.7 GB | Report |
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| EGAF00008071165 | fastq.gz | 2.0 GB | Report |
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| EGAF00008071166 | fastq.gz | 2.0 GB | Report |
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| EGAF00008071167 | fastq.gz | 4.8 GB | Report |
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| EGAF00008071168 | fastq.gz | 4.9 GB | Report |
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| EGAF00008071169 | fastq.gz | 2.4 GB | Report |
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| EGAF00008071170 | fastq.gz | 2.5 GB | Report |
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| EGAF00008071171 | fastq.gz | 2.6 GB | Report |
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| EGAF00008071172 | fastq.gz | 2.6 GB | Report |
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| EGAF00008071173 | fastq.gz | 2.1 GB | Report |
|
| EGAF00008071174 | fastq.gz | 2.1 GB | Report |
|
| EGAF00008071175 | fastq.gz | 2.8 GB | Report |
|
| EGAF00008071176 | fastq.gz | 2.9 GB | Report |
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| EGAF00008071177 | fastq.gz | 1.3 GB | Report |
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| EGAF00008071178 | fastq.gz | 1.4 GB | Report |
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| EGAF00008071179 | fastq.gz | 2.3 GB | Report |
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| EGAF00008071180 | fastq.gz | 2.3 GB | Report |
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| EGAF00008071181 | fastq.gz | 2.0 GB | Report |
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| EGAF00008071182 | fastq.gz | 2.0 GB | Report |
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| EGAF00008071183 | fastq.gz | 2.9 GB | Report |
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| EGAF00008071184 | fastq.gz | 2.9 GB | Report |
|
| EGAF00008071185 | fastq.gz | 1.7 GB | Report |
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| EGAF00008071186 | fastq.gz | 1.8 GB | Report |
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| EGAF00008071187 | fastq.gz | 2.4 GB | Report |
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| EGAF00008071188 | fastq.gz | 2.5 GB | Report |
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| EGAF00008071189 | fastq.gz | 2.9 GB | Report |
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| EGAF00008071190 | fastq.gz | 2.9 GB | Report |
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| EGAF00008071191 | fastq.gz | 3.0 GB | Report |
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| EGAF00008071192 | fastq.gz | 3.0 GB | Report |
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| EGAF00008071193 | fastq.gz | 4.2 GB | Report |
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| EGAF00008071194 | fastq.gz | 4.3 GB | Report |
|
| EGAF00008071195 | fastq.gz | 2.8 GB | Report |
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| EGAF00008071196 | fastq.gz | 2.8 GB | Report |
|
| EGAF00008071197 | fastq.gz | 3.3 GB | Report |
|
| EGAF00008071198 | fastq.gz | 3.4 GB | Report |
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| EGAF00008071199 | fastq.gz | 3.1 GB | Report |
|
| EGAF00008071200 | fastq.gz | 3.1 GB | Report |
|
| EGAF00008071201 | fastq.gz | 3.5 GB | Report |
|
| EGAF00008071202 | fastq.gz | 3.6 GB | Report |
|
| EGAF00008071203 | fastq.gz | 3.2 GB | Report |
|
| EGAF00008071204 | fastq.gz | 3.2 GB | Report |
|
| EGAF00008071205 | fastq.gz | 3.3 GB | Report |
|
| EGAF00008071206 | fastq.gz | 3.4 GB | Report |
|
| EGAF00008071207 | fastq.gz | 3.2 GB | Report |
|
| EGAF00008071208 | fastq.gz | 3.3 GB | Report |
|
| EGAF00008071209 | fastq.gz | 3.5 GB | Report |
|
| EGAF00008071210 | fastq.gz | 3.5 GB | Report |
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| EGAF00008071211 | fastq.gz | 3.1 GB | Report |
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| EGAF00008071212 | fastq.gz | 3.2 GB | Report |
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| EGAF00008071213 | fastq.gz | 3.5 GB | Report |
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| EGAF00008071214 | fastq.gz | 3.6 GB | Report |
|
| EGAF00008071215 | fastq.gz | 4.0 GB | Report |
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| EGAF00008071216 | fastq.gz | 4.0 GB | Report |
|
| EGAF00008071217 | fastq.gz | 3.2 GB | Report |
|
| EGAF00008071218 | fastq.gz | 3.3 GB | Report |
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| EGAF00008071219 | fastq.gz | 5.4 GB | Report |
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| EGAF00008071220 | fastq.gz | 5.4 GB | Report |
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| EGAF00008071221 | fastq.gz | 3.7 GB | Report |
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| EGAF00008071222 | fastq.gz | 3.8 GB | Report |
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| EGAF00008071223 | fastq.gz | 3.2 GB | Report |
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| EGAF00008071224 | fastq.gz | 3.4 GB | Report |
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| EGAF00008071225 | fastq.gz | 2.7 GB | Report |
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| EGAF00008071226 | fastq.gz | 2.7 GB | Report |
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| EGAF00008071227 | fastq.gz | 3.0 GB | Report |
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| EGAF00008071228 | fastq.gz | 3.0 GB | Report |
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| EGAF00008071229 | fastq.gz | 4.7 GB | Report |
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| EGAF00008071230 | fastq.gz | 4.8 GB | Report |
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| EGAF00008071231 | fastq.gz | 2.8 GB | Report |
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| EGAF00008071232 | fastq.gz | 2.8 GB | Report |
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| EGAF00008071233 | fastq.gz | 3.1 GB | Report |
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| EGAF00008071234 | fastq.gz | 3.2 GB | Report |
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| EGAF00008071235 | fastq.gz | 4.1 GB | Report |
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| EGAF00008071236 | fastq.gz | 4.4 GB | Report |
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| EGAF00008071237 | fastq.gz | 5.3 GB | Report |
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| EGAF00008071238 | fastq.gz | 4.4 GB | Report |
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| EGAF00008071239 | fastq.gz | 4.8 GB | Report |
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| EGAF00008071240 | fastq.gz | 4.0 GB | Report |
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| EGAF00008071241 | fastq.gz | 3.4 GB | Report |
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| EGAF00008071242 | fastq.gz | 2.8 GB | Report |
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| EGAF00008071243 | fastq.gz | 4.8 GB | Report |
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| EGAF00008071244 | fastq.gz | 4.0 GB | Report |
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| EGAF00008071245 | fastq.gz | 3.9 GB | Report |
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| EGAF00008071246 | fastq.gz | 3.3 GB | Report |
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| EGAF00008071247 | fastq.gz | 2.9 GB | Report |
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| EGAF00008071248 | fastq.gz | 2.4 GB | Report |
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| EGAF00008071249 | fastq.gz | 1.3 GB | Report |
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| EGAF00008071250 | fastq.gz | 1.1 GB | Report |
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| EGAF00008071251 | fastq.gz | 3.4 GB | Report |
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| EGAF00008071252 | fastq.gz | 2.9 GB | Report |
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| EGAF00008071253 | fastq.gz | 6.1 GB | Report |
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| EGAF00008071254 | fastq.gz | 5.1 GB | Report |
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| EGAF00008071255 | fastq.gz | 5.7 GB | Report |
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| EGAF00008071256 | fastq.gz | 4.8 GB | Report |
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| EGAF00008071257 | fastq.gz | 2.7 GB | Report |
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| EGAF00008071258 | fastq.gz | 2.4 GB | Report |
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| EGAF00008071259 | fastq.gz | 3.8 GB | Report |
|
| EGAF00008071260 | fastq.gz | 3.9 GB | Report |
|
| EGAF00008071261 | fastq.gz | 972.1 MB | Report |
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| EGAF00008071262 | fastq.gz | 976.5 MB | Report |
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| EGAF00008071263 | fastq.gz | 2.8 GB | Report |
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| EGAF00008071264 | fastq.gz | 2.9 GB | Report |
|
| EGAF00008071265 | fastq.gz | 4.4 GB | Report |
|
| EGAF00008071266 | fastq.gz | 4.6 GB | Report |
|
| EGAF00008071267 | fastq.gz | 3.3 GB | Report |
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| EGAF00008071268 | fastq.gz | 3.4 GB | Report |
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| EGAF00008071269 | fastq.gz | 6.0 GB | Report |
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| EGAF00008071270 | fastq.gz | 6.3 GB | Report |
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| EGAF00008071271 | fastq.gz | 3.2 GB | Report |
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| EGAF00008071272 | fastq.gz | 3.3 GB | Report |
|
| EGAF00008071273 | fastq.gz | 5.5 GB | Report |
|
| EGAF00008071274 | fastq.gz | 5.6 GB | Report |
|
| EGAF00008071275 | fastq.gz | 3.2 GB | Report |
|
| EGAF00008071276 | fastq.gz | 3.3 GB | Report |
|
| EGAF00008071277 | fastq.gz | 5.2 GB | Report |
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| EGAF00008071278 | fastq.gz | 5.3 GB | Report |
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| EGAF00008071279 | fastq.gz | 2.6 GB | Report |
|
| EGAF00008071280 | fastq.gz | 2.7 GB | Report |
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| EGAF00008071281 | fastq.gz | 6.2 GB | Report |
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| EGAF00008071282 | fastq.gz | 6.4 GB | Report |
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| EGAF00008071283 | fastq.gz | 2.3 GB | Report |
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| EGAF00008071284 | fastq.gz | 2.4 GB | Report |
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| EGAF00008071285 | fastq.gz | 4.7 GB | Report |
|
| EGAF00008071286 | fastq.gz | 4.8 GB | Report |
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| EGAF00008071287 | fastq.gz | 2.9 GB | Report |
|
| EGAF00008071288 | fastq.gz | 2.9 GB | Report |
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| EGAF00008071289 | fastq.gz | 6.4 GB | Report |
|
| EGAF00008071290 | fastq.gz | 6.5 GB | Report |
|
| EGAF00008071291 | fastq.gz | 3.2 GB | Report |
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| EGAF00008071292 | fastq.gz | 3.4 GB | Report |
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| EGAF00008071293 | fastq.gz | 4.9 GB | Report |
|
| EGAF00008071294 | fastq.gz | 5.1 GB | Report |
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| EGAF00008071295 | fastq.gz | 3.1 GB | Report |
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| EGAF00008071296 | fastq.gz | 3.2 GB | Report |
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| EGAF00008071297 | fastq.gz | 5.1 GB | Report |
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| EGAF00008071298 | fastq.gz | 5.3 GB | Report |
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| EGAF00008071299 | fastq.gz | 2.6 GB | Report |
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| EGAF00008071300 | fastq.gz | 2.7 GB | Report |
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| EGAF00008071301 | fastq.gz | 5.8 GB | Report |
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| EGAF00008071302 | fastq.gz | 6.0 GB | Report |
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| EGAF00008071303 | fastq.gz | 3.0 GB | Report |
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| EGAF00008071304 | fastq.gz | 3.2 GB | Report |
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| EGAF00008071305 | fastq.gz | 6.3 GB | Report |
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| EGAF00008071306 | fastq.gz | 6.5 GB | Report |
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| EGAF00008071307 | fastq.gz | 3.7 GB | Report |
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| EGAF00008071308 | fastq.gz | 3.9 GB | Report |
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| EGAF00008071309 | fastq.gz | 5.2 GB | Report |
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| EGAF00008071310 | fastq.gz | 5.4 GB | Report |
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| EGAF00008071311 | fastq.gz | 2.5 GB | Report |
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| EGAF00008071312 | fastq.gz | 2.6 GB | Report |
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| EGAF00008071313 | fastq.gz | 5.7 GB | Report |
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| EGAF00008071314 | fastq.gz | 5.9 GB | Report |
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| EGAF00008071315 | fastq.gz | 2.2 GB | Report |
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| EGAF00008071316 | fastq.gz | 2.3 GB | Report |
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| EGAF00008071317 | fastq.gz | 5.2 GB | Report |
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| EGAF00008071318 | fastq.gz | 5.4 GB | Report |
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| EGAF00008071319 | fastq.gz | 1.7 GB |
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| EGAF00008071320 | fastq.gz | 1.6 GB |
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| EGAF00008071321 | fastq.gz | 1.5 GB |
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| EGAF00008071322 | fastq.gz | 1.4 GB |
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| EGAF00008071323 | fastq.gz | 2.7 GB |
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| EGAF00008071324 | fastq.gz | 2.5 GB |
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| EGAF00008071325 | fastq.gz | 1.6 GB |
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| EGAF00008071326 | fastq.gz | 1.5 GB |
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| EGAF00008071327 | fastq.gz | 1.6 GB |
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| EGAF00008071328 | fastq.gz | 1.5 GB |
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| EGAF00008071329 | fastq.gz | 1.7 GB |
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| EGAF00008071330 | fastq.gz | 1.5 GB |
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| EGAF00008071331 | fastq.gz | 1.3 GB |
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| EGAF00008071332 | fastq.gz | 1.2 GB |
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| EGAF00008071333 | fastq.gz | 2.4 GB | Report |
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| EGAF00008071334 | fastq.gz | 1.8 GB | Report |
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| EGAF00008071335 | fastq.gz | 1.8 GB | Report |
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| EGAF00008071336 | fastq.gz | 1.9 GB | Report |
|
| EGAF00008071337 | fastq.gz | 789.7 MB | Report |
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| EGAF00008071338 | fastq.gz | 362.8 MB | Report |
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| EGAF00008071339 | fastq.gz | 2.4 GB | Report |
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| EGAF00008071340 | fastq.gz | 2.1 GB | Report |
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| EGAF00008071341 | fastq.gz | 2.4 GB | Report |
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| EGAF00008071342 | fastq.gz | 1.8 GB | Report |
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| EGAF00008071343 | fastq.gz | 2.0 GB | Report |
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| EGAF00008071344 | fastq.gz | 2.0 GB | Report |
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| EGAF00008071345 | fastq.gz | 1.4 GB | Report |
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| EGAF00008071346 | fastq.gz | 2.0 GB | Report |
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| EGAF00008071347 | fastq.gz | 2.0 GB | Report |
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| EGAF00008071348 | fastq.gz | 2.7 GB | Report |
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| EGAF00008071349 | fastq.gz | 1.4 GB | Report |
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| EGAF00008071350 | fastq.gz | 2.0 GB | Report |
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| EGAF00008071351 | fastq.gz | 998.6 MB | Report |
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| EGAF00008071352 | fastq.gz | 1.4 GB | Report |
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| EGAF00008071353 | fastq.gz | 1.0 GB | Report |
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| EGAF00008071354 | fastq.gz | 1.4 GB | Report |
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| EGAF00008071355 | fastq.gz | 3.0 GB | Report |
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| EGAF00008071356 | fastq.gz | 4.0 GB | Report |
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| EGAF00008071357 | fastq.gz | 2.6 GB | Report |
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| EGAF00008071358 | fastq.gz | 3.5 GB | Report |
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| EGAF00008071359 | fastq.gz | 1.6 GB | Report |
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| EGAF00008071360 | fastq.gz | 2.3 GB | Report |
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| EGAF00008071361 | fastq.gz | 1.8 GB | Report |
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| EGAF00008071362 | fastq.gz | 1.8 GB | Report |
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| EGAF00008071363 | fastq.gz | 1.5 GB | Report |
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| EGAF00008071364 | fastq.gz | 1.5 GB | Report |
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| EGAF00008071365 | fastq.gz | 1.9 GB | Report |
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| EGAF00008071366 | fastq.gz | 2.0 GB | Report |
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| EGAF00008071367 | fastq.gz | 2.7 GB | Report |
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| EGAF00008071368 | fastq.gz | 2.7 GB | Report |
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| EGAF00008071369 | fastq.gz | 1.4 GB | Report |
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| EGAF00008071370 | fastq.gz | 1.4 GB | Report |
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| EGAF00008071371 | fastq.gz | 1.6 GB | Report |
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| EGAF00008071372 | fastq.gz | 1.6 GB | Report |
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| EGAF00008071373 | fastq.gz | 1.5 GB | Report |
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| EGAF00008071374 | fastq.gz | 1.5 GB | Report |
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| EGAF00008071375 | fastq.gz | 1.3 GB | Report |
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| EGAF00008071376 | fastq.gz | 1.4 GB | Report |
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| EGAF00008071377 | fastq.gz | 1.3 GB | Report |
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| EGAF00008071378 | fastq.gz | 1.3 GB | Report |
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| EGAF00008071379 | fastq.gz | 1.7 GB | Report |
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| EGAF00008071380 | fastq.gz | 1.7 GB | Report |
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| EGAF00008071381 | fastq.gz | 1.5 GB | Report |
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| EGAF00008071382 | fastq.gz | 1.5 GB | Report |
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| EGAF00008071383 | fastq.gz | 1.4 GB | Report |
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| EGAF00008071384 | fastq.gz | 1.4 GB | Report |
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| EGAF00008071385 | fastq.gz | 1.4 GB | Report |
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| EGAF00008071386 | fastq.gz | 1.4 GB | Report |
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| EGAF00008071387 | fastq.gz | 1.2 GB | Report |
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| EGAF00008071388 | fastq.gz | 1.2 GB | Report |
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| EGAF00008071389 | fastq.gz | 597.3 MB | Report |
|
| EGAF00008071390 | fastq.gz | 615.7 MB | Report |
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| EGAF00008071391 | fastq.gz | 6.3 GB | Report |
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| EGAF00008071392 | fastq.gz | 1.8 GB | Report |
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| EGAF00008071393 | fastq.gz | 7.8 GB | Report |
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| 257 Files (796.7 GB) | ||||