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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.

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DEPArray-based sorting of pure carcinoma and stromal populations from formalin-fixed paraffin-embedded (FFPE) tissues followed by shallow whole genome sequencing

To overcome the challenges of low DNA yields, degraded DNA by formalin fixation and diluted signal of genomic aberrations by non-carcinoma components in the heterogeneous FFPE samples, we isolated pure carcinoma and stromal cells using the DEPArray™ NxT system, a microchip-based digital sorter that allows isolation of pure, homogeneous subpopulations of cells from FFPE samples. We isolated pure carcinoma and stromal cell populations from 12 FFPE tissues, including tissues from 9 primary and metastatic breast cancer and 3 primary ovarian high-grade serous carcinomas. This was followed by downstream shallow whole genome sequencing (WGS) for copy number landscape profiling for 10 samples. Seven out of 10 samples (even some with low tumour content or of old age) produced good quality genomic data, detecting sCNA in all carcinoma population samples but not in the stromal populations.

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DUO:0000028
version: 2021-02-23

institution specific restriction

This data use modifier indicates that use is limited to use within an approved institution.

institution specific restriction

institution specific restriction

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
EGAS50000001328 Whole Genome Sequencing

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
EGAF50000452227 fastq.gz 202.0 MB
EGAF50000452228 fastq.gz 212.6 MB
EGAF50000452229 fastq.gz 155.3 MB
EGAF50000452230 fastq.gz 156.7 MB
EGAF50000452231 fastq.gz 167.3 MB
EGAF50000452232 fastq.gz 192.2 MB
EGAF50000452233 fastq.gz 202.2 MB
EGAF50000452234 fastq.gz 137.1 MB
EGAF50000452235 fastq.gz 145.5 MB
EGAF50000452236 fastq.gz 192.0 MB
EGAF50000452237 fastq.gz 203.7 MB
EGAF50000452238 fastq.gz 187.1 MB
EGAF50000452239 fastq.gz 194.3 MB
EGAF50000452240 fastq.gz 217.7 MB
EGAF50000452241 fastq.gz 229.3 MB
EGAF50000452242 fastq.gz 226.3 MB
EGAF50000452243 fastq.gz 234.7 MB
EGAF50000452244 fastq.gz 262.3 MB
EGAF50000452245 fastq.gz 274.9 MB
EGAF50000452246 fastq.gz 141.5 MB
EGAF50000452247 fastq.gz 162.5 MB
EGAF50000452248 fastq.gz 148.0 MB
EGAF50000452249 fastq.gz 160.3 MB
EGAF50000452250 fastq.gz 119.5 MB
EGAF50000452251 fastq.gz 137.5 MB
EGAF50000452252 fastq.gz 175.8 MB
EGAF50000452253 fastq.gz 181.1 MB
EGAF50000452254 fastq.gz 143.3 MB
EGAF50000452255 fastq.gz 151.3 MB
EGAF50000452256 fastq.gz 141.0 MB
EGAF50000452257 fastq.gz 164.2 MB
EGAF50000452282 fastq.gz 297.1 MB
EGAF50000452283 fastq.gz 315.1 MB
EGAF50000452284 fastq.gz 384.9 MB
EGAF50000452285 fastq.gz 408.4 MB
EGAF50000452286 fastq.gz 340.1 MB
EGAF50000452287 fastq.gz 356.1 MB
EGAF50000452288 fastq.gz 323.5 MB
EGAF50000452289 fastq.gz 352.4 MB
EGAF50000452290 fastq.gz 163.0 MB
40 Files (8.6 GB)