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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MATISSE Whole-exome sequencing data

Sample availability: WES was performed on 41 available baseline tumor and blood samples (22 CCRs/MPRs, 5 PPRs, 14 CRN/NPRs). Tumor DNA was extracted from formalin-fixed paraffin-embedded (FFPE) primary tumor and lymph node metastasis sections containing at least 10% viable tumor cells present in the sample. A pathologist (LS) scored the tumor percentage and indicated the most tumor-dense region on a hematoxylin and eosin (H&E) stain slide for subsequent DNA isolation. According to the manufacturer's protocol, five to 10 FFPE slides (10 µm) were used for DNA isolation using the AllPrep DNA FFPE isolation kit (Qiagen, 80234) and the QIAcube. Germline DNA was isolated from baseline PBMCs using the AllPrep DNA / RNA / miRNA Universal isolation kit (Qiagen, 80224) and the QIAcube, according to the manufacturer’s protocol. Genetic Diagnostics and Sequencing Services (CeGaT) performed whole-exome sequencing sequencing in Germany. Data processing: Demultiplexing of the sequencing reads was performed with Illumina bcl2fastq (v2.20). Adapters of the reads were trimmed with Skewer (v0.2.2), without quality trimming. Sequencing reads were aligned with BWA (v0.7.17) to the human reference genome GRCh38 (Ensemble, v105). Duplicated reads were marked using Picard (v2.25.0) MarkDuplicates, after which quality scores were recalibrated using GATK4 (4.2.2.0) BaseRecalibrator. FastQC (v0.12.1), MultiQC (v1.14), Mosdepth (v0.3.3) and NGScheckmate (v1.0.1) were used for assessing data quality, on FASTQ files and intermediate processing steps.

Request Access

Netherlands Cancer Institute - Antoni van Leeuwenhoek (NKI-AVL) general policy

Data is available under reasonable request. All data requests will be reviewed by the NKI IRB and must be supported by the Principal Investigator of the study. The researcher will need to sign a data access agreement with the NKI after approval.

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
EGAS50000001003 RNASeq

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
EGAF50000370754 fastq.gz 6.3 GB
EGAF50000370755 fastq.gz 9.6 GB
EGAF50000370756 fastq.gz 10.6 GB
EGAF50000370757 fastq.gz 9.2 GB
EGAF50000370758 fastq.gz 10.8 GB
EGAF50000370759 fastq.gz 10.4 GB
EGAF50000370760 fastq.gz 7.8 GB
EGAF50000370761 fastq.gz 8.7 GB
EGAF50000370762 fastq.gz 7.5 GB
EGAF50000370763 fastq.gz 9.3 GB
EGAF50000370764 fastq.gz 6.6 GB
EGAF50000370765 fastq.gz 6.6 GB
EGAF50000370766 fastq.gz 13.5 GB
EGAF50000370767 fastq.gz 13.7 GB
EGAF50000370768 fastq.gz 7.7 GB
EGAF50000370769 fastq.gz 6.9 GB
EGAF50000370770 fastq.gz 7.2 GB
EGAF50000370771 fastq.gz 9.6 GB
EGAF50000370772 fastq.gz 9.9 GB
EGAF50000370773 fastq.gz 7.9 GB
EGAF50000370774 fastq.gz 8.0 GB
EGAF50000370775 fastq.gz 7.9 GB
EGAF50000370776 fastq.gz 8.1 GB
EGAF50000370777 fastq.gz 7.1 GB
EGAF50000370778 fastq.gz 3.9 GB
EGAF50000370779 fastq.gz 4.1 GB
EGAF50000370780 fastq.gz 3.9 GB
EGAF50000370781 fastq.gz 4.0 GB
EGAF50000370782 fastq.gz 3.7 GB
EGAF50000370783 fastq.gz 4.4 GB
EGAF50000370784 fastq.gz 4.5 GB
EGAF50000370785 fastq.gz 4.6 GB
EGAF50000370786 fastq.gz 5.3 GB
EGAF50000370787 fastq.gz 7.0 GB
EGAF50000370788 fastq.gz 3.8 GB
EGAF50000370789 fastq.gz 4.0 GB
EGAF50000370790 fastq.gz 11.4 GB
EGAF50000370797 fastq.gz 3.7 GB
EGAF50000370798 fastq.gz 9.5 GB
EGAF50000370799 fastq.gz 6.8 GB
EGAF50000370800 fastq.gz 8.8 GB
EGAF50000370801 fastq.gz 8.7 GB
EGAF50000370802 fastq.gz 3.9 GB
EGAF50000370803 fastq.gz 3.6 GB
EGAF50000370804 fastq.gz 3.6 GB
EGAF50000370805 fastq.gz 3.7 GB
EGAF50000370806 fastq.gz 5.2 GB
EGAF50000370807 fastq.gz 3.4 GB
EGAF50000370808 fastq.gz 3.6 GB
EGAF50000370809 fastq.gz 3.4 GB
EGAF50000370810 fastq.gz 7.6 GB
EGAF50000370811 fastq.gz 3.5 GB
EGAF50000370812 fastq.gz 3.4 GB
EGAF50000370813 fastq.gz 4.1 GB
EGAF50000370814 fastq.gz 5.5 GB
EGAF50000370815 fastq.gz 3.5 GB
EGAF50000370816 fastq.gz 3.5 GB
EGAF50000370817 fastq.gz 3.9 GB
EGAF50000370818 fastq.gz 3.6 GB
EGAF50000370819 fastq.gz 7.4 GB
EGAF50000370828 fastq.gz 8.6 GB
EGAF50000370839 fastq.gz 9.3 GB
EGAF50000370847 fastq.gz 4.1 GB
EGAF50000370848 fastq.gz 4.1 GB
EGAF50000370849 fastq.gz 4.3 GB
EGAF50000371074 fastq.gz 9.4 GB
EGAF50000371075 fastq.gz 9.8 GB
EGAF50000371076 fastq.gz 6.3 GB
EGAF50000371077 fastq.gz 6.7 GB
EGAF50000371078 fastq.gz 6.6 GB
EGAF50000371079 fastq.gz 7.1 GB
EGAF50000371080 fastq.gz 17.4 GB
EGAF50000371081 fastq.gz 18.3 GB
EGAF50000371082 fastq.gz 5.2 GB
EGAF50000371083 fastq.gz 9.3 GB
EGAF50000371084 fastq.gz 7.7 GB
EGAF50000371085 fastq.gz 8.1 GB
EGAF50000371086 fastq.gz 6.4 GB
EGAF50000371087 fastq.gz 6.6 GB
EGAF50000371088 fastq.gz 7.3 GB
EGAF50000371089 fastq.gz 5.9 GB
EGAF50000371090 fastq.gz 5.9 GB
EGAF50000371091 fastq.gz 6.2 GB
EGAF50000371092 fastq.gz 6.3 GB
EGAF50000371093 fastq.gz 8.4 GB
EGAF50000371094 fastq.gz 8.7 GB
EGAF50000371095 fastq.gz 7.7 GB
EGAF50000371096 fastq.gz 8.2 GB
EGAF50000371097 fastq.gz 11.1 GB
EGAF50000371098 fastq.gz 11.3 GB
EGAF50000371099 fastq.gz 9.1 GB
EGAF50000371100 fastq.gz 6.6 GB
EGAF50000371101 fastq.gz 7.5 GB
EGAF50000371102 fastq.gz 7.7 GB
EGAF50000371103 fastq.gz 8.2 GB
EGAF50000371104 fastq.gz 8.3 GB
EGAF50000371105 fastq.gz 10.2 GB
EGAF50000371106 fastq.gz 10.4 GB
EGAF50000371107 fastq.gz 10.8 GB
EGAF50000371108 fastq.gz 8.0 GB
EGAF50000371109 fastq.gz 8.2 GB
EGAF50000371110 fastq.gz 10.7 GB
EGAF50000371111 fastq.gz 10.9 GB
EGAF50000371112 fastq.gz 7.6 GB
EGAF50000371113 fastq.gz 7.7 GB
EGAF50000371114 fastq.gz 8.8 GB
EGAF50000371115 fastq.gz 8.8 GB
EGAF50000371116 fastq.gz 9.0 GB
EGAF50000371117 fastq.gz 7.5 GB
EGAF50000371118 fastq.gz 9.5 GB
EGAF50000371119 fastq.gz 8.7 GB
EGAF50000371120 fastq.gz 7.3 GB
EGAF50000371121 fastq.gz 3.8 GB
EGAF50000371122 fastq.gz 3.9 GB
EGAF50000371123 fastq.gz 10.9 GB
EGAF50000371124 fastq.gz 4.0 GB
EGAF50000371125 fastq.gz 4.1 GB
EGAF50000371126 fastq.gz 4.1 GB
EGAF50000371127 fastq.gz 3.4 GB
EGAF50000371128 fastq.gz 3.5 GB
EGAF50000371129 fastq.gz 3.4 GB
EGAF50000371130 fastq.gz 3.8 GB
EGAF50000371131 fastq.gz 4.0 GB
EGAF50000371132 fastq.gz 4.0 GB
EGAF50000371133 fastq.gz 4.1 GB
EGAF50000371134 fastq.gz 3.7 GB
EGAF50000371135 fastq.gz 3.9 GB
EGAF50000371136 fastq.gz 5.3 GB
EGAF50000371137 fastq.gz 4.2 GB
EGAF50000371138 fastq.gz 4.5 GB
EGAF50000371139 fastq.gz 3.5 GB
EGAF50000371140 fastq.gz 4.5 GB
EGAF50000371141 fastq.gz 4.7 GB
EGAF50000371142 fastq.gz 4.4 GB
EGAF50000371143 fastq.gz 4.5 GB
EGAF50000371144 fastq.gz 3.5 GB
EGAF50000371145 fastq.gz 3.7 GB
EGAF50000371146 fastq.gz 3.9 GB
EGAF50000371147 fastq.gz 4.0 GB
EGAF50000371148 fastq.gz 3.7 GB
EGAF50000371149 fastq.gz 3.8 GB
EGAF50000371150 fastq.gz 3.8 GB
EGAF50000371151 fastq.gz 8.5 GB
EGAF50000371152 fastq.gz 8.8 GB
EGAF50000371153 fastq.gz 4.8 GB
EGAF50000371154 fastq.gz 3.7 GB
EGAF50000371155 fastq.gz 3.9 GB
EGAF50000371156 fastq.gz 3.9 GB
EGAF50000371157 fastq.gz 3.8 GB
EGAF50000371158 fastq.gz 3.8 GB
EGAF50000371159 fastq.gz 3.5 GB
EGAF50000371160 fastq.gz 3.8 GB
EGAF50000371161 fastq.gz 3.9 GB
EGAF50000371162 fastq.gz 3.7 GB
EGAF50000371163 fastq.gz 5.1 GB
EGAF50000371164 fastq.gz 4.3 GB
EGAF50000371165 fastq.gz 4.5 GB
EGAF50000371166 fastq.gz 3.6 GB
EGAF50000371167 fastq.gz 3.9 GB
EGAF50000371168 fastq.gz 3.7 GB
EGAF50000371169 fastq.gz 3.8 GB
EGAF50000371170 fastq.gz 4.0 GB
EGAF50000371171 fastq.gz 8.2 GB
EGAF50000371211 fastq.gz 4.2 GB
164 Files (1.1 TB)