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 bulk RNA-sequencing data

Tumor availability: Bulk RNA sequencing was performed on tumor biopsies of 48 patients at baseline and 45 patients across time points (baseline n=48, week 1 n=38, week 2 n=34, week 4 n=37), including lymph node metastasis that were sequenced in addition to the primary tumor. Tumor RNA 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, except for on-treatment samples with a complete pathological response in which we isolated samples with at least 10% immune-infiltration with no viable tumor cells. 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 RNA isolation. According to the manufacturer's protocol, five to 10 FFPE slides (10 µm) were used for RNA isolation using the AllPrep DNA/RNA FFPE isolation kit (Qiagen, 80234) and the QIAcube. Genetic Diagnostics and Sequencing Services (CeGaT) performed RNA sequencing in Germany. Data processing: Demultiplexing of the sequencing reads was performed with Illumina bcl2fastq (v2.20). Adapters of the reads (Pico v2 SMART adapter, first three nucleotides of the second sequencing read) were trimmed with Skewer (v0.2.2), without quality trimming. RNA-sequencing data was aligned to GRCh38 (Ensembl v109) using STAR (v2.7.9) in 2-pass mode with default settings. Gene counts were generated with the HTSeq (v2.0.2). FastQC (v0.12.1) and MultiQC (v1.14) 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
EGAF50000370734 fastq.gz 3.3 GB
EGAF50000370735 fastq.gz 3.4 GB
EGAF50000370736 fastq.gz 4.8 GB
EGAF50000370737 fastq.gz 3.5 GB
EGAF50000370738 fastq.gz 3.6 GB
EGAF50000370739 fastq.gz 3.7 GB
EGAF50000370740 fastq.gz 4.7 GB
EGAF50000370741 fastq.gz 2.4 GB
EGAF50000370742 fastq.gz 2.4 GB
EGAF50000370743 fastq.gz 3.7 GB
EGAF50000370744 fastq.gz 4.1 GB
EGAF50000370745 fastq.gz 4.3 GB
EGAF50000370746 fastq.gz 4.3 GB
EGAF50000370747 fastq.gz 3.4 GB
EGAF50000370748 fastq.gz 3.4 GB
EGAF50000370749 fastq.gz 3.4 GB
EGAF50000370750 fastq.gz 6.5 GB
EGAF50000370751 fastq.gz 2.9 GB
EGAF50000370752 fastq.gz 3.4 GB
EGAF50000370753 fastq.gz 3.0 GB
EGAF50000370791 fastq.gz 2.8 GB
EGAF50000370792 fastq.gz 4.6 GB
EGAF50000370793 fastq.gz 3.8 GB
EGAF50000370794 fastq.gz 4.1 GB
EGAF50000370795 fastq.gz 3.6 GB
EGAF50000370796 fastq.gz 4.3 GB
EGAF50000370820 fastq.gz 3.3 GB
EGAF50000370821 fastq.gz 4.3 GB
EGAF50000370822 fastq.gz 4.2 GB
EGAF50000370823 fastq.gz 6.4 GB
EGAF50000370824 fastq.gz 4.0 GB
EGAF50000370825 fastq.gz 4.2 GB
EGAF50000370826 fastq.gz 2.8 GB
EGAF50000370827 fastq.gz 4.1 GB
EGAF50000370829 fastq.gz 4.1 GB
EGAF50000370830 fastq.gz 4.1 GB
EGAF50000370831 fastq.gz 4.2 GB
EGAF50000370832 fastq.gz 4.1 GB
EGAF50000370833 fastq.gz 2.4 GB
EGAF50000370834 fastq.gz 2.5 GB
EGAF50000370835 fastq.gz 2.7 GB
EGAF50000370836 fastq.gz 5.0 GB
EGAF50000370837 fastq.gz 5.1 GB
EGAF50000370838 fastq.gz 3.4 GB
EGAF50000370840 fastq.gz 4.9 GB
EGAF50000370841 fastq.gz 5.0 GB
EGAF50000370842 fastq.gz 4.7 GB
EGAF50000370843 fastq.gz 4.9 GB
EGAF50000370844 fastq.gz 4.5 GB
EGAF50000370845 fastq.gz 4.5 GB
EGAF50000370846 fastq.gz 3.3 GB
EGAF50000370850 fastq.gz 3.4 GB
EGAF50000370851 fastq.gz 4.2 GB
EGAF50000370852 fastq.gz 4.2 GB
EGAF50000370853 fastq.gz 4.5 GB
EGAF50000370854 fastq.gz 4.5 GB
EGAF50000370855 fastq.gz 2.7 GB
EGAF50000370856 fastq.gz 2.6 GB
EGAF50000370857 fastq.gz 3.8 GB
EGAF50000370858 fastq.gz 3.9 GB
EGAF50000370859 fastq.gz 4.6 GB
EGAF50000370860 fastq.gz 4.6 GB
EGAF50000370861 fastq.gz 4.7 GB
EGAF50000370862 fastq.gz 4.6 GB
EGAF50000370863 fastq.gz 3.7 GB
EGAF50000370864 fastq.gz 5.4 GB
EGAF50000370865 fastq.gz 5.4 GB
EGAF50000370866 fastq.gz 4.8 GB
EGAF50000370867 fastq.gz 5.7 GB
EGAF50000370868 fastq.gz 5.7 GB
EGAF50000370869 fastq.gz 2.8 GB
EGAF50000370870 fastq.gz 6.6 GB
EGAF50000370871 fastq.gz 6.6 GB
EGAF50000370872 fastq.gz 4.2 GB
EGAF50000370873 fastq.gz 4.3 GB
EGAF50000370874 fastq.gz 4.7 GB
EGAF50000370875 fastq.gz 3.4 GB
EGAF50000370876 fastq.gz 3.4 GB
EGAF50000370877 fastq.gz 3.7 GB
EGAF50000370878 fastq.gz 5.7 GB
EGAF50000370879 fastq.gz 5.8 GB
EGAF50000370880 fastq.gz 3.7 GB
EGAF50000370881 fastq.gz 3.8 GB
EGAF50000370882 fastq.gz 2.7 GB
EGAF50000370883 fastq.gz 2.7 GB
EGAF50000370884 fastq.gz 4.6 GB
EGAF50000370885 fastq.gz 3.7 GB
EGAF50000370886 fastq.gz 3.7 GB
EGAF50000370887 fastq.gz 2.4 GB
EGAF50000370888 fastq.gz 2.4 GB
EGAF50000370889 fastq.gz 18.7 GB
EGAF50000370890 fastq.gz 18.9 GB
EGAF50000370891 fastq.gz 3.7 GB
EGAF50000370892 fastq.gz 3.7 GB
EGAF50000370893 fastq.gz 4.0 GB
EGAF50000370894 fastq.gz 4.0 GB
EGAF50000370895 fastq.gz 3.0 GB
EGAF50000370896 fastq.gz 3.1 GB
EGAF50000370897 fastq.gz 3.1 GB
EGAF50000370898 fastq.gz 3.1 GB
EGAF50000370899 fastq.gz 4.0 GB
EGAF50000370900 fastq.gz 4.1 GB
EGAF50000370901 fastq.gz 2.9 GB
EGAF50000370902 fastq.gz 2.9 GB
EGAF50000370903 fastq.gz 4.2 GB
EGAF50000370904 fastq.gz 4.3 GB
EGAF50000370905 fastq.gz 4.3 GB
EGAF50000370906 fastq.gz 4.4 GB
EGAF50000370907 fastq.gz 4.7 GB
EGAF50000370908 fastq.gz 4.7 GB
EGAF50000370909 fastq.gz 3.5 GB
EGAF50000370910 fastq.gz 3.5 GB
EGAF50000370911 fastq.gz 4.6 GB
EGAF50000370912 fastq.gz 4.5 GB
EGAF50000370913 fastq.gz 3.8 GB
EGAF50000370914 fastq.gz 3.8 GB
EGAF50000370915 fastq.gz 2.9 GB
EGAF50000370916 fastq.gz 2.9 GB
EGAF50000370917 fastq.gz 4.2 GB
EGAF50000370918 fastq.gz 4.4 GB
EGAF50000370919 fastq.gz 4.8 GB
EGAF50000370920 fastq.gz 4.8 GB
EGAF50000370921 fastq.gz 3.8 GB
EGAF50000370922 fastq.gz 5.7 GB
EGAF50000370923 fastq.gz 5.9 GB
EGAF50000370924 fastq.gz 4.4 GB
EGAF50000370925 fastq.gz 3.2 GB
EGAF50000370926 fastq.gz 3.2 GB
EGAF50000370927 fastq.gz 3.5 GB
EGAF50000370928 fastq.gz 3.5 GB
EGAF50000370929 fastq.gz 3.8 GB
EGAF50000370930 fastq.gz 3.8 GB
EGAF50000370931 fastq.gz 4.6 GB
EGAF50000370932 fastq.gz 4.7 GB
EGAF50000370933 fastq.gz 3.3 GB
EGAF50000370934 fastq.gz 3.3 GB
EGAF50000370935 fastq.gz 4.1 GB
EGAF50000370936 fastq.gz 4.1 GB
EGAF50000370937 fastq.gz 4.2 GB
EGAF50000370938 fastq.gz 5.1 GB
EGAF50000370939 fastq.gz 5.1 GB
EGAF50000370940 fastq.gz 4.2 GB
EGAF50000370941 fastq.gz 4.2 GB
EGAF50000370942 fastq.gz 4.7 GB
EGAF50000370943 fastq.gz 4.7 GB
EGAF50000370944 fastq.gz 3.8 GB
EGAF50000370945 fastq.gz 3.9 GB
EGAF50000370946 fastq.gz 4.4 GB
EGAF50000370947 fastq.gz 4.2 GB
EGAF50000370948 fastq.gz 4.2 GB
EGAF50000370949 fastq.gz 3.6 GB
EGAF50000370950 fastq.gz 3.6 GB
EGAF50000370951 fastq.gz 4.6 GB
EGAF50000370952 fastq.gz 4.7 GB
EGAF50000370953 fastq.gz 4.0 GB
EGAF50000370954 fastq.gz 4.2 GB
EGAF50000370955 fastq.gz 5.8 GB
EGAF50000370956 fastq.gz 5.8 GB
EGAF50000370957 fastq.gz 3.6 GB
EGAF50000370958 fastq.gz 4.3 GB
EGAF50000370959 fastq.gz 4.4 GB
EGAF50000370960 fastq.gz 4.6 GB
EGAF50000370961 fastq.gz 4.6 GB
EGAF50000370962 fastq.gz 4.2 GB
EGAF50000370963 fastq.gz 6.2 GB
EGAF50000370964 fastq.gz 6.3 GB
EGAF50000370965 fastq.gz 6.3 GB
EGAF50000370966 fastq.gz 3.5 GB
EGAF50000370967 fastq.gz 3.2 GB
EGAF50000370968 fastq.gz 4.5 GB
EGAF50000370969 fastq.gz 4.5 GB
EGAF50000370970 fastq.gz 2.9 GB
EGAF50000370971 fastq.gz 3.0 GB
EGAF50000370972 fastq.gz 5.0 GB
EGAF50000370973 fastq.gz 5.0 GB
EGAF50000370974 fastq.gz 5.3 GB
EGAF50000370975 fastq.gz 5.4 GB
EGAF50000370976 fastq.gz 3.1 GB
EGAF50000370977 fastq.gz 3.1 GB
EGAF50000370978 fastq.gz 2.5 GB
EGAF50000370979 fastq.gz 2.6 GB
EGAF50000370980 fastq.gz 5.4 GB
EGAF50000370981 fastq.gz 5.4 GB
EGAF50000370982 fastq.gz 4.8 GB
EGAF50000370983 fastq.gz 4.9 GB
EGAF50000370984 fastq.gz 4.1 GB
EGAF50000370985 fastq.gz 4.1 GB
EGAF50000370986 fastq.gz 3.5 GB
EGAF50000370987 fastq.gz 3.5 GB
EGAF50000370988 fastq.gz 4.0 GB
EGAF50000370989 fastq.gz 4.0 GB
EGAF50000370990 fastq.gz 5.3 GB
EGAF50000370991 fastq.gz 5.3 GB
EGAF50000370992 fastq.gz 4.2 GB
EGAF50000370993 fastq.gz 3.5 GB
EGAF50000370994 fastq.gz 3.6 GB
EGAF50000370995 fastq.gz 3.9 GB
EGAF50000370996 fastq.gz 3.9 GB
EGAF50000370997 fastq.gz 3.0 GB
EGAF50000370998 fastq.gz 3.0 GB
EGAF50000370999 fastq.gz 2.3 GB
EGAF50000371000 fastq.gz 2.3 GB
EGAF50000371001 fastq.gz 2.4 GB
EGAF50000371002 fastq.gz 2.4 GB
EGAF50000371003 fastq.gz 2.9 GB
EGAF50000371004 fastq.gz 3.0 GB
EGAF50000371005 fastq.gz 4.6 GB
EGAF50000371006 fastq.gz 5.1 GB
EGAF50000371007 fastq.gz 5.1 GB
EGAF50000371008 fastq.gz 3.1 GB
EGAF50000371009 fastq.gz 3.1 GB
EGAF50000371010 fastq.gz 4.3 GB
EGAF50000371011 fastq.gz 2.5 GB
EGAF50000371012 fastq.gz 2.5 GB
EGAF50000371013 fastq.gz 3.4 GB
EGAF50000371014 fastq.gz 3.5 GB
EGAF50000371015 fastq.gz 3.4 GB
EGAF50000371016 fastq.gz 3.4 GB
EGAF50000371017 fastq.gz 3.2 GB
EGAF50000371018 fastq.gz 3.2 GB
EGAF50000371019 fastq.gz 3.5 GB
EGAF50000371020 fastq.gz 3.6 GB
EGAF50000371021 fastq.gz 6.5 GB
EGAF50000371022 fastq.gz 3.2 GB
EGAF50000371023 fastq.gz 3.3 GB
EGAF50000371024 fastq.gz 3.8 GB
EGAF50000371025 fastq.gz 3.8 GB
EGAF50000371026 fastq.gz 3.1 GB
EGAF50000371027 fastq.gz 3.5 GB
EGAF50000371028 fastq.gz 3.6 GB
EGAF50000371029 fastq.gz 3.5 GB
EGAF50000371030 fastq.gz 3.4 GB
EGAF50000371031 fastq.gz 6.4 GB
EGAF50000371032 fastq.gz 3.0 GB
EGAF50000371033 fastq.gz 3.2 GB
EGAF50000371034 fastq.gz 3.3 GB
EGAF50000371035 fastq.gz 4.0 GB
EGAF50000371036 fastq.gz 3.1 GB
EGAF50000371037 fastq.gz 3.1 GB
EGAF50000371038 fastq.gz 4.7 GB
EGAF50000371039 fastq.gz 4.8 GB
EGAF50000371040 fastq.gz 3.4 GB
EGAF50000371041 fastq.gz 3.3 GB
EGAF50000371042 fastq.gz 3.3 GB
EGAF50000371043 fastq.gz 4.1 GB
EGAF50000371044 fastq.gz 3.0 GB
EGAF50000371045 fastq.gz 3.2 GB
EGAF50000371046 fastq.gz 3.4 GB
EGAF50000371047 fastq.gz 3.3 GB
EGAF50000371048 fastq.gz 3.3 GB
EGAF50000371049 fastq.gz 3.5 GB
EGAF50000371050 fastq.gz 3.6 GB
EGAF50000371051 fastq.gz 3.1 GB
EGAF50000371052 fastq.gz 3.2 GB
EGAF50000371053 fastq.gz 3.6 GB
EGAF50000371054 fastq.gz 3.6 GB
EGAF50000371055 fastq.gz 2.8 GB
EGAF50000371056 fastq.gz 2.9 GB
EGAF50000371057 fastq.gz 4.2 GB
EGAF50000371058 fastq.gz 4.3 GB
EGAF50000371059 fastq.gz 6.0 GB
EGAF50000371060 fastq.gz 6.1 GB
EGAF50000371061 fastq.gz 4.0 GB
EGAF50000371062 fastq.gz 4.3 GB
EGAF50000371063 fastq.gz 4.4 GB
EGAF50000371064 fastq.gz 3.0 GB
EGAF50000371065 fastq.gz 3.1 GB
EGAF50000371066 fastq.gz 5.0 GB
EGAF50000371067 fastq.gz 5.0 GB
EGAF50000371068 fastq.gz 2.6 GB
EGAF50000371069 fastq.gz 2.6 GB
EGAF50000371070 fastq.gz 3.7 GB
EGAF50000371071 fastq.gz 3.7 GB
EGAF50000371072 fastq.gz 6.8 GB
EGAF50000371073 fastq.gz 6.9 GB
EGAF50000371172 fastq.gz 3.9 GB
EGAF50000371173 fastq.gz 4.0 GB
EGAF50000371174 fastq.gz 4.3 GB
EGAF50000371175 fastq.gz 4.4 GB
EGAF50000371176 fastq.gz 5.6 GB
EGAF50000371177 fastq.gz 5.7 GB
EGAF50000371178 fastq.gz 2.9 GB
EGAF50000371179 fastq.gz 2.9 GB
EGAF50000371180 fastq.gz 2.6 GB
EGAF50000371181 fastq.gz 2.6 GB
EGAF50000371182 fastq.gz 2.4 GB
EGAF50000371183 fastq.gz 2.4 GB
EGAF50000371184 fastq.gz 3.8 GB
EGAF50000371185 fastq.gz 3.7 GB
EGAF50000371186 fastq.gz 3.2 GB
EGAF50000371187 fastq.gz 3.3 GB
EGAF50000371188 fastq.gz 5.4 GB
EGAF50000371189 fastq.gz 5.4 GB
EGAF50000371190 fastq.gz 5.1 GB
EGAF50000371191 fastq.gz 5.1 GB
EGAF50000371192 fastq.gz 4.0 GB
EGAF50000371193 fastq.gz 4.0 GB
EGAF50000371194 fastq.gz 3.3 GB
EGAF50000371195 fastq.gz 3.2 GB
EGAF50000371196 fastq.gz 4.1 GB
EGAF50000371197 fastq.gz 3.3 GB
EGAF50000371198 fastq.gz 3.0 GB
EGAF50000371199 fastq.gz 3.1 GB
EGAF50000371200 fastq.gz 3.9 GB
EGAF50000371201 fastq.gz 4.0 GB
EGAF50000371202 fastq.gz 3.5 GB
EGAF50000371203 fastq.gz 3.5 GB
EGAF50000371204 fastq.gz 2.9 GB
EGAF50000371205 fastq.gz 3.0 GB
EGAF50000371206 fastq.gz 2.6 GB
EGAF50000371207 fastq.gz 2.7 GB
EGAF50000371208 fastq.gz 6.4 GB
EGAF50000371209 fastq.gz 4.7 GB
EGAF50000371210 fastq.gz 2.9 GB
314 Files (1.3 TB)