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• DESIGN-NKI RNA-seq

  RNA-Seq data of 36 HPV-negative HNSCC specimens from patients treated at The Netherlands Cancer Institute, Amsterdam. HNSCC biopsy samples obtained prior to treatment (chemo-radiotherapy) were used for polyA mRNA sequencing.

  Dataset EGAD00001005715

• DESIGN-NKI low coverage WGS

  Low-coverage whole genome sequencing data of 37 HPV-negative HNSCC specimens from patients treated at The Netherlands Cancer Institute. HNSCC biopsy samples obtained prior to treatment (chemo-radiotherapy) were used for WGS to a depth of approx. 0.5X.

  Dataset EGAD00001005718

• DESIGN-VUMC low coverage WGS

  Low-coverage whole genome sequencing data of 37 HPV-negative HNSCC specimens from patients treated at the VU Medical Centre, Amsterdam. HNSCC biopsy samples obtained prior to treatment (chemo-radiotherapy) were used for WGS to a depth of approx. 0.5X.

  Dataset EGAD00001005719

• NKI-MET HNSCC RNA-Seq

  RNA-Seq data of 8 HNSCC specimens from patients diagnosed with metastatic disease at The Netherlands Cancer Institute, Amsterdam. Primary HNSCC biopsy samples obtained prior to treatment were used for polyA mRNA sequencing.

  Dataset EGAD00001005720

• DESIGN-VUMC RNA-seq

  RNA-Seq data of 55 HPV-negative HNSCC specimens from patients treated at the VU medical Centre, Amsterdam, The Netherlands. HNSCC biopsy samples obtained prior to treatment (chemo-radiotherapy) were used for polyA mRNA sequencing.

  Dataset EGAD00001005716

• DESIGN-MAASTRO RNA-seq

  RNA-Seq data of 17 HPV-negative HNSCC specimens from patients treated at the MAASTRO clinic, Maastricht, The Netherlands. HNSCC biopsy samples obtained prior to treatment (chemo-radiotherapy) were used for polyA mRNA sequencing.

  Dataset EGAD00001005717

• SF11956 snATAC Seq GBM

  IDHR132H Wildtype GBM. Male, 63 Single Nuclei ATAC seq data from high grade human glioma samples. NovaSeq6000 was used for ATAC seq. The files uploaded are bam files created with grch38 reference.

  Dataset EGAD00001005406

• GATCI whole exome germline variants

  Exome sequences were aligned to the GRCH38 reference genome. Aligned sequence was analyzed with GATK Haplotype Caller to generate germline variant calls. Variant calls are in VCF format. Details for the call can be found in the VCF header

  Dataset EGAD00001005916

• GATCI whole exome somatic variants (MuTect)

  Exome sequences were aligned to the GRCH38 reference genome. Aligned sequence was analyzed with GATK/MuTect, to generate somatic variant calls. Somatic variant calls are in VCF format. Details for the mutect call can be found in the vcf header.

  Dataset EGAD00001005917

• GATCI whole exome somatic variants (SomaticSniper)

  Exome sequences were aligned to the GRCH38 reference genome. Aligned sequence was analyzed with GATK/SomaticSniper, to generate somatic variant calls. Somatic variant calls are in VCF format. Details for the mutect call can be found in the vcf header.

  Dataset EGAD00001005918