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• LSC RNA-Sequencing

  To infer the proteomic Mito signature in the LSC subcompartiment, myeloid blasts for 10 patients from the discovery cohort were FACS-sorted into CD34-GPR56+NKG2DLigands- (CD34-), alias 61dc5fb798e2520001702c03 CD34+GPR56+NKG2DLigands- (CD34+), alias 61dc5fb798e2520001702c03 Detailed gating strategy will be described in Donato, Correia, Andresen and Trumpp et al., (manuscript in preparation)

  Dataset EGAD00001008488

• Drug-induced epigenomic plasticity reprograms circadian rhythm regulation to drive prostate cancer towards androgen-independence

  ChIP-seq for AR, FOXA1 and H3K27ac in primary prostate tumors before and after 3 months of neoadjuvant enzalutamide treatment. RNA-seq expression data of primary prostate tumors before and after 3 months of neoadjuvant enzalutamide treatment.

  Dataset EGAD00001008562

• Fastq and reference alignment of 19 samples for defining structural variation associated with breast cancer susceptibility by long-read genome sequencing

  Long-read genome sequencing performed on the Oxford Nanopore Technologies' PromethION to resolve variants underlying breast cancer susceptibility in sixteen individuals with pathogenic germline SVs in BRCA1, BRCA2, CHEK2 or PALB2.

  Dataset EGAD00001008690

• Stromal and dendritic cells from lymph nodes: single-cell RNA-seq

  Although cross-species transcriptional analysis has been generated for DCs, transcriptomic conservation between mouse and human FRCs at single-cell resolution has been unclear. To test whether GREM1+ FRCs might also play a role in DC homeostasis in humans, we performed scRNA-seq of CD45–PDPN+ stromal cells, as well as CD45+CD11c+ immune cells from healthy human LNs of three human donors. Data was generated using the 10x platform.

  Dataset EGAD00001008731

• Dataset for upper_gastrointestinal_tumor-EXON

  Rare cancer sequencing data of 85 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

  Dataset EGAD00001008902

• Whole genome sequencing of multifocal ileal neuroendocrine tumors

  This dataset includes whole genome sequences of 75 synchronous primary tumors, 15 metastases, and corresponding normal samples from 13 patients with multifocal ileal neuroendocrine tumors. The whole genomes were sequenced on Illumina HiSeq X Ten to generate 151-bp paired-end reads, which were aligned to GRCh38/hg38 reference assembly using BWA–MEM and duplicate-marked with Picard tools. GATK was utilized for base score recalibration and local indel re-alignments. The whole genomes are provided as CRAM files.

  Dataset EGAD00001008831

• ATAC-seq of metastatic prostate tumors

  This dataset includes Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) data, in FASTQ format, from 70 metastatic castration-resistant prostate cancer tumor samples from the SU2C/PCF West Coast Dream Team (WCDT) project. The sequencing data is paired-end, 150 bp sequencing data from an Illumina NovaSeq 6000 machine. ATAC-seq libraries were prepared following the protocol described in Buenrostro et al. Nature Methods. 2013 (PMID: 24097267) and Corces et al. Nature Methods. 2017 (PMID: 28846090).

  Dataset EGAD00001009654

• Dataset of 4 WGS and 35 WES tumor and control runs linked for the ImmuNEO publication out of EGAS00001004813

  Sequencing data of 39 tumor and control runs (different tumors and blood controls), which were uploaded to EGAS00001004813 and reused in this ImmuNEO publication. The sequencing was always paired.

  Dataset EGAD00001009671

• Single-cell RNA and TCR sequencing of BALF from 11 ICI-pneumonitis patients and 6 controls

  Dataset containing the FASTQ files of RNA (scr*) and TCR (vdj*) sequencing of 17 bronchoalveolar lavage fluid samples collected from ICI pneumonitis (n=11) and control (n=6) patients. To comply with GDPR regulations, please note that individual sample identifiers used for this data deposit (alphabetical ID) are different from and cannot be traced back to the patient identifiers used throughout the manuscript (numerical ID).

  Dataset EGAD00001009723

• Papua New Guinean Genome Altitude Project Dataset 2

  The PGAP dataset 2 includes 82 whole genome sequences for Papua New Guinean individuals sampled in Daru (N=1), Port Moresby (N=64) and Mount Wilhelm (N=17). DNA was extracted from saliva samples (Oragen kit). Sequencing libraries were prepared using the TruSeq DNA PCR-Free HT kit. 150 bp paired-end sequencing was performed on the Illumina HiSeq X5 sequencer. The PGAP dataset provides Fastq, mapped cram files (GRCh38) and phenotype measurements.

  Dataset EGAD00001010142