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• McGill EMC Community projects Release 7 for cell line "lung epithelial"

  Complete reference epigenome (as defined by IHEC) of a lung epithelial cell line with non-small Cell Lung Adenocarcinoma

  Dataset EGAD00001007679

• The Xq22.3 contiguous gene deletion syndrome (ATS-ID): from genotype to further delineation of the phenotype

  Approximately 200 ng of high-quality of genomic DNA samples were used for library preparation. DNA libraries were prepared using the Human Core Exome Kit according to manufacturer’s recommendations (Twist Bioscience, San Francisco, CA, USA) and then sequenced on Illumina NovaSeq 6000 (Illumina, Inc., san Diego, CA, USA). Detailed protocol of WES data processing and variant analysis are available in Supplementary data.

  Dataset EGAD00001007740

• Paired-WGS Sequencing of Primary lymphomas of the central nervous system (PCNSL)

  Paired WGS samples, 24 tumor/control pairs of primary CNS lymphoma, sequenced on HiSeq X Ten using Illumina TruSeq Nano DNA for library preparation.

  Dataset EGAD00001007810

• Dataset for linked files from Master-RNA

  RNA sequencing data of thymic epithelias tumors (TETs), 23 runs, which were uploaded to umbrella studies. The sequencing was always paired

  Dataset EGAD00001009096

• 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

• 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

• Whole exome data from PMID27216186

  This dataset comprises complete exome data from from the study PMID27216186 (Harbst & Lauss et al, Cancer Research 2016). These data are from 49 samples (tumor and matched normal) from 8 patients representing multi-region sequencing of human melanoma. Files are in the BAM format and contain aligned and processed data used for e.g. somatic variant calling. The sequencing libraries were constructed using SureSelect target enrichment with Clinical Research Exome Panel (Agilent) and sequenced on a HiSeq2500 (Illumina).

  Dataset EGAD00001008149

• 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