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• Bulk RNA from sorted CD8+ T cells after 48h co-culture with human Mito-DsRed MSCs.

  For human samples, total cellular RNA was isolated from post-sorted Mito+ and Mito CD8+ cells using the RNeasy Mini Kit (Qiagen). Stranded RNA libraries were created using SMARTSeq Stranded.

  Dataset EGAD00001011082

• ICGC PCAWG Dataset: GACA-CN_PCAWG_WGS_BWA

  ICGC PCAWG Dataset for WGS BAM aligned using BWA MEM. Project: GACA-CN.

  Dataset EGAD00001003132

• ICGC PCAWG Dataset: OV-AU_PCAWG_WGS_BWA

  ICGC PCAWG Dataset for WGS BAM aligned using BWA MEM. Project: OV-AU.

  Dataset EGAD00001003227

• ICGC PCAWG Dataset: OV-AU_PCAWG_RNA-Seq_Star

  ICGC PCAWG Dataset for RNA-Seq BAM aligned using Star. Project: OV-AU.

  Dataset EGAD00001003415

• ICGC PCAWG Dataset: OV-AU_PCAWG_RNA-Seq_TopHat2

  ICGC PCAWG Dataset for RNA-Seq BAM aligned using TopHat2. Project: OV-AU.

  Dataset EGAD00001003416

• ICGC PCAWG Dataset: LIRI-JP_PCAWG_RNA-Seq_TopHat2

  ICGC PCAWG Dataset for RNA-Seq BAM aligned using TopHat2. Project: LIRI-JP.

  Dataset EGAD00001003546

• Genomic Landscape of Chordoid Glioma

  This data set consist genomic information of 10 Chordoid Glioma samples: - Exome sequencing: 10 tumors and matched normal DNA for four of them (BAM files) - RNAseq : 10 tumors (fastq files) - CNV array: 9 tumors (IDAT files)

  Dataset EGAD00001004112

• SNV vcf files for CPCG Subclonal Heterogeneity in multiple and single regions

  SNV calls generated using the MuTect-TITAN-PhyloWGS from the CPC-GENE Subclonal Heterogeneity study using single and multiple regions

  Dataset EGAD00001004433

• ICGC PCAWG Dataset: LAML-KR_PCAWG_WGS_BWA

  ICGC PCAWG Dataset for WGS BAM aligned using BWA MEM. Project: LAML-KR.

  Dataset EGAD00001002119

• ICGC PCAWG Dataset: BTCA-SG_PCAWG_WGS_BWA

  ICGC PCAWG Dataset for WGS BAM aligned using BWA MEM. Project: BTCA-SG.

  Dataset EGAD00001002121

• ICGC PCAWG Dataset: BRCA-UK_PCAWG_WGS_BWA

  ICGC PCAWG Dataset for WGS BAM aligned using BWA MEM. Project: BRCA-UK.

  Dataset EGAD00001002122

• ICGC PCAWG Dataset: PAEN-IT_PCAWG_WGS_BWA

  ICGC PCAWG Dataset for WGS BAM aligned using BWA MEM. Project: PAEN-IT.

  Dataset EGAD00001002153

• ICGC PCAWG Dataset: CMDI-UK_PCAWG_WGS_BWA

  ICGC PCAWG Dataset for WGS BAM aligned using BWA MEM. Project: CMDI-UK.

  Dataset EGAD00001002664

• BLUEPRINT DNA methylation profiles of human hematopoietic progenitors

  DNA methylation was analyzed for stem/progenitor cell types and terminally differentiated cell types of the human blood lineage (HSC, MPP, CMP, MEP, GMP, CLP, MLP0, MLP1, MLP2, MLP3, MK, CD4+ Tcell, CD8+ Tcell, Bcell, NK, Neut, Mono).

  Dataset EGAD00001002732

• SF11979 snATAC seq IDHR132H Wildtype GBM Female

  SF11979 snATAC, IDHR132H WT GBM Female, 76 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 EGAD00001005418

• Multi-region sequencing of a RET fusion positive cancer patient

  Deep WGS sequencing (160x) of 2 different sites of disease of a patient with a RET fusion positive cancer. Amplicon sequencing of 19 other sites of the same patients for the RET fusion.

  Dataset EGAD00001005776

• Dataset for RNA and Exome sequencing of Glioblastoma samples

  This dataset contains RNA Seq, 10x scRNA Seq and Exome sequencing of glioblastoma samples. Sequencing was performed on a Illumina NovaSeq 6000 and Illumina HiSeq 4000. The sequencing was always paired.

  Dataset EGAD00001012235

• Exome sequencing data for 40 cases of alopecia areata and vitiligo

  Sequencing of independent unrelated cases of alopecia areata (total/ universal) and vitiligo (>10%, affected family member). DNA obtained from blood

  Study EGAS00001003831

• Single Cell Genome Variation Induced by Mutational Processes in Cancer - HGSOC Trios Study

  Mutational signatures derived from whole genome sequencing have potential prognostic significance. Identification of high grade serous ovarian cancer patients with deficiency in homologous recombination repair pathways could identify a subset of patients that would benefit from homologous recombination deficiency-specific treatments independent of identification of a pathological BRCA1/2 gene mutation. Clinical protocols rely on a pathologist's assessment of formalin-fixed paraffin-embedded (FFPE) tissues, and thus FFPE tissue samples are readily available. However, the bulk of mutational signature analyses have been performed on fresh frozen tissues. In this study, we aimed to assess the reliability of whole genome sequencing, variant calling, and mutational signature analysis from FFPE tissue samples.

  Study phs003036

• Single-Cell Profiling of Premature Neonate Airways Reveals a Continuum of Myeloid Differentiation

  We set out to develop a reference single-cell transcriptomic profile of airway aspirate samples from extremely premature neonates (collected within an hour of birth). In this study, we profiled samples from 10 subjects. We identified cells in the airways of premature neonates representing a continuum of myeloid differentiation, including fetal monocytes, differentiating myeloid cells, and macrophages. Trajectory analysis identified two trajectories consistent with interstitial and alveolar macrophages, and a bridging trajectory providing an alternative route between these terminal states. We defined 259 alveolar-specific genes, 666 interstitial-specific genes, and 285 bridging-specific genes providing the first single-cell transcriptional map of differentiating airway macrophages in humans.

  Study phs003427

• Genomic Characterization of Pediatric Low-Grade Gliomas

  Pediatric low-grade gliomas (PLGGs) are the most common pediatric brain-tumor, with more than ten histologic subtypes recognized by the World Health Organization. We performed a genomic analysis of 230 PLGGs of which 73 had whole genome/RNA sequencing performed and show that MYB-QKI fusions define the seizure associated tumor, Angiocentric Glioma (AG). MYB-QKI fusions present in AGs contribute to tumorigenesis through three mechanisms: MYB activation by truncation, enhancer translocation driving aberrant MYB-QKI expression, and hemizygous loss of QKI, a tumor suppressor gene. Such interplay between three oncogenic mechanisms has diagnostic and therapeutic implications in AGs, and illustrates the functional complexity associated with rearrangements in cancer.

  Study phs001054

• NHLBI TOPMed - NHGRI CCDG: The GENetics in Atrial Fibrillation (GENAF) Study

  The Genetics in AF (GENAF) study enrolled individuals with early-onset lone AF before age 50 in Norway between 2009 and 2016. Early-onset was defined as diagnosis of AF before age 50. Lone AF was defined as AF in the absence of clinical or echocardiographic findings of cardiovascular disease, hypertension, metabolic or pulmonary disease. AF was documented in ECG. All participants underwent clinical examination, including ECG, echocardiography, and blood draw, from which DNA has been extracted. The study conforms to the principles of the Declaration of Helsinki and was approved by the Regional Ethics Committee (REK) in Norway (Protocol reference number: 2009/2224-5). All included patients gave written informed consent.

  Study phs001547

• BLUEPRINT Gene expression analysis during human B-cell differentiation using the Affymetrix Human Genome U219 Array

  We performed gene expression analysis using the Affymetrix Human Genome U219 Array of 9 subpopulations covering the complete B-cell maturation program: hematopoietic progenitor cells (HPC); pre-B-I cells (preB1C); pre-B-II cells (preB2C); naive B cells from peripheral blood (naiBC); naive B cells from tonsil (t-naiBC); germinal center B cells (gcBC); plasma cells from tonsil (t-PC); memory B cells from peripheral blood (memBC) and plasma cells from bone marrow (bm-PC). All the samples were isolated from healthy donors and, with the exception of bm-PC (only 1 replicate), we used 3 to 11 biological replicates of each subtype.

  Study EGAS00001001197

• STREP GENE: Genetics and Severe Streptococcal Infections

  This study investigated host genetic susceptibility to invasive group A streptococcal disease in the UK. Cases were either survivors recruited retrospectively through a patient group or identified from the a tissue bank at Imperial College London. Those recruited through the patient group had survived an episode of invasive GAS disease at a UK hospital since 1980 with microbiological confirmation obtained either through Public Health England or from the treating hospital. Those identified from the tissue bank had been diagnosed with invasive GAS disease at the Hammersmith Hospital, London, UK, since 2006. All cases aged less than 65 years without long-term medical conditions genome-wide genotyped using either the Illumina HumanCore or the Global Screening Array platform.

  Study EGAS00001003421

• Time-dependent characterization of CNS response in COVID-19

  Coronavirus disease 2019 (COVID-19) caused by SARS-CoV-2 primarily affects the respiratory system, but the observation of diverse neurological symptoms indicates that other organs, including the brain, may be involved. The pathophysiological mechanisms of COVID-19-associated effects on the central nervous system (CNS) have become clearer during the past two years. Nevertheless, the precise CNS-specific molecular mechanisms are still elusive and raise several questions. To further elucidate the host response at brain tissue level, we profiled single-nucleus transcriptomes and performed proteomics from olfactory mucosa, olfactory bulb, medulla oblongata and cerebellum at different timepoints of the disease in individuals who died of COVID-19 and underwent rapid autopsy.

  Study EGAS00001006442