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• Understanding_the_multicellular_dynamics_of_clear_cell_renal_cell_carcinoma___visium

  This study will reconstruct the single cellular phylogeny of tumour and immune cells in relation to both genomic, functional, and spatial location. 20 tumours in total will be studied, including non-progressing small renal masses, progressing small renal masses, relatively indolent larger tumours, and high risk tumour with metastatic sampling. We aim to: Generate a focused, comprehensive phylogenetic characterisation of tumour cells Understand the dependencies of the cancer genome, transcriptome, tissue architecture and the single cellular micro-environment Quantify the single cellular composition and functional intra- and inter- tumoural heterogeneity Determine the phylogeny of tumour associated lymphocytes and their relationship to neo-epitopes and the immune microenvironment Investigate the mechanisms by which the tumour-normal interface constrains tumoural growth.

  Study EGAS00001006045

• Memorial Sloan Kettering (MSKCC) Single Cell Mutational Profiling in Myeloid Malignancies

  Myeloid malignancies have previously been characterized by large scale bulk molecular profiling studies on patient samples. These studies, while clinically informative, are unable to delineate mutation order as well as clonal architecture and complexity. To investigate the clonal framework of myeloid malignancies, the Single Cell Mutational Profiling in Myeloid Malignancies study was designed. This study performed sequencing of 148 samples from 117 adult patients diagnosed with clonal hematopoiesis (n = 21), myeloproliferative neoplasms (MPN; n = 14), and acute myeloid leukemia (AML; n = 82) between 20 and 87 years of age. Sequencing of all samples was performed using the Tapestri single cell DNA sequencing platform from Mission Bio, Inc. The platform utilizes a custom amplicon panel covering 109 amplicons across 31 genes frequently mutated in myeloid malignancies (CH, MPN, AML). Using the single cell DNA sequencing data, we were capable of elucidating clonal architecture and clonal complexity in each sample. In a subset of samples, we also performed simultaneous single cell DNA sequencing and cell surface protein expression analysis using the Tapestri DNA + Protein platform. This study allowed us to determine the expression of 7 cell surface proteins (CD3, CD11b, CD19, CD34, CD38, CD45RA, and CD90) at single cell resolution. We performed DNA+ Protein sequencing on samples from CH patients (n = 7) as well as AML patients (n = 17).

  Study phs002049

• Differential methylation positions

  This dataset includes an analyzed DMP file that provide the information about differential methylation positions based on Illumina Infinium MethylationEPIC BeadChip. All samples (5 lung cancer cases vs. 5 benign lung disease controls) were obtained from bronchial washings at the site of the lesion under bronchoscopy manipulation. Of the five lung cancer cases, 3 are adenocarcinoma and 2 are squamous carcinoma.

  Dataset EGAD00001010147

• Whole transcriptome RNA sequencing on bone marrow and peripheral blood samples from patients with acute myeloid leukemia at diagnosis or relapse.

  One hundred cryopreserved bone marrow and peripheral blood samples from patients with acute myeloid leukemia (AML) with 10-90% blasts were selected from the biobank of the Department of Hematology of Leiden University Medical Center (LUMC). The AML cases cover all subtypes, and specifically include known subtype-defining balanced chromosomal translocations according to the WHO classification. The samples were obtained from 96 patients and include three pairs of de novo and relapsed AML and one pair of de novo and presumed therapy-related AML (tAML). Total RNA was isolated from mononuclear cells without prior enrichment for leukemic blasts. The quality and integrity of total RNA was checked and RNA libraries were prepared using the TruSeq RNA library preparation kit v2 (Illumina, San Diego, CA) in an ISO/IEC 17025-accredited protocol. This workflow started with enrichment of messenger RNA by oligo dT magnetic beads. After fragmentation, cDNA synthesis was performed, followed by adaptor ligation and PCR amplification. Paired-end sequencing with a read length of 126 bp was performed on an Illumina HiSeq 2500 v4 sequencer to at least 12.5 Gbp per sample. Image analysis, base calling, and quality check was performed with Illumina data analysis pipeline RTA v1.18.64 and Bcl2fastq v1.8.4. RNAseq reads are provided in compressed Sanger FASTQ format.

  Dataset EGAD00001004187

• Whole Genome Sequencing of 44 Chronic Lymphocytic Leukemia

  Whole Genome Sequencing of 44 patients with Chronic Lymphocytic Leukemia. This dataset comprises 44 .bam files aligned to the hg19 build of the human genome from sequencing reads generated on an Illumina HiSeq instrument.

  Dataset EGAD00001004384

• Multiple Tissue Monitoring in Huntington disease - RNAseq skeletal muscle

  We examined whether peripheral tissues can serve as a source of readily accessible biological signatures at the RNA and protein level in Huntington disease (HD) patients. Under the MTM-HD study we generated large, high-quality human datasets from skeletal muscle, skin and adipose tissue, as well as primary human fibroblast lines to probe molecular changes in human pre-manifest and early manifest HD patients. We document the involvement of inflammation, energy metabolism and extracellular vesicle homeostasis. This demonstrates the potential to identify biological signatures from peripheral tissues in HD suitable as biomarkers in clinical trials.

  Study EGAS00001006474

• Multiple Tissue Monitoring in Huntington disease - RNAseq adipose tissue

  We examined whether peripheral tissues can serve as a source of readily accessible biological signatures at the RNA and protein level in Huntington disease (HD) patients. Under the MTM-HD study we generated large, high-quality human datasets from skeletal muscle, skin and adipose tissue, as well as primary human fibroblast lines to probe molecular changes in human pre-manifest and early manifest HD patients. We document the involvement of inflammation, energy metabolism and extracellular vesicle homeostasis. This demonstrates the potential to identify biological signatures from peripheral tissues in HD suitable as biomarkers in clinical trials.

  Study EGAS00001006473

• Multiple Tissue Monitoring in Huntington disease - RNAseq fibroblasts

  We examined whether peripheral tissues can serve as a source of readily accessible biological signatures at the RNA and protein level in Huntington disease (HD) patients. Under the MTM-HD study we generated large, high-quality human datasets from skeletal muscle, skin and adipose tissue, as well as primary human fibroblast lines to probe molecular changes in human pre-manifest and early manifest HD patients. We document the involvement of inflammation, energy metabolism and extracellular vesicle homeostasis. This demonstrates the potential to identify biological signatures from peripheral tissues in HD suitable as biomarkers in clinical trials.

  Study EGAS00001006472

• LEMA WES files

  This dataset contains WES bam/bai files associated with 133 patients as part of the LEMA Study

  Dataset EGAD50000001311

• ACUITI BAM files

  This dataset contains WES bam/bai files associated with 51 patients as part of the ACUITI Study

  Dataset EGAD50000001401

• Covacta OLINK LOD

  Explore 1536 dataset from serum of patients enrolled in the COVACTA trial. This dataset includes limit of detection values provided by Olink.

  Dataset EGAD00001011161

• Transcriptome analysis of human muscle/myofibers carrying the human nemaline myopathy type 6-associated KBTBD13-R408C variant.

  This dataset contains mRNA-seq results from eleven samples from human donors, each sample being composed of 5-10 rebulked fiber type-specific myofibers. This sample set includes; 1) Three FT-I and three FT-IIa rebulked samples from control individuals 2) Three FT-I and two FT-IIa rebulked samples from NEM6 patients with a KBTBD13R408C variant (NP_001094832.1: p.Arg408Cys)

  Dataset EGAD50000002408

• Clinical panel sequencing of cancer of unknown primary using TruSight Oncology 500 (TSO500)

  TruSight Oncology 500 (TSO500) cancer panel sequencing data on paired tumour and germline DNA from cancer of unknown primary samples. All of the samples in this dataset are matched to WGS data. This data was used to compare biomarker yield against what was achieved with WGS and contains n=51 tumour-only samples. All samples are in BAM format aligned with GRCh38 reference genome.

  Dataset EGAD50000000657

• ICR TYA WES

  Whole exome sequencing of high grade gliomas occurring in teenagers and young adults between the ages of 13 and 30. This study combines methylation array profiling, whole exome sequencing and fusion panel sequencing to provide an integrated molecular description of brain tumours in this age group. Dataset contains 96 BAM files aligned with BWA to GRCh37 from 88 tumours. Tumour DNA was isolated from FFPE material in most cases. 8 germline sequences from peripheral blood DNA are also included.

  Dataset EGAD50000000904

• Whole exome sequencing of SarBC-01- and UroBC-01-related samples.

  This dataset contains raw FASTQ files from DNA of SarBC-01-related samples (SarBC-01 patient Germline, SarBC-01 patient Urothelial tumor, SarBC-01 patient Sarcomatoid tumor, SarBC-01 Passage 6 organoids, SarBC-01 Passage 20 organoids) and UroBC-01 related samples (UroBC-01 patient Germline, UroBC-01 patient Urothelial tumor, UroBC-01 Passage 19 organoids, UroBC-01 Passage 6 organoids). DNA was extracted from FFPE tissue, using RecoverAll RNA/DNA extraction kit (Invitrogen, Carlsbad, CA, USA, AM1975) followed by incubation with Uracil-DNA Glycosylase, and fresh or flash frozen tissue, using Quick-DNA/RNA Miniprep kit (Zymo Research, Irvine, CA, USA, D7001). Twist Human Core Exome + RefSeq + Mito-Panel kit (Twist Bioscience, 102031) was used for the whole exome capturing. Sequencing was performed on Illumina NovaSeq 6000 using paired-end 100-bp reads.

  Dataset EGAD00001011157

• 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

• Covacta OLINK QC metrics

  Olink Explore 1536 dataset from serum of patients enrolled in the COVACTA trial. This dataset includes QC warning flag provided by Olink.

  Dataset EGAD00001011167

• WGS of 125 cord blood hematopoietic stem and progenitor cells

  This dataset contains 125 BAM files of cord blood hematopoietic stem and progenitor cell DNA, sequenced with Illumina Novaseq 6000, and 125 files with the variant calling performed to the sequencing data.

  Dataset EGAD50000000417

• scRNAseq of neuroblastoma PDX and cell lines

  This dataset contains the 22 bam files coresponding to the scRNAseq done in PDX models and cell lines.

  Dataset EGAD00001007870

• Pilocytic Astrocytoma RNA sequencing

  This dataset contains RNA sequencing samples from the Duesseldorf/LIsbon pilocytic astrocytoma cohort which was profiled using Proteogenomics (RNA Sequencing, proteomics and methylation). There are 48 samples which were sequenced using paired-end sequencing at the University Hopstial Dusseldorf.

  Dataset EGAD00001009053

• RNASeq

  The cohort comprised of 48 pediatric patients with 21 different relapsed or refractory solid neoplasms. This cohort was analysed by RNASeq. The corresponding datasets contains fasq files.

  Dataset EGAD00001010041

• NiCOL Study RNA-seq dataset

  15 samples sequenced in RNA-seq. This dataset contains their raw FASTQ data and the raw count table and the TPM count table.

  Dataset EGAD00001010912

• RNA sequencing data from the lungNENomics project

  Raw RNA-seq data from the lungNENomics cohort, comprising 319 pairs of FASTQ files from 179 individuals. This dataset also includes a gene count matrix, gene TPM matrix and gene expression VST matrix from 244 samples.

  Dataset EGAD00001015524

• Altered Blood and Keratinocyte microRNA/transfer RNA Fragment Profiles Related to Fibromyalgia Syndrome and its Severity

  We show dysregulated microRNA and tRNA fragment profiles related to FMS pathopyhsiology and opening new perspectives for FMS diagnostics and symptom monitoring. This dataset includes all sequencing raw files from whole blood (tempus tube) and keratinocyte sequencing.

  Dataset EGAD50000000900

• Sample metadata

  Sample metadata for this experiment. Includes treatment and donor derivation information.

  Dataset EGAD50000000827