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• Genome-wide 5-mC profiling in plasma of metastatic ALK-rearranged non-small cell lung cancer (NSCLC) patients receiving tyrosine kinase inhibitor therapy.

  Longitudinal plasma samples (n = 79) of 21 ALK-positive NSCLC patients and 13 healthy donors were collected alongside 15 ALK-positive tumor tissue and 10 healthy lung tissue specimens. All plasma and tissue samples were analyzed by cell-free DNA methylation immunoprecipitation sequencing to generate genome-wide 5-mC profiles. Paired cfMeDIP on NextSeq 550 using KAPA Hyper Prep Kit was done.

  Dataset EGAD00001009412

• Single cell sequencing on whole bone marrow of NBM and AML

  To generate a cellular taxonomy of the human NBM and AML, representing both rare hematopoietic stem/progenitor cells (HSPCs) and stromal niche populations, allowing assessment of their cellular diversity and predicted intercellular signaling, we performed single cell RNA sequencing (scRNAseq) on viably frozen bone marrow (BM) aspirates from four healthy donors and 6 NPM1+ AML patients at diagnosis

  Dataset EGAD00001011057

• Single-cell transcriptome landscape of developing fetal gonads defines somatic cell lineage specification in humans

  Single-cell RNA-seq dataset recovering the gene expression programs of around 128,000 single cells derived from 17 fetal testes and 16 fetal ovaries from 5 to 12 postconceptional weeks.

  Dataset EGAD00001009811

• ATAC-seq data from primary AML samples with t(3;8)

  Open chromatin regions in the MYC super-enhancer region were investigated by ATAC-seq in t(3;8) AML. ATAC-seq was performed as described (Buenrostro et al, 2013) with a modification in the lysis buffer (0.30 M sucrose, 10 mM Tris pH 7.5, 60 mM KCl, 15 mM NaCl, 5 mM MgCl2, 0.1 mM EGTA, 0.1% NP40, 0.15 mM Spermine, 0.5 mM Spermidine, 2 mM 6AA) to reduce mitochondrial DNA contamination.

  Dataset EGAD00001007910

• Methylation profiling of human lung fibroblasts in COPD

  Primary lung fibroblast were isolated from well-matched control donors (no COPD, n=3) and patients with COPD (GOLD stage I-IV, n=8). Genomic DNA of cultured human lung fibroblast was isolated at passage 3, fragmented by tagmentation, and subjected to bisulfite treatment. 100 bp paired-end reads were generated from DNA libraries on Illumina HiSeq2500 platform.

  Dataset EGAD00001009406

• Targeted sequencing of follicular lymphoma tumour samples from the UK's Haematological Malignancy Research Network

  Targeted sequencing was applied to an unselected population-based follicular lymphoma (FL) cohort (n=548) diagnosed in the UK's Haematological Malignancy Research Network catchment population of ~4 million (14 centres). DNA extracted from FL samples was sequenced with a 293-gene panel using the Illumina HiSeq 2500. All data are provided in the CRAM format.

  Dataset EGAD00001007657

• Single cell RNA sequencing of colorectal cancer with diverse tissue dissociation protocols or fresh vs. frozen cell preparations.

  To evaluate 3 different tissue dissociation protocols or fresh vs. frozen cell preparations, we performed single-cell RNA sequencing on cancer or distant normal tissue dissociates from 2 colorectal cancer patients. Total 18,409 cells from 10 sample preparations were analyzed (5 primary colorectal cancer and 5 matched normal mucosa). The results suggest highly consistent cellular proportions were recovered with different sample preparation methods.

  Dataset EGAD00001005191

• WGS of COH TNBC

  WGS data relative to 42 primary and treatment-naive triple negative breast cancers, from independent donors.

  Dataset EGAD00001008617

• Whole Genome DNA Sequencing of matched brain tumor-normal pairs (ICGC)

  Illumina HiSeq sequence data (with >30x coverage) were aligned to the hg19 human reference genome assembly using BWA (Li and Durbin, 2009); duplicate reads were removed from the final BAM file. No realignment or recalibration was performed.

  Dataset EGAD00001000697

• TERT rearrangements are frequent in neuroblastoma and identify aggressive tumors

  Whole genome sequencing detected structural rearrangements of TERT in 17/75 high stage neuroblastoma with 5 cases resulting from chromothripsis. Rearrangements were associated with increased TERT expression and targeted immediate up- and down-stream regions of TERT, placing in 7 cases a super-enhancer close to the breakpoints. TERT rearrangements (23%), ATRX deletions (11%) and MYCN amplifications (37%) identify three almost non-overlapping groups of high stage neuroblastoma, each associated with very poor prognosis. This submission contains all newly sequenced samples only.study_refcenter AMC

  Dataset EGAD00001001635

• Whole Exome DNA Sequencing of matched brain tumor-normal pairs

  Illumina HiSeq sequence data (with >80x coverage) were aligned to the hg19 human reference genome assembly using BWA (Li and Durbin, 2009); duplicate reads were removed from the final BAM file. No realignment or recalibration was performed.The whole exome sequencing data of 20 SHH medulloblastomas from phs000504.v1.p1 dataset has been used in our study on SHH medulloblastomas: http://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000504.v1.p1

  Dataset EGAD00001000698

• Exome sequencing of Congenital Heart Disease families from the Competence Network Berlin

  This project aims to study exomes from families and trios with congenital heart disease (CHD). The samples have been collected under the Competence Network - Congenital Heart Defects in Berlin, Germany. The phenotypes are mainly left ventricular outflow obstruction (aortic stenosis, bicuspd aortic valve disease coarctation and hypoplastic left heart), but will also include samples with hypoplastic right heart and atrioventricular septal defects. We will perform whole exome sequencing using Agilent sequence capture and Illumina HiSeq sequencing.

  Dataset EGAD00001000800

• 762 whole exome sequencing samples from the Singapore Living Biobank

  The dataset includes a subset of 762 individuals that were found to be closely related (≤3rd degree), including 263 Chinese and 499 Malays from the Singapore Living Biobank. There samples are whole-exome sequenced on Illumina HiSeq2000 platform (125bp paired end) with the exonic regions being captured using the Nimblegen SeqCap EZ Exome v3 kits.All the files are in the BAM format.

  Dataset EGAD00001003819

• Mitochondrial DNA (mtDNA) sequences from subjects with intellectual disability (ID) and austism spectrum disorder (ASD)

  Sequences from 95 subjects presenting intellectual disability (ID) and 98 subjects presenting intellectual disability and a diagnosis of autism spectrum disorder (ASD). The mtDNA was amplified by long-range PCR with 3 pairs of primers producing overlapping fragments. The three fragments were mixed in equimolar ratios and each sample was sequenced in an Ion Torrent Personal Machine according to manufacturer's user guide (reference genome: NC_012920.1 (rCRS)).

  Dataset EGAD00001004213

• Whole Genome Sequencing of JK Family

  In collaboration with Dr David Savage, we have identified a patient with a very unusual phenotype, lacking almost all visceral fat, but showing a massive accumulation of white fat tissue behind her neck and significantly elevated liver fat. Whole exome sequencing of the proband and her unaffected parents and brother has been run previously, however no causative variant has been found and the sequencing coverage was generally poor. We propose to conduct whole genome sequencing of all 4 family members at a depth of 30X.

  Dataset EGAD00001002227

• Chromatin accessibility analysis of hepatocyte-like cell in vitro differentiation from iPSC in comparison to primary human hepatocytes

  Fastq files of ATAC-seq data of induced pluripotent stem cells (iPSC), definitive endoderm (DE), hepatocyte-like cells (HLC) and primary human hepatocytes (PHH). The dataset comprises data from two different in vitro differentiation protocols: Cellartis (Takara Bio, "CEL", n = 4) and as described by Wang et al. (PMID: 28287600, "HAY", n = 1), as well as from 3 PHH donors.

  Dataset EGAD00001005934

• mRNA-seq of in vitro differentiation from induced pluripotent stem cells to hepatocyte-like cells

  Fastq files of mRNA-seq data of induced pluripotent stem cells (iPSC), definitive endoderm (DE) and hepatocyte-like cells (HLC). The dataset comprises data from the in vitro differentiation protocol Cellartis (Takara Bio, "CEL", n = 4) and several interventions (11x3 replicates).

  Dataset EGAD00001005935

• Single-cell RNA-seq data of bronchoalveolar lavage (BAL) fluid in severe COVID-19 and SARS-CoV-2 stimulated classical blood monocytes

  We performed single-cell RNA-sequencing of cells in the bronchoalveolar lavage (BAL) fluid of severe COVID-19. In addition, we performed single-cell RNA-sequencing of SARS-CoV-2 stimulated classical blood monocytes. This study provides detailed insights into the alveolar macrophage response to SARS-CoV-2 infection and reveals a profibrotic macrophage response in severe COVID-19 patients.

  Dataset EGAD00001006827

• MGHBoston_Molpheno_Closed

  This dataset contains Whole Genome Sequencing and, if available, RNA-sequencing and/or ATAC-sequencing data of 17 lymphoblastoid cell lines derived from patients with complex genomic rearrangements. Patients have phenotypes in category of intellectual disability and/or multiple congenital anomalies. Data access is closed.

  Dataset EGAD00001004866

• Tcells_CD_scRNAseq

  This set features unfiltered, aligned, UMI-based single cell RNA sequencing count data for 5290 Blood, intraepithelial ileum (IEL) and lamina propria ileum (LPL) T cells from Crohn's disease patients as published in Uniken Venema et al, Gastroenterology 2019

  Dataset EGAD00010001649

• ChIP-seq ERa in primary breast cancer tissues

  ChIP-seq has been perfomed on 5 tumor fresh-frozen primary breast cancer tissues from female patients. Immunoprecipitation has been performed for ERa (SC-543, Santa Cruz). Raw single-end fastq data have been aligned using bwa-mem using Hg19 genome assebly as reference. Unfiltered aligment bam files are provided.

  Dataset EGAD50000000014

• Exome sequencing for heterogeneity and evolution of DNA mutation rates

  Dataset comprising 27 pairs of high-depth (300x) WES results obtained from 54 PDXs derived from primary CRCs resected synchronously with their corresponding metastases. These exoms sequences are part of a larger study on the heterogeneity and evolution of DNA mutation rates in microsatellite-stable colorectal cancer.

  Dataset EGAD50000000208

• Human Brain Small Extracellular Vesicles Contain Selectively-Packaged, Full-Length mRNA

  sEVs were isolated from postmortem human brain tissue. RNA was extracted from the source brain tissue and the sEVs and prepared for RNA sequencing. cDNA was sequenced on the Illumina HiSeq using a 2x150 paired-end read configuration.

  Dataset EGAD50000000042

• Sputum RNA-Seq from Asthmatic Patients for Microbes and Genes

  RNA-seq files and other data associated with an investigation of the relationship between microbes, genes and immune cells present in the sputum of humans with asthma.

  Study phs002224

• ctDNA diva aggregate data

  ctDNA biomarker and relevant clinical data for divarasib phase I GO42144 study, including tumor type, KRAS G12C mutation detectability in plasma at baseline, baseline SLD, sites of metastasis, lines of therapy, best response, confirmed best response, PFS, ctDNA tumor fraction and KRAS G12C VAF at baseline/C1D15/C3D1.

  Dataset EGAD50000000454