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• The genomic landscape of germinal center derived B-cell lymphomas other than follicular, diffuse-large B-cell and Burkitt lymphom

  As part of the ICGC, the ICGC MMML-Seq project performed whole genome sequencing and RNA sequencing of germinal center derived B-cell lymphoma. Analyses were performed in concordance with the guidelines of the ICGC.

  Study EGAS00001002422

• A Comprehensive Catalogue of Somatic Mutations from a Human Cancer Genome

  We previously reported the whole-genome sequencing of the well-studied human malignant melanoma cell line, COLO-829, and a lymphoblastoid cell line from the same individual, providing the first comprehensive catalogue of somatic mutations from an individual cancer (Pleasance et al. (2010) Nature 463, 191). This initial study was carried out using the Illumina Genome Analyzer II, largely using paired-end reads of 75 bases from standard Illumina paired-end libraries. Here we report the results of sequencing the genomes of COLO-829 and its matched lymphoblastoid sample using HiSeq2000 with v3 cluster-generation and sequencing chemistries. This has significantly improved the evenness and completeness of genomic coverage, particularly in areas of extreme sequence composition that were underrepresented in the initial study.

  Study EGAS00001000245

• Understanding_the_multicellular_dynamics_of_clear_cell_renal_cell_carcinoma___DNA_sequencing

  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 EGAS00001003517

• Understanding_the_multicellular_dynamics_of_clear_cell_renal_cell_carcinoma___single_cell_RNA_sequencing

  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 EGAS00001003519

• TSG_knock_out_in_hiPSCs

  We will perform RNAseq to evaluate the effects of the loss of a list of TSGs on the transcriptome.

  Study EGAS00001002262

• RNA-seq

  The RNA was extracted using the AS1390 PROMEGA kit according to the manufacturer’s instructions. The samples underwent sequencing using a Novaseq 6000 machine, equipped with an SP 200 cycles v1.5 cartridge. The sequencing process varied slightly across batches based on the input RNA and the library preparation kits used.

  Dataset EGAD50000002023

• CTOS colorectal cancer organoids – WES and RNA-seq

  Runs for WES and RNA-seq (excluding C138_WES pending file replacement).

  Dataset EGAD50000002401

• Targeted PacBio long-read scRNA-seq

  Twist custom capture–based targeted PacBio long-read scRNA-seq datasets for human adrenal sampleA and sampleB

  Dataset EGAD50000002212

• Short-read scRNA-seq

  10x Chromium Single Cell 3′ single-cell cDNA sequencing data for adrenal tissue sampleA and sampleB.

  Dataset EGAD50000002210

• RNAseq for 208 patients with medulloblastoma cancer (MB_COMICS cohort)

  This dataset contains 208 paired fastq files sequenced with Illumina HiSeq 2500.

  Dataset EGAD50000000600

• Taste Receptor Genotypes_Centenarians and Young

  This dataset includes targeted genotyping data for six BMI-associated polymorphisms across four candidate genes in young and centenarian individuals.

  Dataset EGAD00010002829

• SAFIR02_Oncoscan

  Genomics to select patients with metastatic breast cancer for targeted therapy (microarray_oncoscan)

  Dataset EGAD00010002241

• INMUNGEN_CoV2_genotype

  Cohort: Raw genotype files for INMUNGEN_CoV2 cohort. Genotype Chip: HumanCore Exome Chip (Illumina) and Axiom Spanish Biobank Array (Thermofisher) genomic build: b37

  Dataset EGAD00010002174

• Reference epigenome CKD23_C_Mesan_mRNA-Seq data generated from KEP study

  A CKD23_C_Mesan_mRNA-Seq paired end data for Mesangial cells(kidney)

  Dataset EGAD00001003481

• Reference epigenome CKD27_C_Mesan_mRNA-Seq data generated from KEP study

  A CKD27_C_Mesan_mRNA-Seq paired end data for Mesangial cells(kidney)

  Dataset EGAD00001003484

• Reference epigenome CKD23_C_Mesan_smRNA-Seq data generated from KEP study

  A CKD23_C_Mesan_smRNA-Seq single end data for Mesangial cells(kidney)

  Dataset EGAD00001003497

• Reference epigenome CKD27_C_Mesan_smRNA-Seq data generated from KEP study

  A CKD27_C_Mesan_smRNA-Seq single end data for Mesangial cells(kidney)

  Dataset EGAD00001003500

• RNA-sequencing of SYSCOL colorectal adenoma-carcinoma samples

  RNA-sequencing alignment for SYSCOL colorectal adenoma-carcinoma samples

  Dataset EGAD00001003318

• Reference epigenome SMC05_ChIP-Seq(H3K27me3) data generated from KEP study

  A SMC05_ChIP-Seq(H3K27me3) paired end data for skeletal muscle cells

  Dataset EGAD00001003849

• Reference epigenome SMC06_ChIP-Seq(H3K27me3) data generated from KEP study

  A SMC06_ChIP-Seq(H3K27me3) paired end data for skeletal muscle cells

  Dataset EGAD00001003850

• Reference epigenome SMC01_ChIP-Seq(H3K27me3) data generated from KEP study

  A SMC01_ChIP-Seq(H3K27me3) paired end data for skeletal muscle cells

  Dataset EGAD00001003845

• Reference epigenome SMC02_ChIP-Seq(H3K27me3) data generated from KEP study

  A SMC02_ChIP-Seq(H3K27me3) paired end data for skeletal muscle cells

  Dataset EGAD00001003846

• Reference epigenome SMC03_ChIP-Seq(H3K27me3) data generated from KEP study

  A SMC03_ChIP-Seq(H3K27me3) paired end data for skeletal muscle cells

  Dataset EGAD00001003847

• Reference epigenome SMC04_ChIP-Seq(H3K27me3) data generated from KEP study

  A SMC04_ChIP-Seq(H3K27me3) paired end data for skeletal muscle cells

  Dataset EGAD00001003848

• Reference epigenome SMC07_ChIP-Seq(H3K27me3) data generated from KEP study

  A SMC07_ChIP-Seq(H3K27me3) paired end data for skeletal muscle cells

  Dataset EGAD00001003851

• Reference epigenome SMC08_ChIP-Seq(H3K27me3) data generated from KEP study

  A SMC08_ChIP-Seq(H3K27me3) paired end data for skeletal muscle cells

  Dataset EGAD00001003852

• Reference epigenome SMC09_ChIP-Seq(H3K27me3) data generated from KEP study

  A SMC09_ChIP-Seq(H3K27me3) paired end data for skeletal muscle cells

  Dataset EGAD00001003853

• Reference epigenome SMC07_WGBS data generated from KEP study

  A SMC07_WGBS paired end data for skeletal muscle cells

  Dataset EGAD00001003875

• Reference epigenome SMC01_WGBS data generated from KEP study

  A SMC01_WGBS paired end data for skeletal muscle cells

  Dataset EGAD00001003871

• Reference epigenome SMC02_WGBS data generated from KEP study

  A SMC02_WGBS paired end data for skeletal muscle cells

  Dataset EGAD00001003872

• Reference epigenome SMC05_WGBS data generated from KEP study

  A SMC05_WGBS paired end data for skeletal muscle cells

  Dataset EGAD00001003873

• Reference epigenome SMC06_WGBS data generated from KEP study

  A SMC06_WGBS paired end data for skeletal muscle cells

  Dataset EGAD00001003874

• Reference epigenome SMC08_WGBS data generated from KEP study

  A SMC08_WGBS paired end data for skeletal muscle cells

  Dataset EGAD00001003876

• Reference epigenome SMC09_WGBS data generated from KEP study

  A SMC09_WGBS paired end data for skeletal muscle cells

  Dataset EGAD00001003877

• Reference epigenome SMC03_WGBS data generated from KEP study

  A SMC03_WGBS paired end data for skeletal muscle cells

  Dataset EGAD00001003888

• Reference epigenome SMC04_WGBS data generated from KEP study

  A SMC04_WGBS paired end data for skeletal muscle cells

  Dataset EGAD00001003889

• Reference epigenome KNIH010 mRNA-seq data generated from KEP study

  A KNIH010 mRNA-seq paired end data for podocytes

  Dataset EGAD00001002176

• Reference epigenome KNIH011 mRNA-seq data generated from KEP study

  A KNIH011 mRNA-seq paired end data for podocytes

  Dataset EGAD00001002177

• Reference epigenome KNIH010 miRNA-seq data generated from KEP study

  A KNIH010 miRNA-seq single end data for podocytes

  Dataset EGAD00001002769

• Reference epigenome KNIH011 miRNA-seq data generated from KEP study

  A KNIH011 miRNA-seq single end data for podocytes

  Dataset EGAD00001002770

• RNA-seq for IgA BMPC project

  7 RNA-seq samples in total: CD19n_IgAn (x2) , CD19n_IgAp (x2) , CD19p_IgAn (x1), CD19p_IgAp (x2)

  Dataset EGAD00001006862

• Methylation tumour profiles for EGAS00001004572

  Bulk methylation tumour profiles from infinium methylation epic bead kit in EGAS00001004572

  Dataset EGAD00001006909

• KCL PRECSION SNP

  KCL SNP array samples for copy number analysis

  Dataset EGAD00001008379

• The Mexican-American Coronary Artery Disease Study (MACAD)

  The MACAD Study, funded by NHLBI, was designed to explore genetic contributions to coronary artery disease and glucose homeostasis traits among Hispanics using a family-based design. The baseline examination of the cohort included the euglycemic hyperinsulinemic clamp test from which the two key phenotypes were obtained: insulin sensitivity (M) and metabolic clearance rate of insulin (MCRI). Genome-wide genotyping was obtained under separate funding by NIDDK as a part of the GUARDIAN (Genetics Underlying Diabetes in Hispanics) Consortium.

  Study phs001397

• The Hypertension-Insulin Resistance Family Study (HTN-IR)

  The HTN-IR Study, funded by NHLBI, was designed to explore genetic contributions to hypertension and glucose homeostasis traits among Hispanics using a family-based design. The baseline examination of the cohort included the euglycemic hyperinsulinemic clamp test from which the two key phenotypes were obtained: insulin sensitivity (M) and metabolic clearance rate of insulin (MCRI). Genome-wide genotyping was obtained under separate funding by NIDDK as a part of the GUARDIAN (Genetics Underlying Diabetes in Hispanics) Consortium.

  Study phs001394

• The genetic analysis of circulating tumor DNA in blood of the digestive cancer patients to investigate the prognostic factors of metastasis and reccurence.

  A Darwinian evolutionary shift occurred early in the neutral evolution of advanced colorectal carcinoma (CRC) and copy number aberrations (CNA) were essential in the transition from adenoma to carcinoma. Subsequent to the primary evolution, we now focus on the evolutionary principle of the genome to foster postoperative recurrence of CRC. SO, We compared CNA, single nucleotide variance (SNV), RNA sequences between 8 primary and 11 metastatic sites from 10 CRCR cases.

  Study JGAS000221

• Whole Exome Sequencing analysis of three tumor biopsies from a LUAD patient

  Whole Exome Sequencing (WES) analysis was performed on three distinct tumor biopsies collected at different time points, along with their matched germline non-tumor sample, from the same LUAD patient. DNA was extracted using the DNeasy Blood and Tissue Kit (Qiagen, Germantown, MD) according to the manufacturer’s instructions and quantified using the Qubit Fluorometer assay (Life Technologies, Carlsbad, CA). To minimize FFPE-related sequencing artifacts (e.g., C:G > T:A transitions), the extracted DNA was treated with the DNA repair enzyme Uracil-DNA-Glycosylase (UDG) following the manufacturer’s protocol (New England Biolabs, Ipswich, MA). Whole-exome capture was performed with the Twist Human Core Exome + RefSeq + Mito-Panel kit (Twist Bioscience), in accordance with the manufacturer’s guidelines. Sequencing generated paired-end 100-bp reads on the Illumina NovaSeq 6000 platform. The resulting reads were aligned to the reference human genome (GRCh38) using the Burrows-Wheeler Aligner (BWA, v0.7.12).

  Dataset EGAD50000001198

• DGCR8 and the six hit, three-step model of schwannomatosis

  In our manuscript, we report the second case of a patient with peripheral schwannomatosis and thyroid alterations cause by the germline pathogenic variant E518K in DGCR8 and analyzed a total of 13 schwannomas from patients in the two kindreds identified up to date. Our analyses revealed how path to tumorigenesis prompted by DGCR8 requires the loss of the wild type allele of Chrm22q and in more than two thirds of the tumors a complete inactivation of NF2.

  Study EGAS00001005665

• 16S-based fecal microbiota composition

  The dataset reports the 16S rRNA gene sequencing of the fecal microbiota of donors from the Milieu Intérieur Cohort. The Milieu Intérieur cohort includes a total of 1,000 healthy individuals of western European ancestry, recruited in France as part of the Milieu Intérieur project. To assess their fecal microbiota composition, 16S rRNA profiles were generated from stool samples of 863 of the 1,000 donors. Human stool samples were produced at home no more than 24 hours before the scheduled medical visit and collected in a double-lined sealable bag maintaining strict anaerobic conditions. Upon reception at the clinical site, the fresh stool samples were aliquoted and stored immediately at -80°C. DNA was extracted from stool and barcoding PCR was carried out using indexed primers targeting the V3-V5 region of the 16S rRNA gene. Equal volumes of normalized PCR reaction were pooled and thoroughly mixed. The amplicon libraries were sequenced on Illumina MiSeq.

  Dataset EGAD00001004979

• Myelodysplastic_Syndrome_Follow_Up_Series

  Agilent whole exome hybridisation capture was performed on genomic DNA derived from MDS and matched normal DNA from the same patients. Next Generation sequencing performed on the resulting exome libraries and mapped to build 37 of the human reference genome to facilitate the identification of novel cancer genes. Now we aim to discover the prevalence of our findings using bespoke pulldown methods and sequencing the products from a larger set of patient DNA.

  Study EGAS00001000224

• GINS3 fibroblast RNAseq

  The eukaryotic CDC45/MCM2-7/GINS (CMG) DNA helicase unwinds the DNA double helix during DNA replication. We report the identification of individuals presenting with a Meier-Gorlin syndrome (MGS) like phenotype, secondary to hypomorphic variants in the GINS3 gene.  To verify whether the GINS3 variant affected the transcriptome, RNA-seq was performed from 3 fibroblast cultures derived from a patient with compound heterozygous GINS3 variants, and 1 replicate of fibroblasts derived from each of the two parents.

  Study EGAS00001006038

• Feasibility and Clinical Utility of Whole Genome Profiling in Pediatric and Young Adult Cancers

  Comprehensive Whole Genome Sequencing and Whole Transcriptome (RNASeq) analyses from 114 pediatric patients at Memorial Sloan Kettering. This dataset was used as a prospective clinical utility and feasibility study. By using our Isabl infrastructure for precision medicine, we developed a 2-week end-to-end pipeline to analyze cfDNA, WGS and WTS, which we refer to as cWGTS.

  Study phs002620

• Genetic and Microenvironmental Analysis of Peripheral T-cell Lymphoma

  This study enrolled 129 patients diagnosed with PTCL, comprising 94 cases of nTFHL and 35 cases of PTCL-NOS. Whole exome sequencing (WES) and RNA sequencing (RNA-seq) were performed using DNA and RNA of sufficient quality extracted from their tumor specimens. WES was conducted for all 129 cases, while RNA-seq was performed on 57 tumor samples.

  Study EGAS50000001258

• RNA seq of intestinal biopsies and blood cells from patients with celiac disease and controls

  This study presents RNA sequenced from several intestinal phenotypes such as from patients with damaged intestinal mucosa as well as from those without a damaged intestine but still an autoantibody response to tissue transglutaminase (“potential celiac disease”) or those with treated celiac disease. By combining phenotypes in a much larger number of tissue samples from both peripheral blood and mucosal biopsies, we found highly differentially expressed genes, but also identify genes involved in controlling and triggering celiac disease associated changes. This study identifies molecular mechanisms involved in celiac disease and new possible targets for treatment and for identification of individuals at risk.

  Dataset EGAD50000001597

• NPC genome-wide human SNP array data for HongKong population

  nasopharyngeal carcinoma genome-wide human SNP array data for 423 NPC cases and 573 controls

  Dataset EGAD00010002298

• Molecular profiling of MBD4-deficient acute myeloid leukaemia

  We describe two cases of MBD4-deficient acute myeloid leukaemia (AML). Clinical samples were used for molecular analysis, including genomic profiling (genome and exomes), methylation analysis (RRBS) and transcriptional profiling (RNA-sequencing). An analysis and methodological description has been published: “MBD4 guards against methylation damage and germline deficiency predisposes to clonal hematopoiesis and early-onset AML” [PMID: 30049810]

  Study EGAS00001002581

• Low_depth_whole_genome_sequencing_across_multiple_isolated_populations

  Isolated populations have unique population genetics characteristics that can help boost power in genetic association studies for complex traits. Leveraging these advantageous characteristics requires an in-depth understanding of parameters that have shaped sequence variation in isolates. This study performs a comprehensive investigation of these parameters using low-depth whole genome sequencing (WGS) across multiple isolates.

  Study EGAS00001001597

• Transcriptome sequencing of myelodysplasia

  Transcriptome sequencing was performed on 214 patients with myelodysplasia in this study. RNA was obtained from bone marrow CD34+ cells (n=100) and/or bone marrow mononuclear cells (n=165). Transcriptome sequencing was performed for both cell fractions in 51 patients. We also studied bone marrow CD34+ cells and bone marrow mononuclear cells obtained from three healthy adults each.

  Study EGAS00001002346

• RNA data for MMML (EGAS00001002422)

  RNA sequencing data for MMML (3 tumor samples and 1 gcbcell)

  Dataset EGAD00001003285

• WGS data for MMML (EGAS00001002422)

  Whole genome sequencing data for MMML (7 tumors and 8 controls)

  Dataset EGAD00001003286

• Transcriptomic analysis of TFEB overexpression in LT-HSC, ST-HSC and MEP

  Long-term hematopoietic stem cells (LT-HSC), Short-term hematopietic stem cells (ST-HSC) and Megakaryocyte-erythrocyte progenitors (MEP) were sorted from human cord blood and cultured overnight before transduction with lentivirus to overexpress GP91 (CTRL) or TFEB. Three (LT-HSC ans ST-HSC) or six (MEP) days later, BFP+ transduced cells were sorted for RNA extraction and sequencing.

  Study EGAS00001004969

• RNA-seq following TBL1XR1 KD in human CD34+CD38- cord blood cells

  We performed RNA-seq on CD34+CD38- human cord blood (CB) cells transduced with sh_Control or sh_TBL1XR1 lentiviruses to identify differentially expressed genes. Sorted CD34+CD38- cells from 3 independent cord blood pools were transduced with lentiviruses containing BFP reporter gene. BFP+ cells were sorted 3 days post-transduction and RNA was harvested for library preparation and sequencing.

  Study EGAS00001005869

• Single cell RNA sequencing of bone marrow mononuclear cells

  Bone marrow aspirates were obtained from patients with relapsed/refractory large B cell lymphoma (rrLBCL), mononuclear cells isolated by ficoll density-gradient centrifugation, and loaded onto a 10X Chromium for single cell RNA-sequencing using 5’ chemistry without prior cryopreservation. Healthy donor bone marrow mononuclear cells were obtained from healthy allogeneic stem cell transplant donors and analyzed following viable cryopreservation.

  Study EGAS00001006836

• TENX069

  Transcriptome profiling by high-throughput sequencing for single cells for library TENX069 1 samples; filetype=fastq

  Dataset EGAD00001006483

• Single Cell Genome Sequence for DLP+ library A96210B

  Single Cell Genome Sequence for high grade serous ovarian carcinoma patient SA1047B on DLP+ library A96210B

  Dataset EGAD00001009475

• The evolution of adult T-cell acute lymphoblastic leukemia

  We profile the whole-genome of 19 primary T-ALLs from adult patients and the corresponding relapse malignancies. Concretely, samples were taken at the time of diagnosis (primary), at time of remission (used as control) and at recurrence of the malignancy after treatment (relapse). The libraries were sequenced on HiSeq 4000 or NovaSeq 6000 (Illumina) with a paired-end read length of 2x151bp.

  Study EGAS00001004750

• Spatial Dynamics of the Developing Heart (single-cell)

  Heart development relies on a topologically defined interplay between diverse cardiac cells. We finely curated spatial and single-cell measurements with high-resolution imaging-based transcriptomics validation to explore spatial dynamics during early human cardiogenesis. Analyzing almost 80,000 individual cells and 70,000 spatially barcoded tissue regions between the 5.5th and 14th postconceptional weeks, we identified 31 coarse- and 72 fine-grained cell states and mapped them to highly resolved cardiac cellular niches. We provide novel insight into the development of the cardiac pacemaker-conduction system, heart valves, and atrial septum, and decipher heterogeneity of the hitherto elusive cardiac fibroblast population. Furthermore, we describe the formation of the cardiac autonomic innervation and present the first spatial account of chromaffin cells in the fetal human heart. Our study, supported by an open-access, spatially centric interactive viewer, delineates the cellular and molecular architecture of the developing heart, offering links to genetic causes of heart disease.

  Study EGAS50000001029

• Spatial Dynamics of the Developing Human Heart

  Heart development relies on a topologically defined interplay between diverse cardiac cells. We finely curated spatial and single-cell measurements with high-resolution imaging-based transcriptomics validation to explore spatial dynamics during early human cardiogenesis. Analyzing almost 80,000 individual cells and 70,000 spatially barcoded tissue regions between the 5.5th and 14th postconceptional weeks, we identified 31 coarse- and 72 fine-grained cell states and mapped them to highly resolved cardiac cellular niches. We provide novel insight into the development of the cardiac pacemaker-conduction system, heart valves, and atrial septum, and decipher heterogeneity of the hitherto elusive cardiac fibroblast population. Furthermore, we describe the formation of the cardiac autonomic innervation and present the first spatial account of chromaffin cells in the fetal human heart. Our study, supported by an open-access, spatially centric interactive viewer, delineates the cellular and molecular architecture of the developing heart, offering links to genetic causes of heart disease.

  Study EGAS50000001122

• Exome sequencing and disease analysis of a single family implicate a mutation in KIF1A in hereditary spastic paraparesis

  The study involves a single consanguineous Palestinian family with Hereditary Spastic Paraparesis (HSP). The affected individuals suffer from spasticity of the lower limbs and abnormal gait. Using exome sequencing and homozygosity mapping, our analysis implicated the causative mutation in the motor domain of KIF1A, a gene that functions in anterograde axonal transportation.

  Study phs000359

• Molecular heterogeneity and commonalities in pancreatic cancer precursors with gastric and intestinal phenotype

  Due to the limited number of modifiable risk factors, secondary prevention strategies based on early diagnosis represent the preferred route to improve the prognosis of pancreatic ductal adenocarcinoma (PDAC). Here, we provide a comparative morphogenetic analysis of PDAC precursors aiming at dissecting the process of carcinogenesis and tackling the heterogeneity of preinvasive lesions.

  Study EGAS00001006793

• The biology of cell-free DNA fragmentation and the roles ofDNASE1, DNASE1L3 and DFFB

  The biology of cell-free DNA fragmentation and the roles of DNASE1, DNASE1L3 and DFFB

  Study EGAS00001003514

• HCA_Gut_Paediatric_Hirschsprung_s_disease_Teichmann_WGS_Managed_Access

  This study involves atlasing the development of the postnatal gut nervous system in order to elucidate the pathogenic mechanisms of Hirschsprung disease.

  Study EGAS00001007437

• HCA_Gut_Paediatric_Hirschsprung_s_disease_Teichmann_Spatial_Managed_Access_

  This study involves atlasing the development of the postnatal gut nervous system in order to elucidate the pathogenic mechanisms of Hirschsprung disease.

  Study EGAS00001007152

• HCA_Gut_Paediatric_Hirschsprung_s_disease_Teichmann_RNA_Managed_Access_

  This study involves atlasing the development of the postnatal gut nervous system in order to elucidate the pathogenic mechanisms of Hirschsprung disease.

  Study EGAS00001007151

• An ancient DNA perspective on the Russian Conquest of Yakutia

  Yakut communities from northeastern Siberia inhabit some of the coldest environments on Earth preserving an extraordinary archaeological record. Their history was profoundly reshaped by the Russian conquest, which introduced cereals, pathogens and Christianity from 1632 CE. However, the biological impact of these transformations remains unknown. Here, we generated extensive ancient DNA data to elucidate contemporary changes in Yakut genomic diversity and oral microbiomes. We found Yakut origins tracing back to local populations that admixed with trans-Baikal groups migrating as the Great Mongol Empire spread. Despite the Russian conquest, the Yakut gene pool and oral microbiomes appeared largely stable, though smallpox strains distinct from those documented in Europe by ~1650 CE circulated. Marital practices generally maintained low consanguinity, with the exception of one female bearing the latest markers of traditional shamanism, who was the daughter of second-degree relatives.

  Study EGAS50000001329

• DAC for "Capturing disease severity in LIS1-lissencephaly reveals proteostasis dysregulation in patient-derived forebrain organoids" with Julia Ladewig(Julia.ladewig@zi-mannheim.de), Moritz Mall(m.mall@dkfz-heidelberg.de), and Matteo Gasparotto(matteo.gasparotto@zi-mannheim.de)

  Dac EGAC00001003588

• Division of Cancer Evolution National Cancer Center Research Institute Data Access Committee

  Data Access Committee for data from Division of Cancer Evolution, National Cancer Center Research Institute

  Dac EGAC50000000737

• SiMSen‑Seq

  High resolution amplicon-bases sequencing o screen for PIK3CA hot spot mutations

  Dataset EGAD50000001668

• GEOCODE Cohort

  Transcriptomic profile for whole blood after 24hours of stimulations

  Dataset EGAD50000001320

• Effects of interferon-gamma treatment on human small intestinal organoids.

  Intestinal organoids treated with interferon-gamma 1 ng/mL either for 6h or 18h.

  Dataset EGAD50000000115

• Medulloblastoma dataset

  This dataset contains a tumor + normal DNA sequence data and tumor RNA seq data for a medulloblastoma patient.

  Dataset EGAD50000000384

• gz_bjREP

  DNA for 2979 individuals from Guangzhou was extract from peripheral blood and genotyped by Sequenom, with digit-number working memory, visuospatial working memory, recent long-term memory measured.

  Dataset EGAD00010001528

• Reference epigenome CKD24_C_Podo_mRNA-Seq data generated from KEP study

  A CKD24_C_Podo_mRNA-Seq paired end data for Podocytes(CD90(-) Podocalyxin(+), kidney)

  Dataset EGAD00001003482

• Reference epigenome CKD25_C_Podo_mRNA-Seq data generated from KEP study

  A CKD25_C_Podo_mRNA-Seq paired end data for Podocytes(CD90(-) Podocalyxin(+), kidney)

  Dataset EGAD00001003483

• Reference epigenome OB57_D_PreA_mRNA-Seq data generated from KEP study

  A OB57_D_PreA_mRNA-Seq paired end data for Preadipocyte(fat)

  Dataset EGAD00001003487

• Reference epigenome OB56_N_PreA_smRNA-Seq data generated from KEP study

  A OB56_N_PreA_smRNA-Seq single end data for Preadipocytes(fat)

  Dataset EGAD00001003495

• Reference epigenome OB57_D_PreA_smRNA-Seq data generated from KEP study

  A OB57_D_PreA_smRNA-Seq single end data for Preadipocyte(fat)

  Dataset EGAD00001003496

• Reference epigenome CKD24_C_Podo_smRNA-Seq data generated from KEP study

  A CKD24_C_Podo_smRNA-Seq single end data for Podocytes(CD90(-) Podocalyxin(+), kidney)

  Dataset EGAD00001003498

• Reference epigenome CKD25_C_Podo_smRNA-Seq data generated from KEP study

  A CKD25_C_Podo_smRNA-Seq single end data for Podocytes(CD90(-) Podocalyxin(+), kidney)

  Dataset EGAD00001003499

• RNA-Seq Pair End

  RNA analysis of two patients 11 and 15 with WGS done on Illumina HiSeq2000. For research purpose and authorised user only.

  Dataset EGAD00001003429

• Illumina HiSeq 2000

  Three files of patients 20, 23 and 25 with WGS done on Illumina HiSeq 2000. For research purpose and authorised user only.

  Dataset EGAD00001003438

• Reference epigenome IPS02_N_NPC_WGBS data generated from KEP study

  A IPS02_N_NPC_WGBS paired end data for Neural progenitor cells(Nestin)

  Dataset EGAD00001003474

• Reference epigenome IPS03_N_ENeuron_WGBS data generated from KEP study

  A IPS03_N_ENeuron_WGBS paired end data for Early neuron cells(Tuj1)

  Dataset EGAD00001003475

• ATAC-seq for placental and buffycoat cells.

  We performed ATAC-seq experiments using 2 placental samples and 2 buffycoat samples.

  Dataset EGAD00001004291

• Uncovering tumor intrinsic and extrinsic factors that regulate hepatocellular carcinoma growth using patient derived xenograft assays

  Exome Sequencing and RNA Sequencing Data for PDX Samples

  Dataset EGAD00001005734

• RNAseq data of polyA+ RNA from Leukocytes from 624 individuals of the SardiNIA cohort.

  We sequenced the polyA+ of the RNA of the leukocytes from 624 sardinian individuals with RNAseq (Illumina 2000, an average of round 60M reads per sample, 51 + 51 nt). Combining the genotype information of the same individuals (already available from the ProgeNIA project) with the transcriptome data we identified 21,183 independent expression quantitative trait loci (eQTLs) and 6,768 independent splicing quantitative trait loci (sQTLs), including 619 novel QTLs that exhibit population-specific trait associations. Using family relationships, we identified 809 segregating expression outliers and provide a new approach to study large effect regulatory variants and their relevance to traits. Our results provide insight into the effects of regulatory variants and their relationship to population history and individual genetic risk.

  Study EGAS00001002105

• Exome sequencing of 1000 population control samples from the UK 1958 birth cohort

  Exome sequencing from 1,000 UK population samples (the ICR1000 Exome series), using samples from the 1958 Birth Cohort Collection, a population-based collection of all individuals born in the UK in one week in 1958 (http://www.cls.ioe.ac.uk). DNA libraries were prepared from genomic DNA using the Illumina TruSeq sample preparation kit. DNA was fragmented using Covaris technology and the libraries were prepared without gel size selection. Target enrichment was performed in pools of six libraries using the Illumina TruSeq Exome Enrichment kit. The captured DNA libraries were PCR amplified using the supplied paired-end PCR primers. Sequencing was performed with an Illumina HiSeq2000 (v3 flow cell, one pool per lane) generating 2x100-bp reads.

  Study EGAS00001000971

• Genomic landscape of IG-MYC positive Burkitt lymphoma with precursor B-cell immunophenotype.

  As part of the ICGC, the ICGC MMML-Seq project performed whole genome sequencing of a rare Burkitt lymphoma subtype with precursor B-cell immunophenotype. Analysis were performed in concordance with the guidelines of the ICGC.

  Study EGAS00001002968

• 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

• Systems Analysis of Single-Cell Heterogeneity Underlying Glioma Drug Resistance

  This study characterizes the transcriptional regulatory mechanisms that drive responses of two patient-derived glioblastoma multiforme (GBM) stem-like cells (PD-GSCs) that have distinct phenotypes - one sensitive and another resistant to the drug pitavastatin. This study investigates the differing mechanisms driving drug response in the two PD-GSCs at the single-cell level, and provides an approach that can be used to infer transcriptional regulatory network models, which can then be used to identify mechanisms driving cell-state transitions, e.g., proneural-to-mesenchymal transitions (PMT), which has been observed experimentally and clinically in GBM. The use of these network models enabled the identification of transcription factor and gene targets that perturbed drug-induced PMT through 1) simulations of network dynamics network, and 2) characterization of gene program activities over the time-course response to drug treatment. These results enabled the identification of multiple siRNAs and the drug vinflunine as secondary components that potentiate the efficacy of pitavastatin. This work demonstrates an approach to uncover the transcriptional network topology (TRN) topology of PD-GSCs, and use it to rationally predict combinatorial treatments that block treatment escape and acquired resistance to drugs in GBM.

  Study phs003501