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• Single-nucleus RNA-sequencing of meningiomas

  Single-nucleus RNA-sequencing of meningiomas for integrative molecular classification

  Dataset EGAD00001007677

• Biomarker data

  Biomarker data for KATHERINE: Biomarker data include RNA-seq time point, Percent of tumor content, PAM50 subtypes, normalized gene expression of ERBB2, CD8 and CD274, normalized immune signature expression.

  Dataset EGAD00001008786

• KCL PRECSION lpWGS

  KCL lpWGS samples for copy number analysis

  Dataset EGAD00001008380

• liCHi-C Samples of B-ALL

  Libraries of liCHi-C for 2 B-ALL (B Acute Lymphocytic Leukaemia) from human patients. Fastq file format.

  Dataset EGAD00001008829

• 7 samples RNA-seq raw data

  Dataset comprising raw paired RNA-seq data in fastq.gz format for 7 samples of rosette forming brain tumors

  Dataset EGAD00001009265

• Hi-C of cohesin-mutated and wildtype adult AMLs

  High-throughput chromosome conformation capture (Hi-C) data generated for cohesin-mutated (STAG2 or RAD21) and cohesin-wildtype AMLs.

  Dataset EGAD00001011198

• 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

• 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

• 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

• Genome-wide Ancestry and Demographic History of African-Descendant Maroon Communities from French Guiana and Surname.

  The transatlantic slave trade (TAST) was the largest forced migration in world history. However, the origins of the enslaved Africans and their admixture dynamics remain unclear. To investigate the demographic history of African-descendant Marron populations, we generated genome-wide SNP data (4.3 million markers) from 107 individuals from three African-descendant populations in South America, as well as 124 individuals from six west African populations to complement underrepresented African data sets. Our study sheds additional light on the demographic consequences of the TAST and illustrates how genetic data can complement historical sources.

  Study EGAS00001002535

• Genome Sequencing Reveals That RAD50 Hypomorphism Results in Enhanced Sensitivity to Checkpoint Kinase Inhibition Combined with Chemotherapy

  Outlier analyses represent a versatile method to identify predictive biomarkers of response to both targeted agents and chemotherapy. We performed whole genome sequencing (WGS) of tumor and germline blood from a patient with metastatic small cell carcinoma of the ureter who experienced a durable complete response to a combination of irinotecan plus AZD7762, a checkpoint kinase inhibitor. The patient initially had resection of the ureter followed by metastatic recurrence within the kidney and lymph nodes and underwent nephrectomy with lymph node dissection. Through WGS of tissue from the second surgery, we detected a hypomorphic L1237F mutation within RAD50, a component of the Mre11 double strand break repair complex, which resulted in heightened sensitivity to the combination of checkpoint inhibition and clastogenic chemotherapy. We validated the WGS findings using a combination of an exon capture assay and validation in model systems. The tumor samples sequenced by exon capture were derived from tissue taken from both the initial and second surgeries.

  Study phs000706

• single cell RNA-seq and ATAC-seq of human fetal forebrain tissue

  Oligodendrogenesis in the human central nervous system has been mainly observed at the second trimester of gestation, a much later developmental stage compared to mouse. Here we characterize the transcriptomic neural diversity in the human forebrain at post conceptual weeks (PCW) 8 to 10, using single-cell RNA-Seq. We find evidence of the emergence of a first wave of oligodendrocyte lineage cells as early as PCW 8, which we also confirm at the epigenomic level with single-cell ATAC-Seq. Using regulatory network inference, we predict key transcriptional events leading to the specification of oligodendrocyte precursor cells (OPCs). Moreover, by profiling the spatial expression of fifty key genes using In Situ Sequencing (ISS), we identify regions in the human ventral fetal forebrain where oligodendrogenesis first occurs. Our results indicate evolutionary conservation of the first wave of oligodendrogenesis between mouse and human and describe regulatory mechanisms involved in human OPC specification.

  Study EGAS00001006136

• Deciphering the mutational landscape and the genome organization of LMS

  Leiomyosarcoma (LMS) are an uncommon group of malignant mesenchymal tumors composed of cells showing distinct smooth muscle differentiation. These tumors occur mainly in adults in any location of the body (soft-tissue, viscera or uterine). Soft-tissue LMS represent 10-15% of all soft-tissue sarcomas. The most frequent locations are the limbs followed by the retroperitoneum and uterine.

  Study EGAS00001001262

• Multiple_Myeloma_Diagnosis_to_Relapse_study_samples

  The study will investigate serial samples from the same patient taken at the time of MGUS or SMM diagnosis, and later at the time of evolution towards MM. Samples will be sequenced by whole genome along with a matched normal to obtain the highest possible amount of information toinvestigate genomic changes at disease evolution.

  Study EGAS00001001299

• PanProstate Cancer Group DK data

  THE PAN PROSTATE CANCER PROJECT: Many groups around the world have generated Whole Genome DNA Sequence (WGS) data from prostate cancer patients. The pan prostate group have gathered with the idea that the accumulated data, should be collected and compared in a common format including common storage, re-analysis through a single pipeline, and investigation to achieve a variety of scientific goals. The combined collection would include the following categories: (i) cancers from different ethnic groups: eg Caucasian, Asian, Black Caribbean; (ii) cancer from different stages of progression from normal, to organ-confined disease, to metastases; (iii) early-onset prostate cancer; (iv) prostate cancer from aggressive and indolent disease; and (v) prostate cancer patients managed by different treatments with information linked to long-term clinical follow up data in many cases.This study contains the samples from the Danish prostate group.

  Study EGAS50000001616

• NHLBI TOPMed: Cleveland Clinic Atrial Fibrillation (CCAF) Study

  The Cleveland Clinic Atrial Fibrillation Study consists of clinical and genetic data of patients with atrial fibrillation and control cohorts from the Cleveland Clinic CV/Arrhythmia Biobank, including the Cleveland Clinic Lone Atrial Fibrillation GeneBank. The Cleveland Clinic Lone AF GeneBank Study has enrolled patients with lone AF, defined as AF in the absence of significant structural heart disease. The CV/Arrhythmia Biobank has also enrolled participants with non-lone atrial fibrillation. All patients provided written informed consent.

  Study phs001189

• Khoe-San Genome Project

  The dataset contains BAM files of whole genome sequencing data of African Khoe-San population (n=169, 30X coverage) recruited from South Africa and Namibia. The population captured the true extent of human genetic diversity as represent the earliest diverged human population. The project described a detailed divergence of human population and identified positive selections associated forager lifestyles in Khoe-San population. These findings emphasise an inclusive catalogue with better representation of the earliest human genomic diversity to better advance biomedical research.

  Study EGAS50000001408

• RNAseq of 704 patients with soft tissue tumors

  The dataset contains transcriptome sequencing (RNA-seq) data of 704 soft tissue tumors (STT) from 704 patients. The sequencing data comes in FASTQ format and contains 1408 files. A total of 56 different STT types were included in the present study and each tumor type was represented by >2 samples. The vast majority of the patients had been diagnosed and treated at the sarcoma centers in Lund (Sweden) or Stockholm (Sweden) during the period 1988-2020, but also a few samples from other centers, obtained through previous collaborative projects, were included. RNA was extracted from fresh frozen tumor material and samples were primary lesions unless otherwise indicated. The sequencing was performed using 2x150 bp paired-end chemistry on a series of Illumina instruments at various facilities during the period 2013-2023.Samples were obtained after informed consent from the patients and the study was approved by the regional ethics committee (Etikprövningsmyndigheten, Uppsala, dnr 2023-01550-01, dnr 2025-02997-02).

  Dataset EGAD50000002120

• RISE-UP study: riboflavin supplementation in Crohn's disease

  Taxonomic classification of the fecal microbiota of Crohn's disease patients showing the shift in the gut bacterial community after riboflavin supplementation.

  Study EGAS50000000982

• DNA-seq from plasma of 14 liver transplantation patients

  We performed DNA sequencing on the plasma of 14 liver transplantation patients to study the liver DNA in the plasma.

  Study EGAS00001003116

• Tagmentation-based Whole Genome Bisulfite Sequencing

  We demonstrated the reliability of the tagmentation-based whole genome bisulfite sequencing in direct comparison with the conventional whole genome bisulfite sequencing.

  Study EGAS00001000528

• Single Cell Genomic Analysis of Lymphoma

  Our study aimed to define the extent of heterogeneity between anatomically separated tumor manifestations in follicular lymphoma at single-cell resolution. We subjected single-cell suspensions derived from nodal, synchronously-acquired fine needle aspirations from two distinct tumor sites to high-throughput microfluidics-based single-cell RNA sequencing. By comparing the relative composition of the tumor subpopulations between the two tumor sites, we found that some patients can exhibit site-to-site differences. While the overall composition of the tumor microenvironment did not differ significantly between sites, we did detect a specific correlation between site-to-site tumor heterogeneity and T follicular helper cell abundance. Our study demonstrates the significant limitations of a solitary biopsy in defining the full scope of a patient's disease.

  Study phs002188

• Whole-genome low pass sequencing of 3,514 Sardinian individuals

  The dataset includes the VCF files with the list of variants, and their frequency, found in 3,514 Sardinian individuals recruited from the SardiNIA longitudinal study (N=2090) and from a case-control study of autoimmune diseases in Sardinia (N=1424).

  Study EGAS00001002212

• 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.

  Dac EGAC50000000247

• McGill Reproductive Genetics Data Access Committee

  Committee at RI-MUHC (Slim Lab) that reviews requests for controlled human genetic/phenotypic data generated in reproductive genetics/infertility studies. Ensures requests comply with participant consent, ethics approvals, and institutional policies.

  Dac EGAC50000000775

• NICOLA Epigenetic Data Wave 1 - Beta values

  Beta values generated from Illumina EPIC methylation array data for a subset of NICOLA Wave 1 samples.

  Dataset EGAD50000001965

• DNA-Methylation data for atypical teratoid/rhabdoid tumoroids study

  We demonstrate that ATRT tumoroids retain subgroup-specific epigenetic and gene expression profiles

  Dataset EGAD00010002400

• Genetic and transcriptomic landscape of DLBCL

  Affymetrix SNP6.0 data for 341 DLBCL patients

  Dataset EGAD00010001980

• PMBCL IL4R DASL

  Expression data for 42 PMBCL patient samples (32 IL4R WT cases and 10 cases with mutations in IL4R)

  Dataset EGAD00010001542

• Sequencing data for oesophageal and related samples - cell-lines (WGS)

  Dataset EGAD00001015467

• iPSC alignment file (CRAM) for EBiSC

  EBiSC Whole Genome Sequencing processed CRAM

  Dataset EGAD00001003942

• iPSC Samples for EBiSC

  EBiSC Whole Genome Sequencing raw FASTQ

  Dataset EGAD00001003882

• HIV exome pilot, exome data part 2 GRCh37_53

  exome sequence data for 25 HIV elite long term non-progressors and rapid progressors. Partial dataset (overlap with EGAD00001000047) of raw BAMs mapped to GRCh37_53.

  Dataset EGAD00001000087

• MiSeq-High Coverage

  Seven files of patients 3, 21, 29, 30, 31, 32 and 33 with WGS done on Illumina MiSeq with high coverage. For research purpose and authorised user only.

  Dataset EGAD00001003436

• Genome - MBD4-deficient AML

  Genome sequencing at diagnosis and post induction for WEHI-AML-1 and WEHI-AML-2. Whole genome sequencing was performed on an Illumina HiSeq X Ten.

  Dataset EGAD00001003568

• BGI study for primary and metastatic Chinese lung adenocarcinomas

  We sequenced 292 patients who were suffering NSCLC with Whole genome sequencing or Exome sequencing method.

  Dataset EGAD00001001397

• FFPE Normal Panel V3 Cancer Panel

  FFPE normal panel generation for use with V3 cancer panel 0618521

  Dataset EGAD00001001122

• ICGC Benchmark 2 (Medulloblastoma)

  Raw fastq files for sequence data generated at 5 sequencing centers from a Medulloblastoma sample and matching blood normal control.

  Dataset EGAD00001001859

• HIV exome pilot, exome data part 1 GRCh37_53

  exome sequence data for 49 HIV elite long term non-progressors and rapid progressors. Partial dataset (overlap with EGAD00001000087) of raw BAMs mapped to GRCh37_53.

  Dataset EGAD00001000047

• DNA sequencing for gastric cancer ascites

  Whole-exome sequencing (WES) was performed on a total of 34 PC specimens, with 15 cases having matched gDNAs extracted from blood.

  Dataset EGAD00001004364

• RnaSeq samples for 25 UPS samples

  Whole Transcriptiome Rnaseq of 25 UPS samples - raw FastQ sequences, 125x2 nc Paired End Reads, min 30M PE, HiSEq technology

  Dataset EGAD00001006355

• RNA-seq data for de-methylation of FOXP3-TSDR study

  22 RNA-seq samples of ex-vivo (TN and Treg), cultured Treg, TET1 and untreated mCherry-MOCK

  Dataset EGAD00001006865

• 1_fibroblasts_HD_vs_Ctrl_DMSO_Branaplam

  n=4 Ctrl and n=4 HD fibroblasts lines were treated with DMSO or 10nM Branaplam for 72h and RNA-seq was performed.

  Dataset EGAD00001008807

• scRNA-seq of HGSC tumor and ascites

  Immune regulatory metabolites are key features of the tumor microenvironment (TME), yet with a few notable exceptions, their identities remain largely unknown. We uncovered the immune regulatory metabolic states and metabolomes of sorted tumor and stromal, CD4+, and CD8+ cells from the tumor and ascites of patients with high-grade serous ovarian cancer (HGSC) using high-dimensional flow cytometry and metabolomics supplemented with single cell RNA sequencing. Flow cytometry revealed that tumor cells show a consistently greater uptake of glucose than T cells, but similar mitochondrial activity. Cells within the ascites and tumor had pervasive metabolite differences, with a striking enrichment in 1-methylnicotinamide (MNA) in T cells infiltrating the tumor compared to ascites. Despite the elevated levels of MNA in T cells, the expression of nicotinamide N-methyltransferase, the gene encoding the enzyme that catalyses the transfer of a methyl group from S-adenosylmethionine to nicotinamide, was restricted to fibroblasts and tumor cells. Treatment of T cells with MNA resulted in an increase in T cell-mediated secretion of the tumor promoting cytokine tumor necrosis factor alpha. Thus, the TME-derived metabolite MNA contributes to an alternative and non-cell autonomous mechanism of immune modulation of T cells in HGSC. Collectively, uncovering the tumor-T cell metabolome may reveal metabolic vulnerabilities that can be exploited using T cell-based immunotherapies to treat human cancer.

  Study EGAS00001004829

• Dataset for GIST-RNA

  Rare cancer sequencing data of 50 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

  Dataset EGAD00001008852

• Dataset for neuroendocrine_adrenal_tumor-EXON

  Rare cancer sequencing data of 164 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

  Dataset EGAD00001008891

• Dataset for other_cancer-EXON

  Rare cancer sequencing data of 137 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

  Dataset EGAD00001008896

• Haplotype-specific assembly of shattered chromosomes in oesophageal adenocarciomas

  Genomic and epigenomic sequencing of 5 oesphageal adenocarciomas with evidence of chromothripsis. Genomic sequencing includes: Pacbio circular consensus sequencing, Pacbio continuous long read sequencing, 10X linked read and Illumia HiSeq X Ten sequencing. Epigenomic sequencing includes: Hi-C chromosome capture, ATAC-seq, ChIP seq (for H3K27ac, H3K4me3, H3K27me3 and CTCF) and long read RNA sequencing. All data types have the bam files which have not undergone haplotype resolution (demarcated as unresolved) and some data types also have haplotype resolved reads (demarcated as resolved).

  Dataset EGAD00001010871