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• WGS data of Japanese including COVID-19 patients and healthy subjects

  This dataset contains WGS data of 234 Japanese, including 88 COVID-19 patients and 146 healthy subjects. Libraries were sequenced on the HiSeqX or NovaSeq 6000 system. Sequenced reads were aligned against the Genome Reference Consortium human genome build 38 using BWA-MEM.

  Dataset EGAD00010002742

• Epigenomic data of HEMa_LP

  To profile the epigenomic landscape of Human Epidermal Melanocytes , adult, lightly pigmented(HEMa-LP), whole genome bisulphite sequencing (WGBS) and ChIP-seq of histone marks data were generated.

  Study EGAS00001004016

• RNA sequencing of human fetal brain at 7, 9, 12, 15 and 21 gestational weeks

  The dataset contains raw sequences (FASTQ files) from the Illumina 2x150bp paired-end RNA sequencing profiles of 11 fetal human brain samples at 7, 9, 12, 15 and 21 gestational weeks

  Dataset EGAD00001003915

• Neuroblastoma Evolution

  Here, we quantify the somatic evolution of neuroblastomas by deep (80x) whole-genome sequencing, molecular clock analysis and population-genetic modeling in a comprehensive cohort (Hipo_K09R) covering all subtypes.

  Study EGAS00001006533

• Potent neutralizing antibodies against SARS-CoV-2

  The COVID-19 pandemic urgently needs therapeutic and prophylactic interventions. Here we report the rapid identification of SARS-CoV-2 neutralizing antibodies by high-throughput single-cell RNA and VDJ sequencing of antigen-enriched B cells from 60 convalescent patients.

  Dataset EGAD00001006130

• Modulation of macrophage inflammatory function through selective inhibition of the epigenetic reader protein SP140

  Transcriptomic (N = 18) and epigenomic (N = 6) characterization of macrophages using RNA-sequencing and ChIP-sequencing (bait = SP140) in the presence of absence of SP140 inhibition.

  Dataset EGAD00001006186

• Inherited CD28 deficiency in otherwise healthy patients with disseminated warts and giant horns

  this dataset corresponds to 3 patient of HPV-driven warts single cell RNA data generated through the 10X genomics platform and aligned on GRCh38 reference using the cell ranger tools.

  Dataset EGAD00001006644

• Variation and transmission of the human gut microbiota across generations - 16S data

  Variation and transmission of the human gut microbiota across generations - 16S sequencing data

  Dataset EGAD00001008195

• Investigating genetic susceptibility to rheumatic heart disease in Oceania

  This case-control study investigated susceptibility to rheumatic heart disease in over 3,000 individuals recruited across eight Oceanian countries. Cases were patients with rheumatic heart disease and controls were members of the general population. In addition to the Illumina HumanCore-24 BeadChip genotyping, a subset of 128 samples were analysed using the higher density Illumina HumanOmniExpressExome BeadChip of which 64 were also analysed using low coverage sequencing with the Illumina HiSeq 4000 platform.

  Study EGAS00001001881

• Siberia.Pakendorf

  The tar archive contains a) the txt file with the genotypes, b) illumina annotation file with info on SNPs, c) sample info file unfiltered illumina data, autosomes only data from Pugach et al MBE 2016 The Complex Admixture History and Recent Southern Origins of Siberian Populations

  Dataset EGAD00010002304

• Deep sequencing of the gut microbiome from donors of the Milieu Intérieur cohort

  This dataset includes 1,359 paired-end shotgun metagenomics samples from 946 healthy donors of the Milieu Intérieur cohort. 413 of the donors provided two samples (V1 and V2).

  Dataset EGAD00001006554

• Analysis of lymphocytes specific gene expression pattern by RNA-Seq in patients with IgG4-related disease: Comparison between submandibular glands and peripheral blood

  We compared the gene expression of PanT and CD19+B cells by RNA-Seq between SMGs versus PBMCs in IgG4-RD, or IgG4-RD versus pSS versus HCs in PBMCs.

  Study JGAS000630

• Clinical Utility of Breast cancer Research by Inocras, Catholic university hospital and Samsung medical center

  Breast cancer remains a major global challenge. To comprehensively characterize its genomic landscape and clinical significance, we analyzed whole genome sequences from 1,364 clinically annotated breast cancers, integrating transcriptome data from most of the tumors.

  Study EGAS50000001062

• Clinical Utility of Breast cancer Research by Inocras, Catholic university hospital and Samsung medical center

  Breast cancer remains a major global challenge. To comprehensively characterize its genomic landscape and clinical significance, we analyzed whole genome sequences from 1,364 clinically annotated breast cancers, integrating transcriptome data from most of the tumors.

  Study EGAS50000001377

• DNA sequencing of sgRNAs in CRISPR-Cas9 screening and RNA sequencing of SF3B4-overexpressing liver organoids

  The dataset contains 18 samples. It includs 12 paired whole genome sequencing, and 2 matched short read and long read RNA sequencing of liver organoids, 2 paired RIP RNA sequencing samples. All the experiments were performed on Illumina platform with raw reads stored in fastq format or bam format.

  Dataset EGAD50000001625

• RNAseq of human intestinal epithelial cell layers cultured in OGM, ENR, and ENRRT

  This dataset contains RNA sequencing data in fastq and bam format from 24 samples of human jejunum organoids grown in 3D configuration or as 2D monolayers on anodisc imaging chambers (AICs) in medium formulations OGM, ENR, and ENRRT. The RNA sequencing samples were sequenced using paired-end sequencing (2x150 bp) on an Illumina NovaSeq 6000 instrument at the SciLifeLab National Genomics Infrastructure (NGI) in Uppsala.

  Dataset EGAD50000001766

• Single-cell Transcriptome Analysis of Plasma Cells Across the Disease Spectrum of Multiple Myeloma

  This dataset includes FastQ files of single-cell RNA sequencing data of 5' GEX and VDJ libraries from CD138+ plasma cells enriched from 72 bone marrow aspirates from patients diagnosed with a monoclonal gammopathy from the multiple myeloma spectrum, including MGUS (n=13), SMM (n = 22), NDMM (n = 17), RRMM (n = 15) and PCL (n = 2); and 3 controls.

  Dataset EGAD50000001179

• APS-1 TCR Sequencing

  Single cell TCR sequencing of expanded regulatory T cells (Tregs) in 9 APS-1 patients and 9 ange and gender matched controls. T-cell receptor (TCR) libraries were generated using the Single Cell Human TCR Amplification Kit and the Library Construction Kit from 10x genomics.

  Dataset EGAD50000000261

• Genetic alterations in benign breast biopsies of subsequent breast cancer patient

  This dataset consists of amplicon sequencing of fibrocystic breast tissues, subsequent cancer tissue and germline control of 17 patients. The target genes include all exons of 27 protein-coding genes and 2 non-coding genes, as well as mutation hotspots in three cancer genes, frequently mutated in breast cancer. Ion AmpliSeq libraries were generated and sequenced on the Ion S5 XL system.

  Dataset EGAD00001004874

• Prognostic and immunomodulatory consequences of ERV expression in ovarian cancer

  The dataset contains transcriptional data obtained using total RNA sequencing on a Illumina machin. 59 samples are from the Hammersmith Hospital (HH) cohort of human primary ovarian tumours and 20 samples are from ovarian cancer cell lines Kuramochi (3 replicates) and Ovsaho (2 replicates) treated with 1 uM DNMTi guadecitabine or vehicle, at an early (day 5) or late (day 8) timepoint.

  Dataset EGAD00001006589

• Acute myeloid leukemia single cell RNA-seq (Diagnosis and Relapse)

  To gain insight into the clonal heterogeneity of diagnosis (Dx) and relapse (Re) pairs, we employed single-cell RNA-seq (SORT-seq) to longitudinally profile two t(8;21) (AML1-ETO = RUNX1-RUNX1T1), and four FLT3-ITD AML cases. All the samples are Bone marrow aspirates.

  Dataset EGAD00001008373

• Megabase scale methylation phasing using Nanopore long reads and NanoMethPhase

  This paper describes the work by Akbari V,. et al. on detection of allele specific methylation using oxford nanopore sequencing data. They have developed set of tools, SNVoter and NanoMethPhase, and workflow which enable the detection of allele specific methylation even in samples with sparse coverage of nanopore sequencing data.

  Dataset EGAD00001007920

• Blueprint: A human variation panel of genetic influences on epigenomes and transcriptomes in three immune cell types, (ChIP-Seq for mature neutrophil, on genome GRCh37)

  ChIP-Seq data for 182 mature neutrophil sample(s). 2847 run(s), 366 experiment(s), 355 analysis(s) on human genome GRCh37. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/blueprint_Epivar/protocols/README_chipseq_analysis_ebi_20160816

  Dataset EGAD00001002670

• Blueprint: A human variation panel of genetic influences on epigenomes and transcriptomes in three immune cell types, (RNA-Seq for mature neutrophil, on genome GRCh37)

  RNA-Seq data for 205 mature neutrophil sample(s). 205 run(s), 205 experiment(s), 205 analysis(s) on human genome GRCh37. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/blueprint_Epivar/protocols/README_rnaseq_analysis_sanger_20160816

  Dataset EGAD00001002675

• Resolution of tumour cell populations enhances specificity of treatment options for precision cancer medicine

  This dataset comprises FASTQ files for single-cell RNA-seq and single-cell ATAC-seq data. These data were generated using 10x Genomics' multiome kit. In this cohort, there are 25 samples from 17 human cancer patients.

  Dataset EGAD00001015782

• Single nucleus and bulk transcriptomics in prefrontal cortex of individuals with alpha synucleinopathies

  We explore cell-specific changes in gene expression across different α-synucleinopathies. We perform single nucleus RNA sequencing using 10X Genomics, and bulk RNA sequencing from the prefrontal cortex of individuals with alpha synucleinopathies - Parkinson's Disese (PD), monogenic LRRK2 PD, and multiple system atrophy (MSA), together with neurologically healthy controls.

  Study EGAS50000000301

• PRO-SPeCT: PROstate cancer heterogeneity deconvolution through Single cell Profiling of Chromatin accessibility and Transcriptomic output

  38 prostate cancer specimens derived from five human patients with ISUP ≥ 3 pathology who underwent radical prostatectomy and pelvic lymph node dissection at surgery as part of the International Cancer Genome Consortium (ICGC) late-onset cohort. Using single-cell multiome (expression and chromatin accessibility from RNA and ATAC, respectively) sequencing assay, we characterized 282,956 nuclei/cells, with a median of 6 primary tumor foci from the prostate gland and 3 locoregional lymph node metastases across all patients.

  Dataset EGAD50000000745

• Congenital mesoblastic nephroma and infantile fibrosarcoma

  The genetic basis of many rare childhood cancers remains unknown. These include a spectrum of infant soft tissue tumors without canonical gene fusions, encompassing congenital mesoblastic nephroma (CMN) of the kidney and infantile fibrosarcoma (IFS). Here, we integrated whole genome and transcriptome sequencing and identified diagnostic markers and novel therapeutic strategies.

  Dataset EGAD00001003884

• The Landscape of N-6 Methyladenosine in Primary Localized Prostate Cancer

  Using meRIP-sequencing, we profiled N-6 methyladenosine (m6A) in a cohort of 148 primary prostate cancer samples as part of the Canadian Prostate Cancer Genome Network project (CPC-GENE). Paired-end sequencing of 150 bp reads were mapped to GRCh38.p13 using annotations from gencode.v34.chr_patch_hapl_scaff.annotation.gtf. Peaks were called using MeTPeak, joint peaks were identified and IP reads were quantitated, normalized and adjusted using Input reads to obtain estimates of m6A abundance.

  Study EGAS00001006925

• WGS of peripheral blood leukocytes from patients with Li-Fraumeni syndrome

  We performed whole genome sequencing on 84 LFS family members from 47 families: 22 with wildtype TP53 and 62 with variant TP53. The variant TP53 cohort consists of 49 individuals who developed cancer and 13 individuals who remain cancer-free; 34 were from 13 families with 2-4 individuals sequenced within a given family and the remaining 28 had no family members sequenced. The wildtype cohort consists of 14 individuals who developed cancer and 8 individuals who are cancer-free, from 6 families.

  Dataset EGAD00001010200

• Mucosal 16S sequencing data

  16S-V4 rRNA gene sequence data for intestinal biopsies from NCT02749630 trial participants. Biopsies from patients were collected at screening, day 30, and day 85 and prepared for 16SV4 rRNA gene sequencing.

  Dataset EGAD00001008843

• T cell receptor repertoire in cell-free DNA as a proxy for tumor infiltrates in patients treated with pembrolizumab

  Bulk TCR sequences from tumor, peripheral blood mononuclear cell (PBMC), and cell-free DNA (cfDNA) samples from 81 patients with solid tumors treated with pembrolizumab.

  Dataset EGAD50000001857

• Dataset for scRNA glioblastoma samples

  This dataset contains 5 scRNA samples of human glioblastoma samples, human cortical spheroid derived from hiPSC line 028-4 and 3 samples of mouse xenografts. Sequencing has been performed on Illumina NovaSeq 6000. Sequencing has always been paired.

  Dataset EGAD50000001117

• Exome sequencing files for "Minimal functional driver gene heterogeneity among untreated metastases"

  Files from whole exome sequencing of 14 tumors from two cancer patients (endometrial and lung cancer) along with a matched normal tissue per patient.

  Dataset EGAD00001004212

• WES and RNA-seq raw sequence data for HIFI project

  WES sequence data from 15 samples, RNA-seq sequence data from 19 samples, all sequence data are raw pair-end sequence data in fastq format, sequenced by Illumina platform.

  Dataset EGAD00001004799

• Indonesian Genome Diversity Project 2

  This dataset reports whole genome sequences for 82 individuals from different populations from Mentawai, New Guinea, Sumatra and Sumba islands.

  Dataset EGAD00001005059

• Bam files for a metastatic bladder cancer patient with BAP1 variants

  This dataset consists of three bam files (two cell-free DNA and one germline DNA) from a metastatic bladder cancer patient with BAP1 variants. Bam files were generated from targeted Illumina sequencing data.

  Dataset EGAD00001005520

• Fecal whole metagenomic shotgun sequencing data.

  Human fecal WMS data from patients treated with combined anti-CTLA-4 and anti-PD-1 immunotherapy for advanced melanoma.

  Dataset EGAD00001006734

• RNA-Seq for SF3B1 splicing signature

  This dataset includes exome-captured RNA-Seq made with exome v8 (Agilent) - library preparation on a MAGNIS XT-HS2 starting from 100ng of RNA. RNA has been extracted from lymphocytes cultures from 2 probands with SF3B1 mutations and 14 controls. All 16 RNA-Seq were sequenced on a single HighOutput flowcell 2x75bp (NextSeq550). Raw fastq files have between 20 and 30M paired-reads.

  Dataset EGAD50000002121

• RNAseq of neuroblastoma PDX and cell lines

  This dataset contains 72 RNAseq (BAM and Fastq files are available for each sample).

  Dataset EGAD00001006558

• Whole-genome and transcriptome sequencing files obtained in monozygotic twins discordant for Mayer-Rokitansky-Küster-Hauser syndrome

  Raw, unfiltered, paired-end fastq files obtained through whole-genome and RNA-sequencing, respectively. RNA-seq of affected individuals in three twin pairs. WGS of blood in five twin pairs as well as uterine rudiment tissue of selected affected individuals.

  Dataset EGAD00001008992

• Sequencing data for oesophageal and related samples - Nowicki-Osuch, Zhuang et al (scRNA)

  Data supporting: “Single-cell RNA sequencing unifies developmental programs of Esophageal and Gastric Intestinal Metaplasia.” Nowicki-Osuch, Zhuang et al. scRNAseq (FASTQ files) 59 samples

  Dataset EGAD00001010074

• Targeted sequencing of genomics regions of interest in depression and obesity

  Data corresponding to the fastq of the 654 individuals included in the study.

  Dataset EGAD50000000476

• Flemish_Gut_Flora_Project_phenotype

  Here, we studied well-phenotyped individuals from the Flemish Gut Flora Project (FGFP, N=1,106, Belgium) and the effect of environments on microbiome. The 69 major significant phenotypes found in this study are provided.

  Dataset EGAD00001001943

• Somatic evolution in the non-neoplastic IBD affected colon

  Whole genome and whole exome sequencing data supporting the manuscript 'Somatic evolution in the non-neoplastic IBD affected colon' by Sigurgeir Olafsson et al.

  Dataset EGAD00001006061

• The Berlin (BLN) panel of glioblastoma cell lines: RNAseq of human gliomasphere cell lines and matched parental tumors

  We generated a panel of nine glioma stem-like cell lines under serum-free cell culture conditions from human glioblastoma samples. In addition to clinical annotation, MR imaging and histological characterization of the parental tumor, as well as xenograft studies of tumorigenecity, transcriptomic profiling of tumor/cell line pairs by RNA sequencing has been performed.

  Study EGAS00001001167

• RNA-Seq of non-canonical t(7;12) AML

  We performed WGS on AutoMACS-separated BM leukemic blasts (CD34 + CD33+) to characterize the breakpoint and genes involved in the translocation. Additionally, we performed RNA-seq of the bone marrow blast cells to explore the functional consequences of the t(7;12) translocation

  Dataset EGAD50000000268

• Post-liver transplant recurrent human hepatocellular carcinoma study (RHCCS)

  The whole exome sequencing showed that HERC5 deletion and under-expression associates with shorter: time to tumor recurrence, progression-free, and overall survival in hepatocellular carcinoma (HCC) in two independent studies (p1=0.004, HR1=1.80; p2=0.018, HR2=3.31) totaling 286 HCC patients. Matched primary and recurrent tumors indicated a clonal selection advantage in somatic single nucleotide and copy number variants (CNVs) in recurrent compared to primary tumors of Chinese HCC patients with Wnt signaling most activated.

  Study phs000782

• Functional analysis of GATA2 synonymous mutations

  Germline mutations in SAMD9 and SAMD9L (SAMD9/9L) genes predispose to myelodysplastic syndromes (MDS) and show high prevalence in pediatric MDS with monosomy 7. Here, we studied an international cohort of children with primary MDS to assess the prevalence, hematological features, genetics, clonal evolution and clinical outcome in patients with germline SAMD9/9L mutations compared to pediatric MDS with either germline GATA2 mutations or pediatric MDS with wildtype status in SAMD9/9L and GATA2 genes

  Study EGAS00001003817

• Long-read sequencing of diagnosis and post-therapy medulloblastoma reveals complex rearrangement patterns and epigenetic signatures

  Cancer genomes harbor a broad spectrum of structural variants (SV) driving tumorigenesis, a relevant subset of which are likely to escape discovery in short reads. We employed Oxford Nanopore Technologies (ONT) sequencing in a paired diagnostic and post-therapy medulloblastoma to unravel the haplotype-resolved somatic genetic and epigenetic landscape. We assemble complex rearrangements and such associated with telomeric sequences, including a 1.55 Megabasepair chromothripsis event. We uncover a complex SV pattern termed "templated insertion thread", characterized by short (mostly less than 1kb) insertions showing prevalent self-concatenation into highly amplified structures of up to 50kbp in size. Templated insertion threads occur in 3% of cancers, with a prevalence ranging to 74% in liposarcoma, and frequent colocalization with chromothripsis. We also perform long-read based methylome profiling and discover allele-specific methylation (ASM) effects, complex rearrangements exhibiting differential methylation, and differential promoter methylation in seven cancer-driver genes. Our study shows the potential of long-read sequencing in cancer.

  Study EGAS00001006576