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• ISCAPE V(D)J libraries from HA-specific single memory B cells of four Influenza A exposed individuals

  Peripheral blood mononuclear cells were used to produce paired, full-length IGM, IGK and IGL V(D)J libraries from HA-binding single memory B cells using the ISCAPE (Individualized Single Cell Analysis of Paired Expressed antigen receptors) technique. Locus-specific multiplexed nested PCR with primer sets targeting the 5’ UTR/leader and 3’ constant region was performed before well and plate indexing and paired chain sequencing with an Illumina MiSeq instrument. Expressed total IGM, IGK and IGL V(D)J libraries from each donor were acquired and analyzed to define personalized IG allele content. The fastq file names include the donor and a numerical plate index for the HA-specific ISCAPE BCR HC and LC V(D)J libraries.

  Dataset EGAD50000002019

• Use_of_Deep_Sequencing_to_Dectect_Clonal_Mutations_In_Sun_Exposed_Skin_Epidermis

  This study aims to define the landscape of somatic mutations in sun exposed human skin by deep sequencing, analyse their frequency and use the data to infer the effect of mutations on proliferating cell behaviour. The frequency of each mutation will reflect the size of the clone of cells in the tissue sample. By analyzing small samples, clones with as few as 100 cells will be detectable. Allele frequency distributions for each mutation will be used to infer cell fate using published methods (Klein et al. 2010). This study will shed unprecedented light on the early clonal events that lead to the emergence of cancer.

  Study EGAS00001000515

• Use_of_Deep_Sequencing_to_Dectect_Clonal_Mutations_In_Sun_Exposed_Skin_Epidermis_PART2

  This study aims to define the landscape of somatic mutations in sun exposed human skin by deep sequencing, analyse their frequency and use the data to infer the effect of mutations on proliferating cell behaviour. The frequency of each mutation will reflect the size of the clone of cells in the tissue sample. By analyzing small samples, clones with as few as 100 cells will be detectable. Allele frequency distributions for each mutation will be used to infer cell fate using published methods (Klein et al. 2010). This study will shed unprecedented light on the early clonal events that lead to the emergence of cancer.

  Study EGAS00001000603

• GoT2D: Genetics of Type 2 Diabetes, a study of the the genetic architecture of type 2 diabetes

  The GoT2D study includes ~2800 samples, half T2D cases and half T2D controls, of Northern European ancestry sequenced over 3 three technologies: deep whole exome sequencing, low-pass (4x) whole genome sequencing, and OMNI 2.5M genotyping. Samples were ascertained to be phenotypically "extreme" (e.g. leaner, younger cases and older, more obese controls). Genotypes (SNVs, INDELs, and SVs) were called separately for each technology and then integrated via genotype refinement into a single phased reference panel; samples and variants were then excluded based on QC procedures described in Fuchsberger et al. Please note that 2 of the samples in the GoT2D vcf do not have phenotype data.

  Dataset EGAD00001002247

• Lymphocyte Gut WGS H38 (2021-02-02)

  We study lymphocyte somatic evolution through the sequencing of normal healthy lymphocytes. We perform whole-genome sequencing of single-cell derived T and B cell colonies to identify somatic mutations, and perform targeted deep-sequencing of these mutations. The lineages of T and B cells, and the frequencies of these mutations reveals the neutral and non-neutral evolutionary processes underlying lymphocyte growth and function. . This dataset contains all the data available for this study on 2021-02-02.

  Dataset EGAD00001006934

• Lymphocyte PanBody WGS H38 (2021-02-02)

  We study lymphocyte somatic evolution through the sequencing of normal healthy lymphocytes. We perform whole-genome sequencing of single-cell derived T and B cell colonies to identify somatic mutations, and perform targeted deep-sequencing of these mutations. The lineages of T and B cells, and the frequencies of these mutations reveals the neutral and non-neutral evolutionary processes underlying lymphocyte growth and function. . This dataset contains all the data available for this study on 2021-02-02.

  Dataset EGAD00001006935

• Liquid biopsy for molecular characterization of diffuse large B-cell lymphoma and early assessment of minimal residual disease

  Genomic data from Diffuse-large B-cell lymphomas at diagnosis and during the treatment. The processed samples were : -Circulating tumor DNA: at diagnosis and after2-cycles of treatment. -Tumour lymph node at diagnosis -Genomic DNA

  Dataset EGAD50000000310

• Whole-exome sequences of ovarian clear cell carcinomas and paired normal DNA

  Whole-exome sequencing dataset for the Australian Ovarian Cancer Study (AOCS) and The Jikei University School of Medicine (JIKEI) ovarian clear cell carcinoma (OCCC) clinical outliers project, representing 10 donors. Consists of 20 fastq files: one normal and one tumour from each patient.

  Dataset EGAD00001006004

• Whole-exome sequencing of liver cancer organoids

  Whole-exome sequencing was performed from organoids derived from 10 liver cancer biopsies (7 hepatocellular carcinoma and 3 cholangiocarcinoma), corresponding liver and non-tumoral biopsies. For 3 of the organoids, both early and late passage organoids were sequenced. Whole-exome sequencing was performed using the Agilent Clinical Research Exome capture kit followed by Illumina sequencing. BAM files are provided in this dataset.

  Dataset EGAD00001004205

• Targeted next-generation sequencing of plasma samples

  Targeted next-generation sequencing was performed on circulating cell-free DNA extracted from plasma samples of patients in the Neo-Pembro trial. For each patient, circulating cell-free DNA from the baseline plasma sample was extracted and sequenced using the AVENIO Expanded Kit v2.

  Dataset EGAD50000001415

• EFFORT occupationally exposed human stool metagenomes (148 samples)

  Metagenomes of stool samples from 54 pig farmers, 24 broiler farmers and 70 slaughter line workers. Note: Access to the data will only be granted for antibiotic resistance studies in accordance with the EFFORT consents issued by the participants.

  Dataset EGAD00001005444

• scRNA-seq dataset for AD and Pso patients

  This dataset contains scRNA-seq fastq files to the paper entitled "Single-cell profiles reveal distinctive immune response in atopic dermatitis in contrast to psoriasis". The details of experiment setup was described in the paper.

  Dataset EGAD00001010106

• Single-Cell Transcriptomic Characterization of Microscopic Colitis

  Patients with microscopic colitis (MC), chronic diarrhea without histological signs of MC, or unaffected controls were profiled using single-cell RNA sequencing (scRNA-seq; inDrops and 10X Genomics were used). One profiled patient without clinical symptoms was found to have histological signs of MC (asymptomatic MC). Some of the subjects from dbGaP study phs003418 are controls in this study. T-Cell Receptor sequencing (TCR-Seq) was also performed on a subset of patients. Individual transcriptomes were analyzed to characterize the cellular profile associated with MC and search for mediators of disease pathology. Raw reads and processed count matrices will be available through dbGaP.

  Study phs003876

• Single-cell RNA sequencing of SI-NET

  Small intestinal neuroendocrine tumors (SI-NETs) arise from hormone-producing cells in the gut, yet the molecular changes driving malignant transformation remain poorly understood. Bulk tissue-based analyses make it challenging to distinguish signals derived from normal cells from those of normal hormone-producing cells. In this study, we analyzed SI-NETs at single-cell resolution and directly compared tumor cells with their corresponding normal hormone-producing counterparts using single-cell RNA sequencing. Tissue samples were obtained from two patients undergoing tumor resection surgery. Cells from corresponding normal intestinal mucosa and SI-NET tumors were isolated using specific markers and analyzed for direct comparison.

  Study EGAS50000001584

• Truncated FOS impairs osteogenic differentiation and induces prostaglandin and NFkB signalling in an in vitro cell-of-origin model for osteoid osteoma and osteoblastoma

  The effect of FOS truncation on osteogenic differentiation and proliferation was investigated in an in vitro model for osteoid osteoma and osteoblastoma. In this model, truncated FOS (FOSΔ) was overexpressed in human foetal mesenchymal stem cells through a lentiviral vector. Osteogenic differentiation - assessed by measuring mineralization, ALPL expression and ALP activity - and proliferation rate were reduced in cells overexpressing FOSΔ compared to mesenchymal stem cells with an empty lentiviral vector (pLV). Transcriptome-sequencing and differential gene expression analysis revealed decreased gene expression of genes in pathways involving cell cycling and mitosis, and osteogenic differentiation, including WNT signalling, extracellular matrix (ECM) organization and matrix metalloproteinases (MMPs), in FOSΔ as compared to empty vector cells, indicating decreased proliferation and osteogenesis.

  Study EGAS50000001291

• A Single-cell Atlas of Progressive TKI Resistance in Chronic Myeloid Leukemia

  High-dimensional scRNA seq and CyTOF were used to identify features predictive of treatment outcome at diagnosis. An optimal TKI response was characterised by erythroid lineage skewing of the CD34+ HSPC compartment. While TKI-resistant CP was reminiscent of a BC-like state, where HSPCs were enriched for inflammation, stemness and quiescence. We designed a machine-learning approach which assessed the prognostic potential of all 32 sub-populations of our scRNA seq dataset. LSCs and NK populations harboured the highest prognostic power at diagnosis. Within the LSCs, erythroid lineage priming and MYC activation were features of an optimal and poor TKI responses, respectively. With the NK cell compartment, apart from a higher abundance of NK cells in TKI optimal responders, a memory-like HLA-DR+ adaptive NK and KLRC1+ NK populations were hallmarks of an optimal and poor TKI responses, respectively. Mechanistically, both cell intrinsic and extrinsic mechanisms contributed towards the higher sensitivity of EPs to TKI therapy. In summary, our high-dimensional single-cell atlas of TKI resistance highlights pivotal transcriptional features associated with TKI-resistance disease, some of which have the potential to be exploited as biomarkers.

  Study EGAS00001005509

• Dataset for "HPV integration induces gene fusions" (Illumina)

  Illumina whole-genome sequencing data for "HPV integration induces gene fusions" We performed short read whole-genome sequencing of five HPV+ head and neck cancer samples using Illumina. The reads are submitted in bam or fastq file format.

  Dataset EGAD50000001305

• Whole genome sequencing raw data for fragile X associated unmethylated expansion carrier 1

  Whole genome sequencing raw data for fragile X associated unmethylated expansion carrier 1. DNA was sequenced using the illumina NovaSeq6000 system. 8x paired end FASTQ files from one DNA sample (UFM 1), 4x R1 files and 4x R2 files.

  Dataset EGAD50000000917

• Whole genome sequencing raw data for fragile X associated unmethylated expansion carrier 2

  Whole genome sequencing raw data for fragile X associated unmethylated expansion carrier 2. DNA was sequenced using the illumina NovaSeq6000 system. 8x paired end FASTQ files from one DNA sample (UFM 2), 4x R1 files and 4x R2 files.

  Dataset EGAD50000000921

• Study the differences at the trascriptome level between iNKT and T cells

  Chimeric antigen receptor anti-CD19 (CAR19)-T cell immunotherapy-induced clinical remissions in CD19+ B cell lymphomas are often short-lived. We tested whether CAR19-engineering of the CD1d-restricted invariant NKT (iNKT) cells would result in enhanced anti-lymphoma activity. CAR19-iNKT cells co-operatively activated by CD1d- and CAR19-CD19-dependent interactions are more effective than CAR19-T cells against CD1d-expressing lymphomas in vitro and in vivo. The swifter in vivo anti-lymphoma activity of CAR19-iNKT cells and their enhanced ability to eradicate brain lymphomas underpinned an improved tumor-free and overall survival. CD1d transcriptional de-repression by all-trans retinoic acid results in further enhanced cytotoxicity of CAR19-iNKT cells against CD19+ chronic lymphocytic leukemia cells. Thus, iNKT cells are a highly efficient platform for CAR-based immunotherapy of lymphomas and possibly other CD1d-expressing cancers.

  Study EGAS00001003176

• Somatic mutation and clonal evolution in the human pancreas - WGS (2019-12-17)

  In this study we aim to characterise the landscape of mutation and clonal selection in the human pancreas. The study combines targeted sequencing and whole-genome sequencing of microbiopsies from the pancreas. The range of patients studied will include healthy individuals, both smokers and non-smokers, and patients with pancreatic ductal adenocarcinoma. This dataset contains all the data available for this study on 2019-12-17.

  Dataset EGAD00001005751

• Raw sequencing data - Intra-tumor heterogeneity and clonal evolution patterns towards platinum-resistant high-grade serous ovarian cancer

  This dataset includes 69 sampels of whole-exome sequencing data of high-grade serous ovarian carcinoma (HGSOC). We included patients with advanced (International Federation of Gynecology and bstetrics [FIGO] stage IIIeIV) HGSOC for which biopsies were obtained during debulking surgery, the first at initial diagnosis and the second at disease relapse. Where possible, matched normal DNA from each participating patient was obtained from a whole-blood sample. Written informed consent was obtained from all patients and approved by the local ethics committee.

  Dataset EGAD00001001381

• H3Africa - Respiratory Microbiota of African Children

  Shotgun metagenomic sequencing of nasopharyngeal (NP) samples, from children enrolled in a PCV13-vaccinated South African birth cohort was used to explore strain-level pneumococcal colonization patterns and transmission dynamics, and associated antimicrobial-resistance determinants. NP swabs were collected at two-week intervals from birth through the first year of life from 137 infants. Pneumococcal isolates were serotyped and tested for phenotypic antimicrobial resistance. 196 NP samples from a subset of 23 infants were then selected based on changes in serotype or antimicrobial resistance. DNA was extracted directly from the enriched NP samples and shotgun metagenomic sequencing performed. Reads were assembled and aligned against reference pneumococcal genomes. in silico pneumococcal capsular, multilocus sequence typing, and resistome analyses were performed.

  Study EGAS00001004401

• Comprehensive characterization of cell-free tumor DNA in plasma and urine of patients with renal tumors

  Cell-free tumour-derived DNA (ctDNA) allows non-invasive monitoring of various cancers but its utility in renal cell cancer (RCC) has not been well established. A combination of untargeted and targeted sequencing methods, applied to two independent cohorts of patients (n=90) with various renal tumour subtypes, were used to determine ctDNA content in plasma and urine. Our data revealed lower plasma ctDNA levels in RCC relative to other cancers, with untargeted detection of ~33% for both cohorts. A highly sensitive personalised approach, applied to plasma and urine from select patients (n=22), improved detection to ~50%, including in patients with early stage and even benign lesions. A machine-learning based model, applied to untargeted data, predicted this detection, potentially offering a means of triaging patient samples for personalised analysis. We observed that plasma, and for the first time, urine ctDNA may better represent tumour heterogeneity than a single tissue biopsy. Longitudinal sampling of >200 plasma samples revealed that ctDNA can track disease course. These data highlight low ctDNA levels in RCC but indicate potential clinical utility provided improvement in isolation and detection approaches.

  Study EGAS00001003530

• Integration of human pancreatic islet genomic data refines regulatory mechanisms at Type 2 Diabetes susceptibility loci

  Human genetic studies have emphasised the dominant contribution of pancreatic islet dysfunction to development of Type 2 Diabetes (T2D). However, limited annotation of the islet epigenome has constrained efforts to define the molecular mechanisms mediating the, largely regulatory, signals revealed by Genome-Wide Association Studies (GWAS). We characterised patterns of chromatin accessibility (ATAC-seq, n=17) and DNA methylation (whole-genome bisulphite sequencing, n=10) in human islets, generating high-resolution chromatin state maps through integration with established ChIP-seq marks. We found enrichment of GWAS signals for T2D and fasting glucose was concentrated in subsets of islet enhancers characterised by open chromatin and hypomethylation, with the former annotation predominant. At several loci (including CDC123, ADCY5, KLHDC5) the combination of fine-mapping genetic data and chromatin state enrichment maps, supplemented by allelic imbalance in chromatin accessibility pinpointed likely causal variants. The combination of increasingly-precise genetic and islet epigenomic information accelerates definition of causal mechanisms implicated in T2D pathogenesis.

  Study EGAS00001002592