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• Genetically unique biospecimens derived from individuals with or without Type 1 Diabetes

  In this dataset, samples correspond to pools of genetically unique biospecimens derived from individuals with or without Type 1 Diabetes. Each sample alias contains all the DNA test numbers for that pool. Each experiment corresponds to scmxGEX (multiome RNA gene expression), scmxATAC (multiome ATAC sequencing), scRNA (single cell RNA sequencing), scATAC (single cell ATAC sequencing) for each pool. Runs link the appropriate fastq files to each experiment. Deconvolution using genetic information is required for single sample-based testing.

  Dataset EGAD50000001257

• CITEseq data of Reactive Lymph Nodes

  Mononuclear cells were isolated as cell suspensions by dissociation in a BD Horizon™ Dri Tumor & Tissue Dissociation Reagent (BD Biosciences) using a gentleMACS dissociator (Miltenyi Biotec). A totalseq-C antibody cocktail (Biolegend) was used, and the cell suspensions were diluted to a concentration of 1,000 cells/μL. Library sequencing was performed using the NovaSeq6000 System (Illumina). The FASTQ files were aligned to the 10x provided reference genome using 10x Genomics Cell Ranger software v7.1.0 to create unique molecular identifier count tables of gene expression of the samples.

  Dataset EGAD50000000538

• Single-cell RNA-Seq analysis of thymic ILC1 progenitors and NK cell differentiation This analysis involved a multiplexed sequencing run to study thymic innate lymphoid cells (ILCs) and NK progenitors. The generated data requires a demultiplexing file to separate and identify the individual sample tags for downstream analysis.

  This dataset contains multiplexed single-cell RNA sequencing (scRNA-seq) data from human thymic tissue, focusing on ILC1 progenitors and NK cell differentiation. The data were generated using the BD Rhapsody system and sequenced on the Illumina NovaSeq S4 platform. A demultiplexing file is required to assign sample identities.

  Dataset EGAD50000001157

• Application of targeted long-read methylation sequencing to dissected breast cancer tissues

  Four regions defined by pathological view were dissected from fresh frozen sections of breast cancer tissue using Millisect system. DNA and RNA extracted from the dissected tissues were applied to short-read WGS, short-read RNA-seq, short-read EM-seq, and targeted long-read methylation analysis t-nanoEM.

  Study JGAS000758

• Chromatin profiling of baseline and Notch inhibitor treated HCC PDX model

  We generated chromatin accessibility profiles for anti-Notch2 (n=3) and anti-gD (n=3) treated LIV78 tumors. Tumors were isolated, snap frozen in liquid nitrogen and stored at -80C. Tumor tissue was pulverized using a Covaris CP02 CryoPrep Pulverizer. Flash frozen pulverized tumor samples were sent to Active Motif to perform the ATAC-seq assay. Resulting material was quantified using the KAPA Library Quantification Kit for Illumina platforms (KAPA Biosystems), and sequenced with PE42 sequencing on the NextSeq 500 sequencer (Illumina) to produce FASTQ sequencing files.

  Dataset EGAD50000000735

• Multiple paralogues and recombination mechanisms contribute to the high incidence of 22q11.2 Deletion Syndrome

  To enable haplotype-specific assembly and rearrangement mapping in LCR22 clusters, we combined fiber-FISH optical mapping with whole genome (ultra-)long read sequencing or rearrangement-specific long-range PCR on 254 duos families (22q11.2DS patient and parent-of-origin) comprising several different LCR22-mediated rearrangements.

  Study EGAS50000000601

• WES to explore mutational landscape of blood and non blood liquids in female patients with metastatic breast cancer.

  Whole Exome Sequencing (WES) to explore mutational landscape of blood and non blood liquids in female patients with metastatic breast cancer. 11 patients. 86 liquid samples, 11 matched normal samples. Median coverage 67X. Illumina paired-end sequencing. Fastq files are provided. WES from Richard et al., Nature Communications, 2025 low-pass Whole Genome Sequencing (lpWGS) to assess the representativeness of seven body liquids from female patients with metastatic breast cancer. 216 liquid samples, 745 solid samples, 20 matched normal samples. 0.5X coverage. lpWGS from Richard et al., Nature Communications, 2025.

  Dataset EGAD50000001852

• A distinct monocyte cellular state links systemic immune dysregulation to pulmonary impairment in long COVID

  This is an independent cohort of Long COVID patients recruited from a rehabilitation centre. These patients had Long COVID from 8 months to more than 2 years since their acute COVID-19 disease. PBMC from these patients were collected and single cell transcriptomics dataset was generated.

  Study EGAS50000001216

• WGBS analysis corresponding to representative cases of iBCP-ALL patients

  In this study, we performed whole genome bisulfite sequencing (WGBS) to characterize the methylome of representative iBCP-ALL cases from the Interfant study discovery cohort, including 2 pools of B-cell progenitors from healthy donors, 2 MLL-AF4+, 2 MLL-AF9+ and 2 non-MLLs from iBCP-ALL patients.

  Study EGAS00001003650

• Mechanism and targeted therapy of Vemurafenib-Resistant Hairy-Cell Leukemia

  The discovery of the BRAF V600E mutation in almost all cases of hairy-cell leukemia has led to the widespread adoption of the BRAF inhibitor vemurafenib for treatment of chemotherapy-resistant cases. Impressive responses are reported; however, acquired resistance is common. Whilst diverse mechanisms of vemurafenib resistance have been elucidated in melanoma, the basis of resistance in HCL is unclear. Here we apply whole genome and deep targeted sequencing to investigate resistance mechanisms and potential therapeutic strategies in a patient with aquired resistance to vemurafenib.

  Dataset EGAD00001003923

• Mechanism and targeted therapy of Vemurafenib-Resistant Hairy-Cell Leukemia

  The discovery of the BRAF V600E mutation in almost all cases of hairy-cell leukemia has led to the widespread adoption of the BRAF inhibitor vemurafenib for treatment of chemotherapy-resistant cases. Impressive responses are reported; however, acquired resistance is common. Whilst diverse mechanisms of vemurafenib resistance have been elucidated in melanoma, the basis of resistance in HCL is unclear. Here we apply whole genome and deep targeted sequencing to investigate resistance mechanisms and potential therapeutic strategies in a patient with aquired resistance to vemurafenib.

  Dataset EGAD00001003924

• Precursor lesions, clonal architecture and relapse in Wilms nephroblastoma

  Targeted resequencing at high depth (21 genes, 9 chromosomal regions): at least 4 FFPE samples per case and matched germline DNA: * 100 cases with detailed outcome data, including 15 cases with tumour relapse (515 samples) * 40 cases with matched pre-chemotherapy biopsies (240 samples) * 50 nephrogenic rests matched to above cases (50 samples) We expect a proportion (possibly 10%) of cases to be mutationally silent on the above studies, and propose to subsequently carry out integrated whole-genome, methylome and transcriptome studies on matched frozen tissue from these cases

  Dataset EGAD00001003217

• IBD Whole Genome Sequencing Phase 1 (2018-08-03)

  We will sequence at 15X coverage the genomes of 960 IBD patients. These samples are currently onsite at Sanger and made available for sequencing via our collaboration with the UK IBD Genetics consortium. During the next quinquennium we intend to sequence the genomes of many thousand IBD patients and these 960 represent the first stage of this effort. Ultimately we will perform association tests comparing these genomes to similar numbers of control genomes to identify rare and low-frequency variants underlying IBD. . This dataset contains all the data available for this study on 2018-08-03.

  Dataset EGAD00001004272

• Chordoma Sequencing Project RNAseq

  This is a continuation of the Chordoma Sequencing Project. All cancers arise due to somatically acquired abnormalities in DNA sequence. Systematic sequencing of cancer genomes allows acquisition of complete catalogues of all classes of somatic mutation present in cancer. These mutation catalogues will allow identification of the somatically mutated cancer genes that are operative and characterise patterns of somatic mutation that may reflect previous exogenous and endogenous mutagenic exposures. In this application, we aim to perform whole genome sequencing on 10 chordoma matched genome pairs. RNA Sequencing/Methylation and SNP6 and an additional sequencing of three cancer cell lines will be added to this work.

  Dataset EGAD00001000653

• Transcriptomics of human olfactory mucosa

  The olfactory gene repertoire is largely species-specific, shaped by the nature and necessity of chemosensory information for survival in each species' niche. We are intrigued by this interspecific variation and started to investigate the olfactory transcriptome in primates for evidence of selection at the level of receptor gene choice. Having collected this data from two primates, we now wish to extend the analysis to humans. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/

  Dataset EGAD00001003213

• Application of short-RNA-seq in post-mortem human hippocampi from the Calgary Brain Bank (CBB) to assess transcriptome-wide deregulation in processing of SINE Alu RNAs in Alzheimer’s disease

  Here, we investigate through short-RNA_seq in human hippocampi from the Calgary Brain Bank (CBB) whether Alu RNAs are processed in human brains, and whether their processing ratio is deregulated in brains of AD patients compared to healthy aging individuals.

  Study EGAS00001004973

• MutWP5: CRUK Mutographs of Cancer: BRCA Carriers (WG)(Novaseq)

  Sequencing of LCM-derived microbiopsies from 20 women who underwent risk-reducing reduction mastecomies due to germline BRCA1/2. Goal to assess the mutational burden, spectrum, and clonal dynamics within the tissue. Exome data will be used as a driver and clonality screen, highly clonal or driver-containing samples will subsequenctly be sent for whole-genome sequencing. Results from this poriton of the study will be compared to women who had cosmetic breast reduction surgeries and those with cancer. . This dataset contains all the data available for this study on 2023-03-08.

  Dataset EGAD00001010112

• Development and Validation of a Prognostic and Predictive 32-Gene Signature for Gastric Cancer

  We applied this signature to a 567-patient GC cohort to establish genomic-based molecular subtypes and then used a support vector machine to build a molecular subtype-based risk-scoring model. Both source code and supplementary datasets for risk score prediction are available at https://github.com/hwanglab/Yonsei_gastric_cancer_32genes.

  Dataset EGAD00001008091

• MutWP5: CRUK Mutographs of Cancer: BRCA Carriers (Exome)(Novaseq)

  Sequencing of LCM-derived microbiopsies from 20 women who underwent risk-reducing reduction mastecomies due to germline BRCA1/2. Goal to assess the mutational burden, spectrum, and clonal dynamics within the tissue. Exome data will be used as a driver and clonality screen, highly clonal or driver-containing samples will subsequenctly be sent for whole-genome sequencing. Results from this poriton of the study will be compared to women who had cosmetic breast reduction surgeries and those with cancer. . This dataset contains all the data available for this study on 2023-03-08.

  Dataset EGAD00001010115

• Whole genome sequencing of Osteosarcoma clonal evolution

  Multiple large-scale genomic profiling efforts have been undertaken in osteosarcoma to define the genomic drivers of tumorigenesis, therapeutic response, and disease recurrence. The spatial and temporal intratumor heterogeneity could also play a role in promoting tumor growth and treatment resistance. Here, we conducted longitudinal whole-genome sequencing of 37 tumor samples from eight patients with osteosarcoma that relapsed or became refractory to initial therapy. We found that the chemoresistant population in recurrent osteosarcoma is subclonal at diagnosis, emerges at the time of primary resection due to selective pressure from neoadjuvant chemotherapy, and is characterized by unique oncogenic amplifications.

  Dataset EGAD00001011285

• TRACERx Reduced-representation bisulfite sequencing (RRBS)

  RRBS data from TRACERx non-small cell lung cancer (NSCLC) tumours and matched normal adjacent tissue. TRACERx (TRAcking Cancer Evolution through therapy (Rx)) is a prospective cohort study designed to investigate intratumor heterogeneity (ITH) in relation to clinical outcome, and to determine the clonal nature of driver events and evolutionary processes in early stage non-small cell lung cancer (NSCLC).

  Dataset EGAD00001009707

• Dataset for identification of the dismal subtype of B-ALL with dysregulation of CDX2 and UBTF

  WGS (tumor and germline samples) was performed to identify structural variants in the UBTF/CDX2 subgroup. RNA-seq was performed to detect gene fusion in the UBTF/CDX2 subgroup. HiChIP was performed to investigate 3D chromatin architecture and enhancer landscapes of representative patient samples and cell lines harboring Type I and II FLT3-PAN3 deletions and amplifications.

  Dataset EGAD00001008416

• Gene expression profile of mesothelial-derived carcinoma-associated fibroblasts

  RNA-sequencing was carried out on ascetic fluid-isolated mesothelial cells from low-grade serous ovarian cancer patients, high-grade serous ovarian cancer patients, chemotherapy-treated high-grade serous ovarian cancer patients and control mesothelial cells obtained from non-oncologic patients to identify differentially expressed genes associated to mesothelial-to-mesenchymal transition process. The dataset contains 18 samples: - Control mesothelial cells: 4 samples - Group 1, high-grade serous ovarian cancer patients: 3 samples - Group 2, chemotherapy-treated high-grade serous ovarian cancer patients: 5 samples - Group 3, low-grade serous ovarian cancer patients: 6 samples

  Dataset EGAD00001005133

• Congenital anosmia 1

  Congenital anosmias can be complete (the lack of a sense of smell) or specific (the inability to detect specific smells). To date, only a single recessive gene underlying complete anosmia has been identified. Here we sequenced the exomes of 10 individuals from a single family, including three with complete anosmia, across three generations to identify the genetic basis of congenital anosmia in this family. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/

  Dataset EGAD00001002210

• Whole genome sequencing

  This dataset contains whole genome sequencing data from 22 samples of FACS-purified bone marrow CD34+ haematopoietic stem and progenitor cells and matched hair follicle controls collected from individuals undergoing hip replacement surgery. Additionally, it contains whole genome sequencing data from unseparated bone marrow mononuclear cells, CD3-CD34- bone marrow mononuclear cells, and peripheral blood granulocytes of the same 14 samples. Haematopoietic samples were sequenced to a target coverage of 90-120x; 19 of them were re-sequenced to a total target coverage of 270x. Hair follicle controls were sequenced to a target coverage of 30x.

  Dataset EGAD00001015178