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• Single cell and spatial transcriptomics of adult human adrenal glands

  The data set is composed of single cell transcriptomics data for adrenal glands from 11 deceased organ donors (10x 3') and spatial transcriptomic data for adrenal glands from 4 deceased organ donors (10x Visium).

  Dataset EGAD50000000394

• WGS data for Pancreatic Cancer samples (misc.)

  WGS data for pancreatic cancer samples. These are miscellaneous samples which are part of a tandem duplicator phenotype paper (Farooq et al, NPJ Precision Oncology, 2025). The dataset includes tumour and normal BAM files sequenced on Illumina NovaSeq 6000 and aligned against GRCh38 (n=7 tumour/normal pairs).

  Dataset EGAD50000001833

• Epi2Diag raw methylation array data for patients with neurodevelopmental disorders

  Raw methylation array data (Illumina Infinium EPIC v2.0) from patients with rare neurodevelopmental disorders. IDAT files were generated from DNA extracted from whole blood at the ASGARD platform, Inserm U1245, Univ Rouen, CHU Rouen, to investigate new episignatures and provide independent validation datasets for existing episignatures.

  Dataset EGAD00010002724

• A95720A

  Whole genome sequencing for single cells for library A95720A 1467 cells; filetype=bam

  Dataset EGAD00001007613

• A96240B

  Whole genome sequencing for single cells for library A96240B 1683 cells; filetype=bam

  Dataset EGAD00001007122

• Single-cell RNA-seq counts and merged data for 28 Hodgkin lymphomas and 5 reactive lymph nodes

  This dataset contains raw count data (10X CellRanger) for 28 Hodgkin lymphoma samples and 5 reactive lymph nodes, and merged data from all samples (RData object) including cell cluster assignments.

  Dataset EGAD00001008270

• Single Cell Genome Sequence for DLP+ library A118389B

  Single Cell Genome Sequence for Telomerase immortalized breast epithelium cell line 184-hTERT 85.14 p20 cell line AT135 on DLP+ library A118389B

  Dataset EGAD00001009433

• A96233B

  Whole genome sequencing for single cells for library A96233B 1601 cells; filetype=bam

  Dataset EGAD00001007623

• Single Cell Genome Sequence for DLP+ library A110660A

  Single Cell Genome Sequence for triple negative breast cancer patient-derived xenograft SA610 passage 3 on DLP+ library A110660A

  Dataset EGAD00001009430

• CBD-RAW-REPERTOIRE-B: B cell bulk repertoire sequence files

  fastq and filtered fasta files for B-cell receptor sequencing. For further information regarding this dataset, please contact Rachael Bashford-Rogers at contact@combat.ox.ac.uk.

  Dataset EGAD00001007960

• Breast implant-associated anaplastic large cell lymphoma shallow whole genome sequencing for copy number analysis and Whole exome sequencing data.

  Shallow whole genome sequencing of 29 BIA-ALCL patients for copy number analysis and 24 Alk-negative ALCL samples as control cohort. 7 Whole exome sequencing BIA-ALCL samples.

  Dataset EGAD00001006433

• A96174B

  Whole genome sequencing for single cells for library A96174B 1447 samples; filetype=bam

  Dataset EGAD00001008242

• Single Cell Genome Sequence for DLP+ library A118857B

  Single Cell Genome Sequence for high grade serous ovarian carcinoma patient-derived xenograft SA1184D passage 1 on DLP+ library A118857B

  Dataset EGAD00001009445

• Single Cell Genome Sequence for DLP+ library A95663A

  Single Cell Genome Sequence for high grade serous ovarian carcinoma patient-derived xenograft SA1053F passage 1 on DLP+ library A95663A

  Dataset EGAD00001009446

• Single Cell Genome Sequence for DLP+ library A96187A

  Single Cell Genome Sequence for triple negative breast cancer patient-derived xenograft SA501 passage 11, patient-derived xenograft SA609 passage 7 on DLP+ library A96187A

  Dataset EGAD00001009464

• A96177B

  Whole genome sequencing for single cells for library A96177B 683 samples; filetype=bam

  Dataset EGAD00001008244

• Single Cell Genome Sequence for DLP+ library A98181A

  Single Cell Genome Sequence for triple negative breast cancer patient-derived xenograft SA919 passage 7, patient-derived xenograft SA1050A passage 1 on DLP+ library A98181A

  Dataset EGAD00001009479

• Single Cell Genome Sequence for DLP+ library A96109A

  Single Cell Genome Sequence for triple negative breast cancer patient-derived xenograft SA501 passage 2 on DLP+ library A96109A

  Dataset EGAD00001009452

• Single Cell Genome Sequence for DLP+ library A118782A

  Single Cell Genome Sequence for high grade serous ovarian carcinoma patient-derived xenograft SA1050B passage 1, patient-derived xenograft SA1050E passage 1 on DLP+ library A118782A

  Dataset EGAD00001009435

• Genotyping of GM samples

  This dataset contains a vcf file for 99 GM individuals genotyped on the Illumina HumanOmni2.5 array . The vcf file is originated after imputation (IMPUTE2) and filtering for minor allele frequency MAF≥0.05, imputation confidence score INFO of >0.4 and Hardy-Weinberg Equilibrium (HWE) p>1e-06, yielding ~6.3 million variants.

  Dataset EGAD00001010255

• A95707A

  Whole genome sequencing for single cells for library A95707A 1359 samples; filetype=bam

  Dataset EGAD00001008228

• A96155B

  Whole genome sequencing for single cells for library A96155B 1028 samples; filetype=bam

  Dataset EGAD00001008236

• A96165A

  Whole genome sequencing for single cells for library A96165A 779 samples; filetype=bam

  Dataset EGAD00001008239

• Single Cell Genome Sequence for DLP+ library A118812B

  Single Cell Genome Sequence for high grade serous ovarian carcinoma patient-derived xenograft SA1180C passage 1 on DLP+ library A118812B

  Dataset EGAD00001009442

• 16S bacterial amplicon sequencing data for Guangzhou cohort

  16S bacterial amplicon sequencing data for Guangzhou cohort

  Dataset EGAD00001010268

• BLUEPRINT release August 2015, DNase-Hypersensitivity for monocyte, on genome GRCh38

  DNase-Hypersensitivity data for 2 monocyte sample(s). 4 run(s), 2 experiment(s), 2 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_dnaseseq_analysis_20150820

  Dataset EGAD00001001560

• BLUEPRINT release January 2015, RNA-Seq for monocyte

  RNA-Seq data for 8 monocyte sample(s). 8 run(s), 8 experiment(s), 8 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_rnaseq_analysis_crg_20140811

  Dataset EGAD00001001191

• Carcinoid study - WGS dataset

  Fernandez-Cuesta et al., 2014, Nature Communication, Whole genome sequencing was performed using a read length of 2x100 bp for all samples. On average, 110 Gb of sequence were produced per sample, aiming a mean coverage of 30x for both tumour and matched normal.

  Dataset EGAD00001000813

• BLUEPRINT release January 2015, DNase-Hypersensitivity for macrophage

  DNase-Hypersensitivity data for 14 macrophage sample(s). 18 run(s), 14 experiment(s), 14 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_dnaseseq_analysis_20140811

  Dataset EGAD00001001198

• BLUEPRINT release August 2014, DNase-Hypersensitivity for macrophage

  DNase-Hypersensitivity data for 1 macrophage sample(s). 1 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT release August 2014. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_dnaseseq_analysis_20140811

  Dataset EGAD00001000931

• Whole Exome Sequencing of healthy Spanish individuals - Fastq files

  The need for a detailed catalogue of local variability for the study of rare diseases within the context of the Medical Genome Project motivated the whole exome sequencing of 267 unrelated individuals, representative of the healthy Spanish population.

  Dataset EGAD00001001012

• NHLBI GO-ESP: Early-Onset Myocardial Infarction Exome Chip (Broad EOMI)

  The NHLBI "Grand Opportunity" Exome Sequencing Project (GO-ESP), a signature project of the NHLBI Recovery Act investment, was designed to identify genetic variants in coding regions (exons) of the human genome (the "exome") that are associated with heart, lung and blood diseases. These and related diseases that are of high impact to public health and individuals from diverse racial and ethnic groups will be studied. These data may help researchers understand the causes of disease, contributing to better ways to prevent, diagnose, and treat diseases, as well as determine whether to tailor prevention and treatments to specific populations. This could lead to more effective treatments and reduce the likelihood of side effects. GO-ESP is comprised of five collaborative components: 3 cohort consortia - HeartGO, LungGO, and WHISP - and 2 sequencing centers - BroadGO and SeattleGO. As part of this initiative, the Broad has performed genotyping on several thousand subjects from 4 different cohorts on Illumina's ExomeChip platform as described below: The Duke Study: The Duke study enrolled cases from the Duke University Medical Center with myocardial infarction or coronary artery stenosis > 50%. Controls were individuals who were > 50 years old without coronary stenosis > 30% and without history of myocardial infarction, coronary artery bypass grafting, percutaneous coronary intervention, or heart transplant. The InterMountain Heart Study: The Intermountain Heart Study is an observational registry of individuals with coronary artery disease and healthy controls who received care at participating Intermountain Healthcare facilities. The Ottawa Heart Study: The Ottawa heart study enrolled cases with angiographically confirmed coronary artery disease (> 1 coronary artery with > 50% stenosis) who did not have type 2 diabetes and were ≤ 50 years old for males and ≤ 50 years old for females. Controls were also enrolled who were asymptomatic males > age 65 and females > age 70. PennCATH: PennCATH is a case-control study that recruited individuals undergoing coronary angiography at the University of Pennsylvania Hospital. Cases had angiographically confirmed coronary artery disease (>1 coronary artery with 50% stenosis) and were ≤ 55 years old if male and ≤ 60 years old if female. Controls were men > 40 years old and women > 45 years old with normal coronary angiography.

  Study phs000936

• DAC for OAMZL

  Dac EGAC00001003298

• DAC for EGAS00001002275

  Dac EGAC00001000600

• DAC for IRCR dataset

  Dac EGAC00001000693

• DAC for IL2

  Dac EGAC00001001176

• DAC for Pearl

  Dac EGAC00001002255

• DAC for EGAS00001006660

  Dac EGAC00001002900

• DAC for glioblastoma studies

  Dac EGAC00001003461

• DAC for EGAS00001007510

  Dac EGAC00001003402

• Dana-Farber Cancer Institute (DFCI) Brown Lab CLL Sequencing Study

  Chronic Lymphocytic Leukemia (CLL) is a hematological malignancy characterized by accumulation of CD5+CD19+ B cells in peripheral lymphoid organs, bone marrow and blood. In this study we analyze matched whole genome sequencing and RNA-seq data from CLL patients to characterize the mutational processes operative throughout tumor evolution. Source of tumor and normal DNA used is patient PBMC or B cells and saliva respectively.

  Study phs000879

• Single-Cell DNA Methylation Profiling with sciMETv2

  In this study we developed a high-throughput single-cell DNA methylation analysis technology, sciMETv2. This technique is rapid, cost-effective, and robust, enabling large-scale single-cell methylome dataset generation. We demonstrate this technology on human middle frontal gyrus, where we identified major cell types. We additionally performed target enrichment using sciMET-cap to enable a reduction in sequencing costs per cell while achieving comparable cell type identification.

  Study phs003091

• ScRNA sequencing and snp-array genotyping of peripheral immune cells in Type 1 diabetes mellitus (T1DM)

  Type 1 diabetes mellitus (T1DM) is a prototypic endocrine autoimmune disease resulting from an immune-mediated destruction of pancreatic insulin-secreting beta-cells. A comprehensive immune cell phenotype evaluation in T1DM has not been performed thus far at the single. In this cross-sectional analysis, we generated a single-cell transcriptomic dataset of peripheral blood mononuclear cells (PBMCs) from 46 manifest T1DM (Stage 3) cases and 31 matched controls.Our study reveals a surprisingly strong systemic dimension at the level of immune cell network in T1DM, defines disease-relevant molecular subtypes and has the potential to guide non-invasive test development and patient stratification.

  Dataset EGAD50000000345

• Whole Exome Sequencing

  The objective of this study was to better understand the molecular changes occurring in tumors during development of ICB (immune checkpoint blockade) resistance. Here, we performed Whole Exome Sequencing (WES) on biopsies from a cohort of melanoma patients after progression on anti-CTLA4 or anti-PD1 monotherapy and matched normal samples. Genetic alterations of antigen presentation and interferon gamma signaling pathways were observed in approximately 25% of ICB resistant cases.

  Study EGAS50000000259

• Clonal Evolution and Blastic Plasmacytoid Dendritic Cell Neoplasm - Two Cases

  Here we present two case studies of sequential whole exome sequencing (WES) in patients, who both developed BPDCN throughout their medical history but primarily presented with lymphoid cancers (clonally related ALK-negative anaplastic large-cell lymphoma (ALCL) and T-lymphoblastic lymphoma (T-LBL)) and whose bone marrow at remission exhibited a CMML phenotype, from which in both cases BPDCN clones arose that subsequently became treatment refractory.

  Study EGAS50000000214

• Rearrangements of Viral and Human Genomes at Human Papillomavirus Integration Events and Their Allele-Specific Impacts on Cancer Genome Regulation

  We discovered genomic and epigenomic dysregulation originating at sites of human papillomavirus (HPV) integration following the Oxford Nanopore long-read analysis of 72 cervical cancer genomes. The integration events had allele-specific effects on the genome, methylome, and transcriptome, which sometimes resulted in the activation of cancer genes. We also examined the 72 samples using Illumina short-read analysis in phs000528.

  Study phs003780

• CLDN14 mutation identifed from Japanese sensorineural hearing loss patient.

  The CLDN14 gene, encoding claudin 14, is reported to be one of the rare causes of non-syndromic autosomal dominant sensorineural hearing loss. The detailed clinical characteristics of CLDN14 associated hearing loss is still remain unclear. In the present study, we performed CLDN14 mutation analysis using massively parallel DNA sequencing (MPS) to reveal the clinical characteristics of CLDN14-related hearing loss in a large hearing loss population.

  Study JGAS000191

• Transcriptomic profiling of myeloid cells from secondary lymphoid organs (lymph nodes and tonsils) from lymphoma patients and controls.

  Despite their recognized impact on the pathogenesis and prognosis of B-cell lymphoma, tumor-associated macrophages (TAM) have not been extensively explored in diffuse large B-cell lymphoma (DLBCL) and follicular lymphoma (FL). We investigated mononuclear phagocyte (MNP) heterogeneity using single cell RNA sequencing (scRNAseq) in B-cell lymphoma lymph nodes compared to reactive secondary lymphoid organs (lymph nodes and tonsils).

  Study EGAS50000001135

• RNAseq_of_ribosomal_footprints

  Cancer genes can affect ribosomal RNA processing and this can underlie their essentiality to cells, making them cell-essential in the same way as ribosomal genes themselves. We want to confirm this, in order to understand the results of our CRISPR drop-out screens.NOTE FROM BESPOKE TEAM: Run a single read 1 (forward read) of 30 bases, then an index 1 read as normal. This would fit a 50cycle kit

  Study EGAS00001001591

• HipSci HumanExome BeadChip analysis - Usher syndrome and congenital eye defects

  The HipSci project brings together diverse constituents in genomics, proteomics, cell biology and clinical genetics to create a UK national iPS cell resource and use it to carry out cellular genetic studies. In this sub-study we performed Genotyping analysis using the Infinium HumanExome BeadChip on iPS cells generated from skin biopsies or blood samples from rare disease patients diagnosed with Usher syndrome and congenital eye defects.

  Study EGAS00001002008

• HipSci HumanExome BeadChip analysis - Bleeding and Platelet disorders

  The HipSci project brings together diverse constituents in genomics, proteomics, cell biology and clinical genetics to create a UK national iPS cell resource and use it to carry out cellular genetic studies. In this sub-study we performed Genotyping analysis using the Infinium HumanExome BeadChip on iPS cells generated from skin biopsies or blood samples from rare disease patients diagnosed with Bleeding and Platelet disorders.

  Study EGAS00001002013

• HipSci HumanHT 12 Expression BeadChip analysis - Hereditary Spastic Paraplegia

  The HipSci project brings together diverse constituents in genomics, proteomics, cell biology and clinical genetics to create a UK national iPS cell resource and use it to carry out cellular genetic studies. In this sub-study we performed Expression analysis using the Illumina HumanHT -12 Expression BeadChip on iPS cells generated from skin biopsies or blood samples from rare disease patients diagnosed with Hereditary Spastic Paraplegia.

  Study EGAS00001002021

• HipSci___Whole_Exome_sequencing___Usher syndrome and congenital eye defects

  The HipSci project brings together diverse constituents in genomics, proteomics, cell biology and clinical genetics to create a UK national iPS cell resource and use it to carry out cellular genetic studies. In this sub-study we perform whole exome sequencing using Agilent whole exome pulldown method on iPS cells generated from skin biopsies or blood samples from rare disease patients diagnosed with Usher syndrome and congenital eye defects.

  Study EGAS00001001985

• HipSci HumanHT 12v4 Expression BeadChip analysis-Rare_BBS

  The HipSci project brings together diverse constituents in genomics, proteomics, cell biology and clinical genetics to create a UK national iPS cell resource and use it to carry out cellular genetic studies. In this sub-study we performed Expression analysis using the Illumina HumanHT -12 Expression BeadChip on iPS cells generated from skin biopsies or blood samples from rare disease patients diagnosed with Bardet-Biedl syndrome.

  Study EGAS00001001276

• HipSci HumanHT 12v4 Expression BeadChip analysis - monogenic diabetes

  The HipSci project brings together diverse constituents in genomics, proteomics, cell biology and clinical genetics to create a UK national iPS cell resource and use it to carry out cellular genetic studies. In this sub-study we performed Expression analysis using the Illumina HumanHT -12 Expression BeadChip on iPS cells generated from skin biopsies or blood samples from rare disease patients diagnosed with monogenic diabetes.

  Study EGAS00001001277

• GILD_ExomeSeq_PTNHL

  This study is meant to gain further knowledge in haematological cancers. Patients samples (mainly DNAs or PCR products) from haematolocical cancer patients will be sequenced, and the outputs will be correlated to their diagnosis and/or prognosis; the findings may also add more insight into the understanding of biology in this type of tumour. We will be sequencing Primary Testicular Lymphomas (PTL) to identify genetic drivers of this rare cancer

  Study EGAS00001001613

• Genetic characterization patients affected by Cancer of Unknown Primary

  The genetic changes sustaining the development of human Cancers of Unknown Primary (CUP) remain elusive. Here we report the genomic profiling of 14 rigorously selected CUP samples. Although no specific recurring mutation in known driver genes was found, a comparison of the mutational landscape of CUPs with that of most other human tumor types revealed a consistent change in diverse genes belonging to the axon guidance KEGG pathway.

  Study EGAS00001006621

• HipSci HumanHT 12 Expression BeadChip analysis - Hereditary Cerebellar Ataxias

  The HipSci project brings together diverse constituents in genomics, proteomics, cell biology and clinical genetics to create a UK national iPS cell resource and use it to carry out cellular genetic studies. In this sub-study we performed Expression analysis using the Illumina HumanHT -12 Expression BeadChip on iPS cells generated from skin biopsies or blood samples from rare disease patients diagnosed with Hereditary Cerebellar Ataxias.

  Study EGAS00001002020

• HipSci HumanHT 12 Expression BeadChip analysis - Primary immune deficiency

  The HipSci project brings together diverse constituents in genomics, proteomics, cell biology and clinical genetics to create a UK national iPS cell resource and use it to carry out cellular genetic studies. In this sub-study we performed Expression analysis using the Illumina HumanHT -12 Expression BeadChip on iPS cells generated from skin biopsies or blood samples from rare disease patients diagnosed with Primary immune deficiency.

  Study EGAS00001002027

• HipSci HumanHT 12 Expression BeadChip analysis - Bleeding and Platelet disorders

  The HipSci project brings together diverse constituents in genomics, proteomics, cell biology and clinical genetics to create a UK national iPS cell resource and use it to carry out cellular genetic studies. In this sub-study we performed Expression analysis using the Illumina HumanHT -12 Expression BeadChip on iPS cells generated from skin biopsies or blood samples from rare disease patients diagnosed with Bleeding and Platelet disorders.

  Study EGAS00001002028

• Population_based_analysis_of_POT1_variants_in_a_cutaneous_melanoma_case_control_cohort

  Pathogenic germline variants in the protection of telomeres 1 gene (POT1) have been associated with predisposition to a range of tumor types, including melanoma, glioma, leukemia and cardioangiosarcoma. We sequenced all coding exons of the POT1 gene in 2,929 European-descent melanoma cases and 3,298 controls, identifying 43 protein-changing genetic variants. We performed functional studies on each of these variants and explored their possible contribution to disease risk.

  Study EGAS00001006870

• Pre-neoplastic somatic mutations including MYD88L265P in lymphoplasmacytic lymphoma

  In this study, we sequenced multiple stages of the B-lineage in elderly individuals and patients with lymphoplasmacytic lymphoma to study whether mutations are accumulated in normal-cell counterparts prior to lymphoma

  Dataset EGAD00001008196

• Multiomics characterisation of the response to stimulation in Long Covid patients

  We generated 10X, droplet-based paired snRNAseq+snATACseq (Multiome) of the response to P. Aeruginosa or RPMI in patients suffering from Long Covid. In total, we included 15 patients. Single nuclei libraries are genetically multiplexed across donors, genotype files are available to enable demultiplexing. Phenotype sheets provide information of pools/donors as well as donor phenotype.

  Dataset EGAD50000000203

• Study on longer adjuvant chemotherapy in Women with Early Breast Cancer

  The Cancer and Leukemia Group B (CALGB) 40101 trial compared four and six cycles of AC or single-agent paclitaxel in early breast cancer. The study was a 2X2 factorial design trial that also examined the effects of AC vs singleagent paclitaxel.

  Study phs000807

• Study of Leukemia Stem Cells in B-ALL

  This study focused on the biologic properties of human B acute lymphoblastic leukemia (ALL) stem cells. We used human leukemia cell lines, primary patient specimens, and patient derived xenografts in experiments using ChIP-seq, bulk RNA sequencing, single cell RNA sequencing, and CITE-seq.

  Study phs002492

• Loss of RREB1 in pancreatic beta cells reduces cellular insulin content and affects endocrine cell gene expression

  Genome-wide studies have uncovered multiple independent signals at the RREB1 locus associated with altered type 2 diabetes risk and related glycaemic traits. However, little is known about the function of the zinc finger transcription factor Ras-responsive element binding protein 1 (RREB1) in glucose homeostasis or how changes in its expression and/or function influence diabetes risk.

  Dataset EGAD50000000515

• Genome-wide association scan in Parkinson's disease

  Genome-wide association scan was performed in 1,705 cases of parkinson's genotyped on the Illumina Human 660W SNP array, and 5,175 controls genotyped on the Illumina1.2M-Duo. Analysis was carried out on the overlaps set of SNPs.

  Study EGAS00000000034

• Determinants of DNA methylation patterning in human placental development and trophoblast stem cell models.

  To assess whether the DNA methylation landscape of human trophoblast stem cells resembles an in vivo cell type, we used post-bisulfite adaptor-tag sequencing to measure genome-wide DNA methylation of preimplantation human trophectoderm and sorted first trimester cytotrophoblast.

  Study EGAS50000000661

• Application of organoid culture system of human gastrointestinal and thoracic cancer in genome medicine

  In order to establish preclinical models, we have established a kind of lung cancer tumoroids derived from a mucus-producing solid pulmonary adenocarcinoma patient. We performed whole exome sequencing and RNA sequencing to analyze genetic background of the tumoroids.

  Study JGAS000664

• Application of organoid culture system of human gastrointestinal and thoracic cancer in genome medicine

  In order to establish preclinical models, we have established three kinds of lung cancer tumoroids derived from three different pulmonary large cell neuroendocrine carcinoma patients. We performed whole exome sequencing to analyze genetic background of these kinds of tumoroids.

  Study JGAS000641

• Application of organoid culture system of human gastrointestinal and thoracic cancer in genome medicine

  In order to establish preclinical models, we have established a kind of lung cancer tumoroids derived from a mucus-producing solid pulmonary adenocarcinoma patient. We performed whole exome sequencing and RNA sequencing to analyze genetic background of the tumoroids.

  Study JGAS000653

• Screening of 2.5 million SNPs in 142 samples from the western Mediterranean area

  The analysis of 2.5 million SNPs in 142 samples from the western Mediterranean area, including southern Spain, Andalusia (Huelva: 35 samples, Granada: 35), southern Portugal (36 samples) and Moroccan Berbers (Asni: 15, Bouhria: 12 and Figuig: 9).

  Study EGAS00001003901

• Landscape of gene mutations in Down syndrome-related myeloid disorders

  To identify the spectrum of gene mutations in Down syndrome-related myeloid disorders, whole genome sequencing of 4 trio samples from TAM/AMKL/complete remission (CR) phases and whole exome sequencing of 15 TAM and 14 DS-AMKL samples were performed.

  Study EGAS00001000546

• WES on tumor DNA and germline DNA in pediatric cancer

  This dataset contains whole exome sequencing (WES) data from tumor DNA samples of various pediatric cancer entities. Files are provided in fastq format. Samples were sequenced on a Novaseq6000 or Hiseq2500 (Illumina). Data analysis is available at https://github.com/rmvpaeme/sWGS_pediatric_cancer.

  Study EGAS00001005429

• DNA-seq FASTQ files from 16 carriers of the BMPR2 p.Arg491Gln mutation in a family affected by HPAH

  Paired-end DNA-seq FASTQ files from 16 carriers of the BMPR2 p.Arg491Gln mutation in a family affected by hereditary pulmonary arterial hypertension (HPAH). Whole genome sequencing of these samples was performed in an Illumina HiSeq 4000 instrument. Libraries were prepared using the Fisher PE Kit (Kapa Biosystems). Each sample was multiplexed across flowcells and lanes, leading to a total number of 86 FASTQ files.

  Dataset EGAD00001005756

• A living biobank of patient-derived ductal carcinoma in situ Mouse-INtraDuctal xenografts identifies factors associated with risk of invasive progression

  Create a living biobank of patient-derived ductal carcinoma in situ (DCIS) Mouse-INtraDuctal (MIND) xenografts to find factors explaining invasive growth. Samples exist of both primary and pdx samples. Invasive growth was scored in the pdx.

  Dataset EGAD00001009336

• WES of germline, nevi, primary and metastatic Cutaneous Melanoma from patient 009 in CASVAC-0401 trial

  Samples: primary cutaneous melanoma (CM) non-associated or distal nevus (A); adjacent or CM-associated nevus (B); Primary-CM (C); and Lymph-Node Metastasis (LN-mts) (D). Whole-exome sequencing (WES) was performed in DNA extracted from the different samples (A-D) paired with the germline reference (G), processed with the Agilent SureSelect All Exon Human V5 Library in an Illumina Hiseq 4000 PE101 platform.

  Dataset EGAD00001009083

• two tables containing RNASeq expression values to patients with RNA-Seq data in the study "Comprehensive genomic characterization of refractory multiple myeloma (H067)"

  two tables containing RNASeq expression values to patients with RNA-Seq data in the study "Comprehensive genomic characterization of refractory multiple myeloma (HIPO_067)". From the bam files gene expression was calculated with the annotation of Gencode.v19. Raw Counts and TPM values are given in one table, the other contains filtered TMM normalized CPM values (genes < 1CPM omitted).

  Dataset EGAD00001008363

• Epigenetic dysregulation in autism spectrum disorder

  Autism spectrum disorder (ASD) is a collection of neuro-developmental disorders characterized by deficits in social interaction and social communication, along with restricted and repetitive behaviour patterns. we globally interrogated the histone acetylomes of enhancers in a large cohort of ASD and control samples by analyzing tissue from three brain regions postmortem: prefrontal cortex (PFC), temporal cortex (TC) and cerebellum (CB). H3K27ac was selected as the representative acetylation mark and 288 ChIP-seq were performed on these postmortem samples.

  Dataset EGAD00001002725

• ATAC-seq data from primary AML samples with t(3;8)

  Open chromatin regions in the MYC super-enhancer region were investigated by ATAC-seq in t(3;8) AML. ATAC-seq was performed as described (Buenrostro et al, 2013) with a modification in the lysis buffer (0.30 M sucrose, 10 mM Tris pH 7.5, 60 mM KCl, 15 mM NaCl, 5 mM MgCl2, 0.1 mM EGTA, 0.1% NP40, 0.15 mM Spermine, 0.5 mM Spermidine, 2 mM 6AA) to reduce mitochondrial DNA contamination.

  Dataset EGAD00001007910

• RNAseq Iron-Treated iPSC-derived Microglia

  Iron accumulation in microglia has been observed in Alzheimer’s disease and other neurodegenerative disorders and is thought to contribute to disease progression through various mechanisms including neuroinflammation. To study the interaction between iron accumulation and inflammation, we treated human induced pluripotent stem cell-derived microglia (iPSC-MG) with an increasing concentration of iron, in combination with inflammatory stimuli such as interferon gamma and amyloid β, and performed RNA sequencing.

  Dataset EGAD00001008660

• Single cell transcriptomes of in vitro differentiated hepatocyte-like cells in comparison to primary human hepatocytes

  Fastq files of deeply sequenced single cell RNA-seq data (Smartseq2, approx. 2 million reads / sample) of hepatocyte-like cells (HLC) and primary human hepatocytes (PHH). The dataset comprises data from two different in vitro differentiation protocols: Cellartis (Takara Bio, "CEL", n = 3) and as described by Wang et al. (PMID: 28287600, "HAY", n = 1), as well as PHH from 3 donors. Each replicate comprises 96 single cells.

  Dataset EGAD00001005946

• TERT rearrangements are frequent in neuroblastoma and identify aggressive tumors

  Whole genome sequencing detected structural rearrangements of TERT in 17/75 high stage neuroblastoma with 5 cases resulting from chromothripsis. Rearrangements were associated with increased TERT expression and targeted immediate up- and down-stream regions of TERT, placing in 7 cases a super-enhancer close to the breakpoints. TERT rearrangements (23%), ATRX deletions (11%) and MYCN amplifications (37%) identify three almost non-overlapping groups of high stage neuroblastoma, each associated with very poor prognosis. This submission contains all newly sequenced samples only.study_refcenter AMC

  Dataset EGAD00001001635

• RNA-seq data from Follicular Lymphoma samples

  Dataset included RNA-seq data (Two Fastq files per sample as paired end sequencing was performed) from ribosomal-depleted total RNA in 28 Follicular Lymphoma (FL) criopreserved samples to analyze long non-coding RNA and coding transcript expression profiles. Sample metadata is referred to histological groups of FL tumors (FL1-3A versus FL3B/DLBCL) either in tumor purified cell samples (N=12) as in unpurified tumor samples including normal cells of the lymph node microenvironment (N=16).

  Dataset EGAD00001004109

• Detection of early seeding of Richter transformation in chronic lymphocytic leukemia

  Dataset accompanying the study entitled “Detection of early seeding of Richter transformation in chronic lymphocytic leukemia” (Nadeu et al. Nature Medicine 2022), which includes the analysis of longitudinal samples of 19 chronic lymphocytic leukemia patients developing Richter transformation.

  Study EGAS00001006327

• Chromatin accessibility analysis of hepatocyte-like cell in vitro differentiation from iPSC in comparison to primary human hepatocytes

  Fastq files of ATAC-seq data of induced pluripotent stem cells (iPSC), definitive endoderm (DE), hepatocyte-like cells (HLC) and primary human hepatocytes (PHH). The dataset comprises data from two different in vitro differentiation protocols: Cellartis (Takara Bio, "CEL", n = 4) and as described by Wang et al. (PMID: 28287600, "HAY", n = 1), as well as from 3 PHH donors.

  Dataset EGAD00001005934

• Somatic variants in 344 colorectal cancer samples

  The dataset contains somatic variants in 344 colorectal cancer samples. Variants are called with Mutect2 (GRCh38). Important: VCF-files include also variants, which have been annotated as "str_contraction" and "panel_of_normals". Please, use only "PASS" variants in studies, which are not microsatellite repeat related. Samples are sequenced with Novaseq 6000, HiSeq 2000, and HiSeq X Ten instruments (average coverage depth ~30+). The dataset consists of 257 MSS, 58 MSI, 25 MSS IBD, and 4 POLE mutant CRCs.

  Dataset EGAD00001006572

• WES_SCLC_MDACC

  To identify genomic drivers present in limited-stage small cell lung cancer (LS-SCLC); To determine the overall tumor mutational burden in LS-SCLC; To determine genomic intratumor heterogeneity (ITH) in LS-SCLC.

  Dataset EGAD00001007004

• IL-17 Signaling in Human iPSC-derived Midbrain Neurons in Parkinson's Disease

  To determine IL-17-induced global transcriptome changes in midbrain neurons derived from induced pluripotent stem cells (iPSC) from three sporadic Parkinson's disease (PD) patients and three age- and sex-machted controls, deep RNA sequencing (RNA-Seq) of IL-17-treated and untreated PD and control iPSC-dderived midbrain neurons was performed. Total RNA was isolated from untreated and IL-17-treated cells with the TruSeq RNA Sample Preparation Kit v2 (Illumina). RNA libraries were quantified using the KAPA SYBR FAST ABI Prism Library Quantification Kit (Kapa Biosystems) and cluster generation was performed on the cBot with the TruSeq SR Cluster Kit v3 (Illumina). The sequencing run was performed on a HiSeq 1000 instrument (Illumina) using the indexed, 50 cycles single read (SR) protocol and the TruSeq SBS v3 Kit (Illumina). Image analysis and base calling resulted in .bcl files that were then converted into .fastQ files by the CASAVA1.8.2 software. FastQ files were aligned to the human genome (hg19) using STAR.and annotated with gencode.v19. DESeq2 was used to determine differential expression. Criteria to determine significantly dysregulated genes were as follows: adjusted p-value below 0.05 and log2FC (fold change) of greater than one. Only genes with a mean expression value of greater than one RPKM (reads per kilobase per million mapped reads) throughout the dataset were considered. Control and PD samples were analyzed as two independent datasets. Upon IL-17 treatment only 17 genes were found to be dysregulated in controls but 125 genes were dysregulated in iPSC-derived midbrain neurons from PD patients. The 125 IL-17-dependent genes in PD iPSC-derived neurons separated the treated from untreated PD samples using an unsupervised, hierarchical clustering applying an Euclidean distance metric. More detailed study information can be found in Sommer A, Maxreiter F, Krach F, Fadler T, Grosch J, Maroni M, Graef D, Eberhardt E, Riemenschneider MJ, Yeo GW, Kohl Z, Xiang W, Gage FH, Winkler J, Prots I, Winner B. Th17 Lymphocytes Induce Neuronal Cell Death in a Human iPSC-Based Model of Parkinson's Disease. Cell Stem Cell. 2018 Jul 5;23(1):123-131.e6. doi: 10.1016/j.stem.2018.06.015. PMID: 29979986

  Study phs001686

• Molecular Subtyping Reveals Immune Alterations Associated with Progression of Bronchial Premalignant Lesions

  Exposure to cigarette smoke creates a field of injury throughout the entire respiratory tract inducing genomic alterations that lead to an "at-risk" airway where lung cancers develop. Lung squamous cell carcinoma (SCC) arises in the epithelial layer of the bronchial airways and is often preceded by the development of premalignant lesions (PMLs). Effective tools to identify and treat premalignant lesions at highest risk of progression to invasive carcinoma are not available. Endobronchial biopsies and brushings were obtained from high-risk subjects undergoing lung cancer screening at approximately 1-year intervals by white light and auto-fluorescence bronchoscopy and computed tomography at the Roswell Park Cancer Institute in Buffalo, NY. Subjects were selected that had biopsies collected in repeat locations via serial bronchoscopies. mRNA sequencing was performed on a discovery cohort (DC) of samples comprising endobronchial biopsies and brushes collected between 2010 and 2012 (n=30 subjects, n=197 biopsies, and n=91 brushings). mRNA sequencing was subsequently performed on a validation cohort (VC) of samples comprising endobronchial biopsies and brushes collected between 2010 and 2015 (n=20 subjects, n=111 biopsies, and n=49 brushings). Data analysis identified four distinct molecular subtypes (Proliferative, Inflammatory, Secretory, and Normal) in the bronchial biopsies that correspond to a spectrum of biological and morphological alterations. The Proliferative subtype was enriched with dysplastic PMLs from current smokers that exhibit up-regulation of metabolic and cell cycle pathways and down-regulation of cilium-associated processes. Molecular subtype classification in the validation cohort biopsies replicated these significant clinical and biological associations. Airway brushes from normal fluorescing areas of the large airway classified as the Proliferative subtype specifically predict the presence of biopsies of this same subtype. Within the Proliferative subtype, genes associated with interferon signaling and antigen processing and presentation were observed to be down-regulated among dysplastic biopsies that persist or progress in the future. Innate and adaptive immune cells were computationally predicted to be depleted in these biopsies and this was confirmed via immunofluorescence staining of adjacent biopsies. These findings provide a proof of concept that molecular biomarkers of endobronchial biopsies can enhance histopathological grading and that immunoprevention strategies are an important future direction in intercepting the progression of PMLs to lung cancer.FASTQ files from the RNA sequencing of these biopsies and brushings will be available via dbGaP.

  Study phs003185

• Exome sequencing identifies frequent mutation of the SWI/SNF complex gene PBRM1 in renal carcinoma

  Exome sequencing identifies frequent mutation of the SWI/SNF complex gene PBRM1 in renal carcinoma

  Dataset EGAD00001000001

• Unraveling the genetic basis of a collagen migration defect in patients with a combined platelet dysfunction and reduced bone density

  Unraveling the genetic basis of a collagen migration defect in patients with a combined platelet dysfunction and reduced bone density

  Dataset EGAD00001000109

• NHGRI Genome Integrity of iPSCs Study

  The purpose of this study is to compare mutation load in induced pluripotent stem cells derived from skin fibroblasts.

  Study phs001277

• 10X single-nuclei RNA sequencing

  Single-nuclei sequencing data from four neuroblastoma patients. Each patient was run on two lanes, resulting in two runs per patient. Data is provided in paired-end fastq files.

  Dataset EGAD50000000727

• RIP-seq of SF3B4 binding RNA fragments

  Project aims to characterize SF3B4 binding RNA fragments within liver organoids to understand its role in splicing regulation

  Study EGAS50000000850

• L1-Architect Project Dataset

  Tumours with high and ultrahigh rates of somatic retrotransposition studied in the publication by Zumalave et al. titled Synchronous L1 retrotransposition events promote chromosomal crossover early in human tumorigenesis

  Dataset EGAD50000000607

• Metastatic_Breast_Cancer_Validation

  Validation of point mutations and small insertions and deletions in primary and associated metastatic breast cancer samples with matched normal tissues.

  Study EGAS00001001968

• Mutational_Screening_of_Human_Acute_Myleloid_Leukaemia_Samples

  Characterization of somatic mutations in Acute Myeloid Leukaemia samples to identify whether they can be classified into three mutually exclusive groups.

  Study EGAS00001000046

• Mosaic_Colorectal_Metastasis

  A comparison of the somatic variation present in a primary colorectal tumour and three different liver metastases from the same patient.

  Study EGAS00001000613

• checup

  Sequencing data from a phase II study of nivolumab and ipilimumab in recurrent or refractory cancer of unknown primary (CheCUP trial)

  Study EGAS00001007403