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• Single-cell multi-omics defines the cell-type-specific impact of splicing aberrations in human hematopoietic clonal outgrowths

  Study EGAS00001007402

• TSO500 on DNA

  Targeted sequencing using the TruSight Oncology 500 DNA probes panel, on samples 162 and 521

  Dataset EGAD50000000270

• MiRNA_Validation

  Rounded Log2 CPM well-expressed miRNA levels in plasma; determined using the HTG EdgeSeq miRNA Whole Transcriptome Assay

  Dataset EGAD00010002752

• MiRNA_TrainTest

  Rounded Log2 CPM well-expressed miRNA levels in plasma; determined using the HTG EdgeSeq miRNA Whole Transcriptome Assay

  Dataset EGAD00010002754

• Gentoypes_Lesotho

  Individuals genotyped on the Illumina GSA v2. Autosome and X chromosome.

  Dataset EGAD00010002468

• Baka_saliva_450K

  Epigenome of 36 rainforest hunther-gathering Baka of Cameroon by Illumina HumanMethylation450 array, used in the EGAS00001002226 study

  Dataset EGAD00010001251

• Metadata file

  "Master" file of patient clinical characteristics and outcomes, samples, and the results of certain analyses, including immunohistochemistry.

  Dataset EGAD00001008792

• ICR MOPOPGEN UK exome control series

  BAM files of individuals from the 1958BC aligned to hg17

  Dataset EGAD00001004396

• AI_NF1glioma_WES

  The dataset includes 59 tumor samples from 56 NF1-glioma patients profiled by Whole Exome Sequencing.

  Dataset EGAD00001004375

• Landscape of AL mutations

  Exome Sequencing to Define the Landscape of Plasma Cells in Systemic Light chain Amyloidosis

  Dataset EGAD00001001861

• IRF5 HL RNASeq dataset

  bam files associated with the study EGAS00001001205

  Dataset EGAD00001001417

• Tracing the origins of relapse in AML to stem cells

  Aligned whole genome sequence from AML relapse project

  Dataset EGAD00001003234

• RNA Editing AZIN1 amplicon sequencing

  AZIN1 amplicon sequencing data of the EGAS00001000495 project.

  Dataset EGAD00001000708

• Exome sequencing Parkinson's disease patients

  In this project we will sequence the exomes of 250 patients with Parkinson's disease

  Dataset EGAD00001000405

• Megabase-scale Haplotyped Genomic Analysis of Normal and Cancer Genomes

  We experimentally determined Mb-scale haplotypes from germline and cancer genome sequencing. Using a microfluidic process that partitions long DNA fragments into hundreds of thousands of barcoded reactions, we determined haplotype blocks from matched colorectal cancer samples in the delineation of haplotypes of allelic imbalances and other genomic instability events.

  Study phs000898

• Integrated Somatic and Germline Molecular Properties Dictating Biological and Clinical Phenotypes in Cancer

  We performed single-nuclei matched RNA- and ATAC-sequencing of frozen biopsies from normal adjacent tissue, primary and metastatic esophageal adenocarcinoma specimens. The data was then further stratified into a tumor microenvironment and malignant compartment and was computationally analyzed to reveal cancer cell subtypes and programs driving malignancy.

  Study phs003438

• Genome Sequencing and Variant Calling of HCM Patients with MYH7 Variants

  To investigate potential genetic causes of cardiomyopathy we recruited 48 patients harboring rare MYH7 variants identified from panel-based testing and with a clinical manifestation of cardiomyopathy. Genome sequencing was performed to identify other potential causative variants and genetic modifiers of the cardiomyopathy phenotype, which varied among patients.

  Study phs004024

• 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

• Elucidation of the association of the HPV integration and oropharyngeal cancer

  Whole-genome sequencing was performed using tumor and blood samples from 14 patients with HPV-associated oropharyngeal cancer. Bulk RNA sequencing was performed using tumor samples from 19 patients with HPV-associated oropharyngeal cancer and 17 patients with non-HPV-associated oropharyngeal cancer and normal tonsil samples from 2 healthy controls.

  Study JGAS000751

• Building a Database of Genomic Structural Variants in Japanese population

  Epstein-Barr virus immortalized B-lymphoblast cell lines were obtained through the Japanese Collection of Research Bioresources (Japanese B cell DNA bank), National Institutes of Biomedical Innovation, Health and Nutrition, and cultured at UNITECH Co., Ltd. We extracted genomic DNAs, sequenced them using Nanopore PromethION, and analyzed genomic structural variations.

  Study JGAS000580

• Liquid-based genomic profiling in high-risk localized prostate cancer.

  In this study, we evaluated the feasibility and performance of tissue and liquid-based genomic profiling in patients with high-risk localized prostate cancer. Genomic DNA from 12 FFPE tissue samples and cell-free DNA from 27 plasma samples were analyzed using Illumina TruSight Oncology (TSO) 500 panels.

  Study EGAS50000001712

• HipSci-RNAseq-healthy volunteers

  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 sup-study we perform RNAseq on iPS cells generated from skin biopsies from healthy volunteers.

  Study EGAS00001000593

• Neversmoker lung adenocarcinoma

  Non-small cell lung cancer whole genome sequencing We performed whole genome sequencing of Korean never-smoker lung adenocarcinoma patients to discover novel pathway except EGFR and ALK patients. We identified estrogen signaling as a novel enriched signaling. Lastly we validated the elevated estrogen signaling through immunohistochemistry experiment in some patients which increased signaling.

  Study EGAS50000000232

• Heterogeneity and evolution of DNA mutation rates in microsatellite-stable colorectal cancer

  A mutation accumulation experiment in colorectal cancer (CRC) derived tumoroids, aimed at measuring the spontaneous rates of accumulation of new single-nucleotide sequence variations in seven microsatellite stable CRCs and one microsatellite unstable CRC. Mutations accumulated over six+six months were identified via whole genome sequencing of clonal tumoroids.

  Study EGAS50000000284

• Growth Hormone (GH) -secreting Pituitary Adenoma

  We profiled the somatic landscape of 21 growth hormone (GH) -secreting pituitary adenomas using somatic copy-number alteration (SCNA), whole-genome sequencing (WGS), bisulfate sequencing, and transcriptome approaches. See details in Valimaki et al. Genetic and epigenetic characterization of growth hormone (GH) - secreting pituitary tumors. Manuscript in preparation, 2019.

  Study EGAS00001003488

• Pediatric B-cell precursor acute lymphoblastic leukemia samples with very early relapse

  In this study we performed a genomic analysis of diagnosis-relapse pairs of 12 children who relapsed very early, followed by a deep-sequencing validation of all identified mutations. In addition, we included one case with a good initial treatment response and on-treatment relapse at the end of upfront therapy.

  Study EGAS00001005615

• Multiregion Whole Exome and Smart-Seq3 single cell RNA sequencing of Breast Tumors

  Multiple regions were cut out of each tumor extracted form breast cancer patients and two experiments were run: - Whole exome sequencing on each of the regions plus an adjacent normal tissue sample - Smart-Seq3 Single cell RNA sequencing on EPCAM+ CD45- sorted cells from different tumor regions

  Study EGAS00001006851

• bulk TCR-seq data IMCISION

  We performed bulk TCR sequencing (Adaptive Biotechnologies, Seattle, WA) on peripheral blood monocytic cells (PBMCs) from 9 HNSCC patients enrolled in the IMCISION trial (Vos et al. 2021) that responded to anti-PD-1 and anti-CTLA4 combination immunotherapy. DNA was extracted from PBMCs that were isolated from pre-treatment and on-treatment blood.

  Study EGAS00001007367

• Whole-genome sequencing data of poorly differentiated thyroid carcinomas and matched blood from six patients

  This dataset contains raw sequencing reads in FASTQ format from 12 samples, comprising paired tumour and matched blood DNA from six patients diagnosed with poorly differentiated thyroid carcinoma (PDTC). Genomic DNA was extracted from fresh-frozen tumour tissue and peripheral blood using standard protocols. Whole-genome sequencing was performed on the Illumina HiSeq X Ten platform, generating paired-end reads at an average depth of approximately 20X. These data support investigations into the somatic mutational landscape and genomic alterations associated with PDTC.

  Dataset EGAD50000001628

• BAM file s of WGS data of Progressive supranuclear palsy patients

  BAM files of healthy controls (3) and Progressive supranuclear palsy (PSP) patients (4). Genomic DNA from donors was fragmented, end-polished, A-tailed, and ligated with Illumina adapters, followed by size selection. Libraries were PCR-amplified (unless PCR-free), purified with AMPure XP, assessed on the Agilent Fragment Analyzer, and quantified using Qubit and qPCR. Qualified libraries were pooled and sequenced on Illumina platforms, and low-quality reads or adapter-contaminated reads were removed. Clean data were then mapped to the hg38 reference genome using BWA.

  Dataset EGAD50000001758

• Epigenomic timecourse of brain organoid development

  Single-cell Cut&Tag of three histone modifications and chromatin accessibility over a timecourse of brain organoid development from pluripotency. We profiled 5 time points of brain organoid development and 2 time points of retinal organoid development. At each time point used scCut&Tag to profile histone modifications (H3K27me3, H3K27ac, H3K4me3) as well as multiome-seq (10X) to jointly profile transcriptome and chromatin accessibility from the same cell suspension. Library preparation was carried out with the 10x genomics platform.

  Dataset EGAD50000000222

• Single-Cell DNA Methylation Profiling via scTAMseq

  This dataset comprises single-cell DNA methylation and nuclear genotyping profiles of 7 total bone marrow aspirates (donors A.1-A.7) and 5 CD34+-enriched bone marrow samples (donors B.1-B.5) generated using the scTAMseq protocol. Sequencing was performed on the Mission Bio Tapestri platform, targeting a panel of 448 CpGs to assess epigenetic patterns and We also included 147 genomic regions commonly mutated in clonal hematopoiesis and 20 regions targeting chromosome Y. Samples B.1 & B.5, B.2 & B.4 and A.2 & A.5 were, in pairs, multiplexed into single tapestri lanes.

  Dataset EGAD00001015498

• RNAseq data from NEN patient derived tumor organoids (PDTOs) and matched parental tumors - NKI/UMCU

  The dataset includes fastq files from 15 NEN tumors or metastases and matched PDTOs. The sequencing was done with either a Nextseq 2000 or a NovaSeq 6000 instrument.

  Dataset EGAD00001009992

• TK-EPN862 - Patient-derived xenograft model of Posterior Fossa A Ependymoma - RNAseq

  In Vivo Loss of Tumorigenicity in a Patient-Derived Orthotopic Xenograft Mouse Model of Ependymoma. Whitehouse et al. 2023 Frontiers in Oncology. We describe the establishment of a patient-derived orthotopic xenograft (PDOX) model of posterior fossa A (PFA) EPN, derived from a metastatic cranial lesion. Patient and PDOX tumors were analyzed using RNA sequencing. RNAseq data (paired end) provided here correspond to Primary tumour, two metastatic lesions (one spinal, one cranial), and a patient-derived xenograft derived from the patient.

  Dataset EGAD00001009870

• 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.

  Dataset EGAD00001009848

• Concatenated long-read single-cell RNA sequencing of momentum biopsies of ovarian cancer patients

  Concatenated long-read single-cell RNA sequencing samples prepared using 10X and the HIT-scIsoSeq protocol. The sequencing was performed on Sequel II Pacbio machine. 3 ovarian cancer patients, 5 omentum biopsies samples: 3 metastasis samples (one per patient), 2 healthy samples (one per patient except Patient2). 4 bam files per metastasis sample, 2 bam files per healthy sample.

  Dataset EGAD00001009814

• Single-nucleus Transcriptome of Down Syndrome Brains (short-read)

  29 DS and Control brain samples were prepared using the 10X Genomics Single Cell 3' v3 kit. The cDNA libraries were sequenced on an Illumina Novaseq 6000.

  Dataset EGAD00001008287

• Spatial transcriptome sequence data from HER2-positive human breast tumors (n=8, with 3 or 6 sections from each)

  Spatial transcriptome sequence data from HER2-positive human breast tumors obtained from the first generation of Spatial Transcriptomics arrays. The dataset contains 8 different tumors with 3 or 6 sections taken from each with paired-end sequencing.

  Dataset EGAD00001008031

• Pediatric Papillary Thyroid Carcinoma Whole Exome Sequencing

  Exome libraries from 47 blood and tissue samples were prepared using Agilent SureSelect Human Exome Library Preparation V5 kit and the Agilent Bravo Automation System fExome libraries were pooled and sequenced with the TruSeq SBS sequencing chemistry using a V4 high throughput flowcell on a HiSeq 2500 platform following Illumina’s recommended protocol. Approximately 6-8 gigabases of raw paired end data of 126-bases were generated per exome library.

  Dataset EGAD00001007502

• Processed microarray gene expression data from NPC samples_Cohort 1

  We retrospectively collected 150 non-metastatic, pretreatment, formalin-fixed, paraffin-embedded (FFPE) nasopharyngeal carcinoma (NPC) samples as validation cohort 1. Also, we prospectively collected 32 FFPE samples from NPC patients enrolled in a trial evaluating anti-PD-1 antibody as validation cohort 2. Total RNA was extracted and hybridised to an Affymetrix HTA 2.0 microarray. In this study, we investigated the immune status of the tumour microenvironment (TME) based on gene expression profiles to classify NPC into biologically distinct immune subtypes, and clarify their associations with prognosis and immunotherapy response.

  Dataset EGAD00001006275

• Processed microarray gene expression data from NPC samples_Cohort 2

  We retrospectively collected 150 non-metastatic, pretreatment, formalin-fixed, paraffin-embedded (FFPE) nasopharyngeal carcinoma (NPC) samples as validation cohort 1. Also, we prospectively collected 32 FFPE samples from NPC patients enrolled in a trial evaluating anti-PD-1 antibody as validation cohort 2. Total RNA was extracted and hybridised to an Affymetrix HTA 2.0 microarray. In this study, we investigated the immune status of the tumour microenvironment (TME) based on gene expression profiles to classify NPC into biologically distinct immune subtypes, and clarify their associations with prognosis and immunotherapy response.

  Dataset EGAD00001006274

• Raw microarray gene expression data from NPC samples_Cohort 1

  We retrospectively collected 150 non-metastatic, pretreatment, formalin-fixed, paraffin-embedded (FFPE) nasopharyngeal carcinoma (NPC) samples as validation cohort 1. Also, we prospectively collected 32 FFPE samples from NPC patients enrolled in a trial evaluating anti-PD-1 antibody as validation cohort 2. Total RNA was extracted and hybridised to an Affymetrix HTA 2.0 microarray. In this study, we investigated the immune status of the tumour microenvironment (TME) based on gene expression profiles to classify NPC into biologically distinct immune subtypes, and clarify their associations with prognosis and immunotherapy response.

  Dataset EGAD00001006273

• Raw microarray gene expression data from NPC samples_Cohort 2

  We retrospectively collected 150 non-metastatic, pretreatment, formalin-fixed, paraffin-embedded (FFPE) nasopharyngeal carcinoma (NPC) samples as validation cohort 1. Also, we prospectively collected 32 FFPE samples from NPC patients enrolled in a trial evaluating anti-PD-1 antibody as validation cohort 2. Total RNA was extracted and hybridised to an Affymetrix HTA 2.0 microarray. In this study, we investigated the immune status of the tumour microenvironment (TME) based on gene expression profiles to classify NPC into biologically distinct immune subtypes, and clarify their associations with prognosis and immunotherapy response.

  Dataset EGAD00001006272

• Whole genome sequencing on HiSeq platform of tumour-normal sample pairs from 183 melanoma cases

  Aligned, merged and deduplicated BAM files from HiSeq whole genome sequencing of 366 samples: matched tumour-normal pairs from 183 melanoma cases comprising 48 primary melanomas, 15 cell lines, and 120 metastases. Sequencing was performed on the Illumina HiSeq 2000 and Xten platforms at Australian and Korean sequencing centres. Data was aligned to the human genome (GRCh37) using BWA-MEM.

  Dataset EGAD00001003388

• Chronic lymphocytic leukemia driven by paradoxical ERK activation during BRAF inhibitor treatment

  Whole-exome sequencing of a chronic lymphocytic leukemia (CLL) developed during vemurafenib treatment of a patient with malignant melanoma. Peripheral blood mononuclear cells were separated by Ficoll gradient centrifugation. DNA was extracted from highly purified (>97%) CD19+CD5+ cells obtained from the patient while being under BRAF inhibition versus CD14+ germline control cells (>90% purity). No alterations that could be linked to aberrant RAS activity or paradoxical RAF/MEK/ERK signaling could be identified in the CLL, which shows characteristic copy number alterations.

  Dataset EGAD00001000997

• IFN-γ and TNF-α drive a CXCL10+ CCL2+ Macrophage Phenotype Expanded in Severe COVID-19 Lungs and Inflammatory Diseases with Tissue Inflammation

  We explored how the human macrophages response to different inflammatory factors, focusing particularly on the effects of antiviral interferons (IFN-β and IFN-γ), pro-inflammatory cytokines such as TNF-α, and other mediators like IL-4. Co-cultured fibroblasts were a component in some conditions to generate factors produced by resident stroma. We used a single-cell antibody-based hashing strategy to multiplex samples from different stimulatory conditions in one sequencing run. This macrophage transcriptomic data reveals distinct macrophage activation states and polarizations shaped by different tissue-related inflammatory conditions at single-cell resolution. We further performed an unbiased integration between tissue-level macrophages and this stimulated human blood-derived macrophages, which pinpoint an IFN-γ and TNF-α synergistically driven inflammatory macrophage phenotype expanded in severe COVID-19 lungs and other inflamed disease tissues.

  Study phs002780

• MYC Inhibition By Omomyc Causes DNA Damage And Overcomes PARPi Resistance In Breast Cancer.

  This study investigates the role of MYC dysregulation in DNA damage response (DDR) and PARP inhibitor (PARPi) resistance in breast cancer. Using Omomyc, a direct MYC inhibitor, we demonstrate that MYC inhibition shuts down DDR genes in triple-negative breast cancer (TNBC), causing DNA repair defects and inducing DNA damage that synergizes with PARPi treatment. Through patient-derived models and clinical samples from metastatic HR-altered breast cancer patients treated with PARPi, we identify MYC transcriptional activity as a predictive biomarker of PARPi resistance. Digital spatial profiling (DSP) analysis of pre-treatment tumor biopsies reveals that patients with progressive disease have significantly elevated MYC signatures compared to responders. These findings support the therapeutic strategy of combining MYC inhibition with PARPi in PARPi-resistant breast cancers where high MYC activity predicts poor response to therapy.

  Study EGAS50000001347

• Translational analyses from a phase II study of pembrolizumab and epigenetic modification with azacitidine in platinum-resistant epithelial ovarian cancer

  Epigenetic modulators may sensitize platinum-resistant ovarian cancer (PROC) to immune checkpoint inhibition by reprogramming the tumor microenvironment. We report clinical and translational findings from a phase II non-randomized study of pembrolizumab and oral azacytidine in 34 women with PROC (NCT02900560). The effect of combined epigenetic and immunotherapy was evaluated by transcriptomic analyses of serially biopsied tumors. Differential gene expression analyses revealed an upregulation of inflammatory and cytolytic genes and co-inhibitory checkpoints 6 weeks on-therapy. Upregulation of interferon signaling, antigen presentation and immune cell adhesion and migration gene sets was prominent on-therapy, together with an increased density of CD8+ T -cells. Patients with a CA-125 and/or clinical response showed an enrichment of adaptive and conserved immune response gene sets on-therapy.

  Study EGAS50000001165

• Genome-wide DNA methylation profiles by MeDIP-seq of cord blood cells and cord blood mononuclear cells obtained from twins conceived through in vitro fertilization and naturally conceived controls

  The study included 47 newborn twins conceived though in vitro fertilisation (IVF) and 60 non-IVF-conceived twins from the Peri/postnatal Epigenetic Twins Study (PETS). Cord blood was collected at birth and used to process mononuclear cells. Whole blood cells (WBCs) from cord blood of 98 twins (40 IVF and 58 non-IVF) and cord blood mononuclear cells (CBMCs) of 82 twins (35 IVF and 47 non-IVF) were subjected to DNA methylation profiling. Methylated DNA immunoprecipitation followed by deep sequencing (MeDIP-seq) was applied to generate genome-wide DNA methylation profiles in a total of 180 samples. Single-end reads were mapped onto hg19 using BWA. Methylation levels were quantified using MEDIPS and used to identify IVF-associated differentially methylated regions.

  Study EGAS00001002248

• Application of high-throughput, high-depth, targeted single-nucleus DNA sequencing in pancreatic cancer

  Despite insights gained by bulk DNA sequencing of cancer it remains challenging to resolve the admixture of normal and tumor cells, and/or of distinct tumor subclones; high throughput single-cell DNA sequencing circumvents these and brings cancer genomic studies to higher resolution. However, its application has been limited to liquid tumors or a small batch of solid tumors, mainly because of the lack of a scalable workflow to process solid tumor samples. Here we optimized a highly automated nuclei extraction workflow that achieved fast and reliable targeted single-nucleus DNA library preparation of 38 samples from 16 pancreatic ductal adenocarcinoma (PDAC) patients, with an average library yield per sample of 2867 single nuclei. We demonstrate that this workflow not only performs well using low cellularity or low tumor purity samples but reveals novel genomic evolution patterns of PDAC as well.

  Study EGAS00001006024

• hereditary BrEAst Case CONtrol study (BEACCON)

  The BEACCON study aimed to address the lack of power of previous studies to identify novel BC predisposition genes by performing extensive sequencing in 12,000 women (11,511 analysed following exclusions) and further enhancing power by using an ‘extreme phenotype’ design with enrichment of familial non-BRCA1 and BRCA2 cases, compared with a control population of older women with ongoing confirmation of cancer-free status at June 2019. Three-quarters of the 1303 candidate genes screened were selected based on empiric evidence from local (69 multi-case BC families) or international whole exome sequencing studies, and the remainder were included to provide detailed coverage of functional pathways with established associations with BC.

  Dataset EGAD00001007025

• Semmelweis University - Biophysics Data Access Committee

  This DAC belongs to the dataset entitled: Next generation sequencing on cardiac samples in Hungarian patients of dilated cardiomyopathy.

  Dac EGAC50000000053

• DAC IBMsnRNAseq

  This DAC manages the data access to our snRNA-seq and spatial transcriptomic data set on healthy and inflamed human skeletal muscle.

  Dac EGAC50000000220

• Czech Roma and non-Roma array data

  42 Roma and 52 non-Roma Czech volunteers genotyped with the Axiom TM genome-wide human origins array

  Dac EGAC50000000478

• Reproducibility of 10x Genomics single cell RNA sequencing method in the immune cell environment

  Study EGAS00001005905

• Metabolic requirements of the metastasis-initiating tumour cell population using oral squamous cell carcinoma (OSCC) as a model system

  Study EGAS00001004765

• cfDNA shallow Whole-Genome sequencing - healthy donors

  sWGS of the blood samples from 14 (fourteen) healthy donors

  Dataset EGAD50000001860

• BCG prime DNA methylation data

  This dataset contains the DNA methylation data of 384 samples from individuals with one or more comorbidities

  Dataset EGAD00010002767

• KIR region SNP genotypes

  KIR gene content imputation from single-nucleotide polymorphisms in the Finnish population

  Dataset EGAD00010002206

• Trained immunity DNA methylation data

  This dataset contains the DNA methylation data of 904 samples from Dutch healthy individuals.

  Dataset EGAD00010002738

• AI_NF1glioma_WES_control

  The dataset includes 43 matched normal samples from 43 NF1-glioma patients profiled by Whole Exome Sequencing.

  Dataset EGAD00001004374

• Ethiopia_Genome_Project_high_coverage_vcf

  Integrated callset of high coverage Ethiopian genomes from the Pagani et al. 2015 AJHG paper (doi: http://dx.doi.org/10.1016/j.ajhg.2015.04.019)

  Dataset EGAD00001003294

• RNA Editing Transcriptome

  Transcriptome sequencing data of tumor and 10 matched normal samples of the EGAS00001000495 project

  Dataset EGAD00001000627

• The UCSF Glioblastoma Genome Project #1

  Dataset contains MeDIP-Seq, MRE-Seq and H3K4me3 ChIP-Seq data on 5 GBM patients.

  Dataset EGAD00001000777

• Genome and transcriptome sequence data from a metastatic high-grade adenocarcinoma of the fallopian tubes patient

  Genome and transcriptome sequence data from a metastatic high-grade adenocarcinoma of the fallopian tubes patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001004709

• Methylation data

  To ellucidate methylation activity in mRCC, methylation data was generated as part of the EuroTarget study

  Dataset EGAD50000002295

• PacBio medulloblastoma datasets

  PacBio data from 5 medulloblastoma tumor-normal pairs. The data consists of BAM files aligned using NGMLR

  Dataset EGAD00001010852

• CONTAGIOUS trial - COVID-19 16S metadata

  Study metadata, containing the clinical information on samples and patients

  Dataset EGAD00001008006

• TRACERx RRBS

  TRACERx 100: RRBS data from a subset of the first 100 TRACERx tumours

  Dataset EGAD00001004798

• 15x WGS HELIC MANOLIS

  15x whole genome sequencing in samples from the Cretan Greek isolate collection HELIC MANOLIS

  Dataset EGAD00001001897

• TOTHER3

  Patritumab deruxtecan in HER2-negative breast cancer: part B results of the window-of-opportunity SOLTI TOT-HER3 trial and biological determinants of early-response

  Dac EGAC50000000255

• Single cell whole genome sequencing of meningiomas

  We sequenced PTA-amplified single cells from meningiomas, the most common primary intracranial tumor, to an average depth of 0.5X.

  Dac EGAC50000000512

• Finding structural variation and functional consequences from primary acute myeloid leukemia cells with complex karyotype (CK-AML) at the single-cell level

  Study EGAS00001007436

• Study1_PeaFiber

  SOMAscan plasma proteome datasets generated from participants consuming the pea fibre snack prototype (study 1)

  Dataset EGAD00010002133

• Study2_FiberBlend

  SOMAscan plasma proteome datasets generated from participants consuming the fiber blend snack prototype (study 2)

  Dataset EGAD00010002132

• Raw count table

  Raw count matrix of the 124 bulk tumor RNAseq samples from patients with hormone sensitive or castration resistant prostate cancer.

  Dataset EGAD00001008762

• AI_NF1glioma_RNAseq

  The dataset includes 29 tumor samples from NF1-glioma patients profiled by RNA sequencing.

  Dataset EGAD00001004376

• Whole Exome Sequencing of INTERVAL

  Whole exome sequencing of a subset of participants from the INTERVAL study.

  Dataset EGAD00001002221

• Res1_PC9_exp1_MC_29.03.22

  8 cell pellet samples for genomic DNA extraction. CRISPR PCR1 and PCR2 indexing - Please use standard Kosuke primers.

  Dataset EGAD00001012232

• Res1_PC9_exp2_MC_01.04.22

  8 cell pellet samples for genomic DNA extraction. CRISPR PCR1 and PCR2 indexing - Please use standard Kosuke primers.

  Dataset EGAD00001012233

• ChIP-seq bulk

  This dataset gather ChIP-seq data produced by immunoprecipitating CTCF factor in own laboratory in MM.1S cell line in EtOH and Dex conditions. It also gather ChIP-seq dataset produced by external laboratory (Active Motif) for H3K27ac mark and GR transcription factor in same cell line and conditions ( MM.1S ETOH/Dex)

  Dataset EGAD00001011136

• Bulk ATAC-Seq HiSeq2500 v4 reagents (100M reads)

  Human data for chromatin accessibility (ATAC-Seq) in eight B-cell precursors: HSC, CLP, pro-B, pre-B, Immature B, Transitional B, Naive B CD5-, Naive B CD5+ cells

  Dataset EGAD00001010909

• Whole-exome sequencing of glioblastomas with long-term relapse interval

  Whole-exome sequencing data (Agilent SureSelectXT Human All Exon V7). Retrospective study of matched pairs of initial and post-therapeutic GBM cases treated with temozolomide+radiotherapy with a recurrence period greater than one year. Matched normal, initial and post-therapeutic samples for 27 patients and 1 patient (GBM046) with a matched normal and two post-therapeutic samples.

  Dataset EGAD00001008568

• McGill EMC Community projects Release 7 for cell line "hTERT RPE1"

  Complete reference epigenome (as defined by IHEC) of normal hTERT RPE1 cell line as well as hTERT RPE1 cell lines engineered to express EPC1-PHF1 and JAZF1-SUZ12 fusion proteins, found in Endometrial Stromal Sarcoma.

  Dataset EGAD00001007680

• ICGC PCAWG Dataset: MALY-DE_PCAWG_RNA-Seq_Star

  ICGC PCAWG Dataset for RNA-Seq BAM aligned using Star. Project: MALY-DE.

  Dataset EGAD00001003560

• ICGC PCAWG Dataset: RECA-EU_PCAWG_RNA-Seq_TopHat2

  ICGC PCAWG Dataset for RNA-Seq BAM aligned using TopHat2. Project: RECA-EU.

  Dataset EGAD00001003559

• ICGC PCAWG Dataset: RECA-EU_PCAWG_RNA-Seq_Star

  ICGC PCAWG Dataset for RNA-Seq BAM aligned using Star. Project: RECA-EU.

  Dataset EGAD00001003558

• ICGC PCAWG Dataset: MALY-DE_PCAWG_RNA-Seq_TopHat2

  ICGC PCAWG Dataset for RNA-Seq BAM aligned using TopHat2. Project: MALY-DE.

  Dataset EGAD00001003561

• ICGC PCAWG Dataset: CLLE-ES_PCAWG_RNA-Seq_Star

  ICGC PCAWG Dataset for RNA-Seq BAM aligned using Star. Project: CLLE-ES.

  Dataset EGAD00001003549

• ICGC PCAWG Dataset: CLLE-ES_PCAWG_RNA-Seq_TopHat2

  ICGC PCAWG Dataset for RNA-Seq BAM aligned using TopHat2. Project: CLLE-ES.

  Dataset EGAD00001003548

• ICGC PCAWG Dataset: LIRI-JP_PCAWG_RNA-Seq_Star

  ICGC PCAWG Dataset for RNA-Seq BAM aligned using Star. Project: LIRI-JP.

  Dataset EGAD00001003547

• ICGC PCAWG Dataset: LIRI-JP_PCAWG_RNA-Seq_TopHat2

  ICGC PCAWG Dataset for RNA-Seq BAM aligned using TopHat2. Project: LIRI-JP.

  Dataset EGAD00001003546

• BIOKEY: A single-cell catalogue of the dynamic changes underlying Checkpoint Immunotherapy response in Early Breast Cancer

  Checkpoint immunotherapy combined with neoadjuvant chemotherapy improves complete pathologic response in a subset of breast cancer patients. Here, we applied single-cell profiling to tumor biopsies collected before and during anti-PD1 therapy. One-third of tumors exhibited proliferative T-cells expanding along CD8+ or CD4+ lineages, which were either characterized by increased cytotoxicity and exhaustion or improved T-helper function, respectively. Lineage tracing in non-expanding tumors revealed at which point in the lineage T-cells were impaired, while gene expression modeling along these lineages revealed novel genes and underlying transcription factors involved in T-cell expansion. Interestingly, different dendritic and myeloid cell phenotypes could either stimulate or inhibit expanding T-cells, while cell-to-cell communication revealed an integrated immune context highly predictive of T-cell expansion, consisting of immune-stimulatory/-inhibitory interactions between cancer and various immune cell types. Our data yield unprecedented insights into the dynamic changes underlying checkpoint immunotherapy response in breast cancer.

  Study EGAS00001004809

• Whole Exome Sequencing data from Neodurvarib Clinical Trial

  Sequencing data related to the genomic profiling of advanced urotelial carcinomas, including tissues from pre and postneoadyuvancy (Olaparib and Durvalumab)

  Dac EGAC50000000471

• Multiregion exome sequencing of ovarian immature teratomas

  Clinicopathologic features of the ten patients with ovarian immature teratomas studied by whole-exome sequencing

  Dataset EGAD50000000421

• PDAC Proteomics After Neoadjuvant Therapy

  Shotgun Proteomics, Proteomic characterization of the residual PDAC tumor mass after neoadjuvant chemo or combined chemo-radiation therapy

  Dataset EGAD00010002388

• Human samples from Southern Chile

  Individuals of Native American ancestry from Southern Chile genotyped with the Human Origins SNP Chip

  Dataset EGAD00010002499

• RiMod Methylation frontal

  Illumina EPIC methylation array of frontal lobe tissue from post-mortem human brains of the RiMod-FTD project

  Dataset EGAD00010002055

• Paired-end snATAC-seq analysis of the 3D spatially mapped GBM samples.

  Dataset contains 11 paired-end snATAC-seq samples from 4 patients.

  Dataset EGAD00001010313

• Paired-end Hi-C analysis of the 3D spatially mapped GBM samples.

  Dataset contains 21 paired-end Hi-C samples from 9 patients.

  Dataset EGAD00001010312