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• Genome and transcriptome sequence data from a metastatic cancer to the breast patient

  Genome and transcriptome sequence data from a metastatic cancer to the breast patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001010959

• 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

• RNA Editing Transcriptome

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

  Dataset EGAD00001000627

• 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

• The UCSF Glioblastoma Genome Project #1

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

  Dataset EGAD00001000777

• AI_NF1glioma_WES_control

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

  Dataset EGAD00001004374

• Leicester Mesothelioma Research Omics Dataset Committee

  This Data Access Committee consists of the mesothelioma research group led by Professor Dean Fennell.

  Dac EGAC50000000965

• 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

• 15x WGS HELIC MANOLIS

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

  Dataset EGAD00001001897

• TRACERx RRBS

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

  Dataset EGAD00001004798

• CONTAGIOUS trial - COVID-19 16S metadata

  Study metadata, containing the clinical information on samples and patients

  Dataset EGAD00001008006

• PacBio medulloblastoma datasets

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

  Dataset EGAD00001010852

• 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

• 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

• 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

• Identifying and Reducing Disparities in Patient-Reported Outcomes Among African American Prostate Cancer Survivors

  This research study aimed to identify disparities in prostate cancer symptom burden and their contributors among African American, Hispanic, and non-Hispanic White prostate cancer survivors. We collected patient-reported outcomes data, focusing on various aspects of the survivors' health and well-being, clinical data, demographics data, and germline genomic data.

  Study phs003745

• Single-cell genotype-to-phenotype (scG2P) data of single nuclei from cell line mixing experiment and six donors

  We developed Single-cell genotype-to-phenotype (scG2P) to profile mutations in driver gene hotspots and capture mRNA targets of interest, validating this assay in a cell line mixing experiment of KYSE-270, KYSE-410, and HCT-116, and applied the assay to esophageal biopsy samples from six donors.

  Study EGAS50000001429

• ChIP-seq analysis of clear cell renal cell carcinoma

  In order to understand the epigenetic basis on ccRCC, we performed ChIP-seq on 3 ccRCC cell lines (786-O, A498, UMRC-2), and 1 normal kidney epithelium cell line (HK-2), cultured under normoxic (20% O2) and hypoxic (0.05% O2) conditions. This study analysed data from H3k4me1, H3K4me3, H3K27ac, H3k27me3, H3k36me3, CTCF, and HIF1A

  Study EGAS50000001322

• Whole-exome sequencing of acute myeloid leukemias with aberrations of chromosome 7

  Deletions and partial losses of chromosome 7 are frequent in acute myeloid leukemia (AML) and are often linked to dismal outcome. However, the genomic landscape and prognostic impact of concomitant genetic aberrations remain incompletely understood. Therefore, we performed whole-exome sequencing of acute myeloid leukemias (N = 60) with aberrations of chromosome 7.

  Study EGAS50000000429

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

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

  Study EGAS50000000301

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

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

  Dataset EGAD50000000745

• Poland WES - The Genomic Map of Poland in Open Access

  This project used NGS (next generation sequencing), using Illumina NOVASEQ 6000 and Illumina DRAGEN aligner. The dataset includes BAM and BAM.BAI files from Whole Exome Sequencing of 450 samples (227 female, 223 male, Poland from POPULOUS collection). Library Construction Protocol: Illumina DNA Prep with Enrichment. Reference Genome: GRCh37.

  Dataset EGAD50000000130

• Triple_Negative_Breast_Cancer_Whole_Genome_Validations

  We propose to definitively characterise the somatic genetics of Triple negative breast cancer through generation of comprehensive catalogues of somatic mutations in 500 cases by high coverage genome sequencing coupled with integrated transcriptomic and methylation analyses. This study will use a bespoke bait set to pulldown regions of interest found in whole genome sequencing to validate mutations found.

  Study EGAS00001000426

• Analysis of Complex Genomic Rearrangements of Lung Adenocarcinomas

  Lung adenocarcinomas (LADC) are heterogeneous disease with distinct etiology. A majority of tumors are related with tobacco smoking, and some tumors arise from never-smoking or young patients, whose clinical history do not support the environmental carcinogen-induced oncogenes. Here we analyzed complex rearrangements in lung adenocarcinomas including tumors with distinct etiologies.

  Study EGAS00001002801

• Congenital mesoblastic nephroma and infantile fibrosarcoma

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

  Dataset EGAD00001003884

• Whole genome sequencing data of normal/tumors pairs from 4 patients with uterine or ovarian carcinosarcoma.

  This dataset provides whole genome sequencing data of normal/tumors pairs from 4 patients with uterine or ovarian carcinosarcoma using the HiSeq 2000 sequencing system. It includes 10 samples (4 normals, 4 uterine tumors and 2 ovarian tumors). Through separate whole genome sequencing of carcinomatous and sarcomatoid components, we analyse and compare the genomic alterations of these components.

  Dataset EGAD00001003898

• Profiling of H3K27ac landscape in immune cells from rheumatoid arthritis patients and healthy controls

  We collected peripheral blood mononuclear cells (PBMC) from 6 RA patients and 4 healthy controls, as well as synovial fluid from the same RA patients. We then sorted B cells, CD4+ and CD8+ T cells, regulatory T cells and monocytes using flow cytometry and profiled regions marked with H3K27ac using CUT&Tag.

  Study EGAS00001005085

• Transposome Bisulfite Sequencing

  DNA belonging to 16 tumour/normal samples were treated with bisulfite, then up to 5 different bisulfite PCRs were performed in each one of the samples. Amplicons form the same sample were pooled and submitted to sequencing on a MiSeq platform.

  Dataset EGAD00001001028

• Exome sequencing of matching primary tumor and venous tumor thrombus (VTT) renal cell carcinoma (RCC) samples

  We performed multiregion whole exome sequencing of a total of 37 samples from five consecutive patients (normal tissue, n=5; primary tumors, n=16; tumor thrombi, n=16) to >35-fold target coverage. Matching primary tumor and venous tumor thrombus samples were analyzed. Four patients had a clear cell RCC, one patient had a poorly differentiated type II papillary RCC (RCC-VTT-04). The latter patient had a friable thrombus, the others were of solid consistency.

  Dataset EGAD00001004887

• Whole Genome Sequencing of CRLF2/IL7RA transduced cells

  There are two samples, 42 (control) and 49 To test the role of activated CRLF2/IL7RA in leukemia initiation we expressed CRLF2 together with IL7RA in human CB hematopoietic progenitors. Human CRLF2 and wild type and/or activated mutant form of human IL7RA (IL7RAwt/ins) were cloned into a lentiviral vector with a bi-cistronic cassette under the expression control of an Eμ-B29 promoter/enhancer to augment expression in B-cell precursors. Backbone vector expressing GFP (BB). Whole genome sequencing Leukemic (49) and BB transduced (42) corresponding CB cells were collected from transplanted mice. Sequencing libraries were prepared from these samples

  Dataset EGAD00001005456

• NABUCCO cohort 1 (NCT03387761) - Neo-Adjuvant Bladder Urothelial Carcinoma COmbination-immunotherapy

  NABUCCO cohort 1 sequencing data. The dataset includes: * Whole exome DNAseq pre-treatment on tumor samples (n=24) matched with blood samples (n=24) * RNAseq pre-treatment on tumor samples (n=18) * RNAseq post-treatment on tumor samples (n=18). Not all pre-treatment samples are linked with pre-treatment samples * High coverage Whole exome DNAseq on pre-treatment tumor samples (n=3) matched with post-treatment metastasized lymph nodes isolated with laser microdissection (n=3) * All samples are labelled with the response phenotype (Complete Responder or Non-Complete Responder)

  Dataset EGAD00001006250

• Cell-free DNA and bone marrow samples from myelodysplastic syndromes

  We have assessed the molecular profile of a cohort of 70 patients with MDS by next-generation sequencing (NGS) using cfDNA and compared the results to paired bone marrow (BM) DNA.

  Dataset EGAD00001008567

• Exome sequencing samples from the Acute Care Flagship.

  Exome sequencing samples from the Acute Care Flagship, Illumina sequencing.

  Dataset EGAD00001008105

• scRNA-seq dataset of patient and healthy donors

  scRNA-seq dataset on a patient (P) presenting with defects of immunity and four healthy donors (C1, C2, C3, C4). This dataset contains raw and processed files from scRNA-seq performed on samples using the 10x Genomics Chromium Controller with the Chromium Single Cell 3′ Reagent Kit (v3 chemistry). There are 15 paired-end fastq files (3 per patient/donor - I1, R1, R2) and 15 processed files generated with 10x Genomics Cell Ranger v3.0.2 software against GRCh38 human reference transcriptome (3 per patient/donor - barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz).

  Dataset EGAD00001008372

• 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