23014 results for "ega"

in 38.68 milliseconds.

• single cell RNA sequencing of resting and IAV-stimulated mononuclear phagocytes of Africans and Europeans

  CD14+ monocytes from 4 African and 4 Europeans individuals with varying degree of ex-vivo susceptibility to Influenza, were either stimulated with Influenza A virus, or left resting. Cells from all 16 samples were collected at 4 time points (0, 2, 4, 6h post infection), and pooled across 13 libraries. Samples were processed on the 10x chromium with 3' reagents kits, V3 chemistry and sequenced with Hiseq X ten.

  Dataset EGAD00001006938

• HELIUS virome sequencing

  The dataset contains fecal WGS samples of 196 participants to the HELIUS study, as well as VLP filtrate sequencing for a subset of 48 participants.

  Dataset EGAD00001008765

• BLUEPRINT release August 2016, ChIP-Seq for Germinal Center B-Cell-Like Diffuse Large B-Cell Lymphoma, on genome GRCh38

  ChIP-Seq data for 3 Germinal Center B-Cell-Like Diffuse Large B-Cell Lymphoma sample(s). 10 run(s), 10 experiment(s), 10 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_chipseq_analysis_ebi_20160816

  Dataset EGAD00001002506

• Whole-genome bisulfite sequencing

  Raw reads from whole-genome bisulfite sequencing. Whole-genome bisulfite sequencing library preparations and Illumina sequencing of DNA samples from TET2 mutation carriers (Ly9, Ly11, Ly14, Id1) and their age-matched controls (Ly8, Ly10, Ly13, Id2, Id3) was done as a service at BGI (BGI Tech Solutions Co., Ltd., China). Bisulfite treatment was done with EZ DNA Methylation-Gold Kit (Zymo Research, CA, USA) for 300-400bp size-range fragments with methylated adapters in 5' and 3' ends. Sequencing was done with the HiSeq X-Ten platform using paired-end 150 base-pair read length.

  Dataset EGAD00001004779

• Identification of drug resistance genes in melanoma by mRNA gene expression

  We aim to sequence the mRNA transcriptome of 22 human melanoma cell lines in biological triplicate in order to define the gene expression profile of each cell line. The data will be correlated to the mutation status and the sensitivity to a panel of drugs in order to identify genes whose deregulation is associated to drug resistance This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/

  Dataset EGAD00001003244

• Dataset for hepatopancreaticobiliary_malignancy-WHOLE_GENOME

  Rare cancer sequencing data of 83 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

  Dataset EGAD00001008884

• TARGET-seq+ single-cell transcriptome sequencing

  Single-cell whole transcriptome sequencing data for bone marrow samples from 9 cases with clonal hematopoiesis and 4 control samples. The TARGET-seq+ protocol was used to generate plate-based 3' transcriptome data. For details on cell sorting and the TARGET-seq+ protocol see the methods section of the manuscript. One FASTQ file is provided per cell. Cells are named with their plate and well IDs and the subject ID. Empty wells (no-cell controls) are named "blank". Corresponding genotyping files use the same naming without the "_transcriptome" suffix.

  Dataset EGAD00001011175

• Dataset for neuroendocrine_adrenal_tumor-WHOLE_GENOME

  Rare cancer sequencing data of 112 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

  Dataset EGAD00001008893

• BLUEPRINT release August 2016, RNA-Seq for cytotoxic CD56-dim natural killer cell, on genome GRCh38

  RNA-Seq data for 4 cytotoxic CD56-dim natural killer cell sample(s). 4 run(s), 4 experiment(s), 4 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_rnaseq_analysis_crg_20160816

  Dataset EGAD00001002321

• BLUEPRINT release August 2016, RNA-Seq for erythroblast, on genome GRCh38

  RNA-Seq data for 8 erythroblast sample(s). 30 run(s), 8 experiment(s), 8 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_rnaseq_analysis_crg_20160816

  Dataset EGAD00001002358

• Whole genome, RNA-seq and single-cell Multiome profile of multiple myeloma

  We analyzed multiple myeloma samples from two patients included in the observational prospective cohort MYRACLE before talquetamab treatment and after relapse. Five other myelomas from the same cohort were included for comparison. Normal plasma cells were also retrieved. All samples were analyzed by whole genome sequencing and single-nucleus Multiome, except one that could only be analyzed by bulk RNA sequencing.

  Dataset EGAD00001010057

• BLUEPRINT release August 2016, ChIP-Seq for CD3-negative, CD4-positive, CD8-positive, double positive thymocyte, on genome GRCh38

  ChIP-Seq data for 2 CD3-negative, CD4-positive, CD8-positive, double positive thymocyte sample(s). 7 run(s), 5 experiment(s), 5 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_chipseq_analysis_ebi_20160816

  Dataset EGAD00001002369

• BLUEPRINT release August 2016, ChIP-Seq for mesenchymal stem cell of the bone marrow, on genome GRCh38

  ChIP-Seq data for 2 mesenchymal stem cell of the bone marrow sample(s). 16 run(s), 14 experiment(s), 14 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_chipseq_analysis_ebi_20160816

  Dataset EGAD00001002381

• Transcriptome sequencing of hepatocellular carcinoma biopsies (TACE study)

  Illumina-based RNA-Seq analysis of 93 liver samples. Biopsies of tumors and non-tumor tissues are included. Samples are stratified by response and non-response to TACE treatment.

  Dataset EGAD00001008158

• ChIP-seq and 4C-seq datasets in megakaryocytes and granulocytes from individuals with QPD and unaffected controls

  ChIP-seq was performed for the following histone modifications in both megakaryocytes and granulocytes: H3K27ac, H3K4me2, and H3K36me3. ChIP-seq was performed for H3K27me3 and CTCF in megakaryocytes only. All ChIP experiments consist of n=3 replicates for each of QPD and Control, with the exception of control granulocyte H3K4me2 for which only n=2 replicates were performed. 4C-seq datasets consist of 2 viewpoints (PLAU promoter and an intergenic enhancer), profiled in megakaryocytes from n=2 controls and n=4 QPD.

  Dataset EGAD00001006048

• Hereditary Cancer Diagnostics with I2HCP gene panel

  Germline blood DNA sequencing data generated in routine diagnostics of hereditary cancer using the I2HCP gene panel (~135 genes). There are 130 samples sequenced in a MiSeq machine and 108 sequenced in a HiSeq machine. There is a partial overlap between those two sets, meaning that some samples were sequenced in both machines. There is a strong enrichment in samples with copy-number variants (CNV), both single- and multi-exon, since this dataset was compiled for a benchmarking effort of CNV calling tools for genetic diagnostics.

  Dataset EGAD00001006171

• SOFT study - sequencing premenopausal breast cancer (2017-11-22)

  Our project will examine the role of PIK3CA mutations and their sensitivity to endocrine therapies and its role, with the addition of complete ovarian suppression. We plan to test our hypotheses using tumour samples collected from patients enrolled in the SOFT/IBCSG24-02 clinical study (Suppression of Ovarian Function Trial - (NCT00066690). SOFT is a phase III trial that randomised 3066 premenopausal women to evaluate if adding ovarian suppression to adjuvant endocrine therapy will improve clinical outcomes. This dataset contains all the data available for this study on 2017-11-22.

  Dataset EGAD00001003811

• BLUEPRINT release January 2015, ChIP-Seq for effector memory CD8-positive, alpha-beta T cell, terminally differentiated

  ChIP-Seq data for 1 effector memory CD8-positive, alpha-beta T cell, terminally differentiated sample(s). 4 run(s), 4 experiment(s), 4 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_chipseq_analysis_ebi_20140811

  Dataset EGAD00001001195

• BLUEPRINT release August 2016, RNA-Seq for central memory CD8-positive, alpha-beta T cell, on genome GRCh38

  RNA-Seq data for 1 central memory CD8-positive, alpha-beta T cell sample(s). 1 run(s), 1 experiment(s), 1 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_rnaseq_analysis_crg_20160816

  Dataset EGAD00001002482

• BLUEPRINT release August 2015, ChIP-Seq for CD4-positive, alpha-beta T cell, on genome GRCh38

  ChIP-Seq data for 7 CD4-positive, alpha-beta T cell sample(s). 39 run(s), 39 experiment(s), 39 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_chipseq_analysis_ebi_20150820

  Dataset EGAD00001001505

• Ither NB in Organoids RNA-Seq dataset - Exploring high-throughput drug sensitivity testing in neuroblastoma cell lines and patient-derived tumor organoids in the era of precision medicine

  Ither NB in Organoids RNA-Seq dataset - We aimed to launch an online repository integrating genomics and transcriptomics with high-throughput drug screening (HTS) of nineteen commonly used neuroblastoma cell lines and fourteen generated neuroblastoma patient-derived organoids (NBL-PDOs) to improve identification of molecularly matched therapies and support clinical uptake.

  Dataset EGAD00001010283

• Targeted sequencing of genes recurrently mutated in AML - part2

  Genomic libraries will be generated from total genomic DNA derived from 4000 samples with Acute Myeloid Leukaemia. Libraries will be enriched for a selected panel of genes using a bespoke pulldown protocol. 64 Samples will be individually barcoded and subjected to up to one lanes of Illumina HiSeq. Paired reads will be mapped to build 37 of the human reference genome to facilitate the characterisation of known gene mutations in cancer as well as the validation of potentially novel variants identified by prior exome sequencing.

  Dataset EGAD00001000747

• 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

• 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

• Discovery of resistance mechanisms to the BRAF inhibitor vemurafenib in metastatic BRAF mutant melanoma

  We propose to biopsy 20 consented BRAF mutant melanoma patients at Addenbrooke's Hospital pre-treatment with vemurafenib and also upon the development of resistant disease, with the aim of using exome sequence and SNP6 data to identify novel sequence variants and copy number alterations that can be used to validate observed resistance mechanisms in our cell line models and also to use these models to inform as to likely candidate small molecule inhibitors to overcome resistance and that could be tested in the clinical trial setting.

  Dataset EGAD00001001046

• 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

• Whole-exome ultra-high throughput sequencing in brain samples of suicide victims who had suffered from major depressive disorder and control subjects who had died from other causes

  Whole exome NGS data of 21 sucide victims and 23 control patients sequenced on Illumina HiSeq 2000 platform using the Agilent SureSelect Human All Exon + UTRs V5 target enrichment kit. The dataset contains the paired-end unfiltered FASTQ files, the GRCh37 (b37) aligned BAM files mapped by the BWA MEM algorithm, and the variant files in VCF 4.1 format called with the GATK HaploType caller (version 3.3).

  Dataset EGAD00001004184

• 10x Genomics VDJ single cell sequencing and 10x Genomics sc RNA-Seq (5 individuals/17 VDJ runs,19 scRNA runs))

  single cell RNAseq and TCR sequencing data of 5 individuals. 10x Genomics VDJ single cell sequencing (17 runs) and 10x Genomics sc RNA-Seq (19 runs). The VDJ sequencing was done on a Nextseq 550 using the Chromium Single Cell VDJ Reagent Kit. The RNA-Seq was done either on HiSeq4000 or NovaSeq 6000 using the Chromium Single Cell 5 Reagent Kit.

  Dataset EGAD00001009986

• Transcriptomic intra-tumor heterogeneity of colorectal cancer evaluated by RNA sequencing of multi-regional biopsies

  RNA sequencing of a total of 41 tumor biopsies taken from a total of 14 patients with colorectal cancer. Ribosomal RNA was removed using the Ribo-Zero Gold rRNA Removal Kit (Illumina, CA, USA) and Paired-end sequencing were performed using ScriptSeq v2 RNA-seq Library preparation Kit (Illumina). Data processing of the paired raw sequence reads was performed using TopHat2, with mapping to the human reference genome HG19. Forty-one BAM files with reads mapping the the human reference genome (HG19) is enclosed.

  Dataset EGAD00001006636

• SCLC study George et al. - RNA-sequencing data set

  RNA-sequencing (RNA-seq) was performed with RNA extracted from fresh-frozen human tumor tissue samples. cDNA libraries were prepared from poly-A selected RNA applying the Illumina TruSeq protocol for mRNA. The libraries were then sequenced with a 2 x 100bp paired-end protocol to a minimum mean coverage of 30x of the annotated transcriptome.

  Dataset EGAD00001001244

• BLUEPRINT release August 2015, RNA-Seq for endothelial cell of umbilical vein (proliferating), on genome GRCh38

  RNA-Seq data for 2 endothelial cell of umbilical vein (proliferating) sample(s). 2 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_rnaseq_analysis_crg_20150820

  Dataset EGAD00001001535

• Systematic Identification of Somatic Non-coding Alterations

  Profiling of 12 megabases of human non-coding DNA (including enhancers, promoters, and boundaries of topologically associating domains) in a longitudinal cohort of patients treated with endocrine therapies. For each patient, DNA from the primary and relapsed (metastatic) tumour, along with normal matched DNA, were profiled.

  Dataset EGAD00001009064

• TRACERx Reduced-representation bisulfite sequencing (RRBS)

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

  Dataset EGAD00001009707

• Facioscapulohumeral muscular dystrophy (FSHD): RNA-seq of isogenic TIRM+, TIRM- muscle and PBMCs from patients and matched controls

  FASTQ files describing paired-end RNA-sequencing of isogenic TIRM+ and TIRM- muscle biopsies from 24 FSHD patients (48 samples) and vastus lateralis muscle biopsies from 11 matched control individuals. FASTQ files are also provided describing RNA-sequencing of 15 FSHD peripheral blood mononuclear samples and 14 matched controls. For muscle biopsies sequencing was at 21.7-35.5 million reads/sample. RNA was extracted from PBMCs followed by globin depletion with sequencing at 19.7-46.5 million reads/sample.

  Dataset EGAD00001011077

• PGDx elio plasma resolve analytical validation

  This dataset consists of 39 noncancerous donor and 62 cancer patient plasma samples (including 29 patients with CRC across a total of 13 tumor types) that were analyzed with the PGDx elio plasma resolve assay. The PGDx elio plasma resolve assay is a hybrid capture approach targeting 33 genes with sequencing performed using the Illumina NextSeq with 150bp paired-end reads. The bam files provided have been adapter masked and contain duplicate reads.

  Dataset EGAD00001009718

• Blueprint: A human variation panel of genetic influences on epigenomes and transcriptomes in three immune cell types, (ChIP-Seq for mature neutrophil, on genome GRCh37)

  ChIP-Seq data for 182 mature neutrophil sample(s). 2847 run(s), 366 experiment(s), 355 analysis(s) on human genome GRCh37. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/blueprint_Epivar/protocols/README_chipseq_analysis_ebi_20160816

  Dataset EGAD00001002670

• Whole genome sequencing of Osteosarcoma clonal evolution

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

  Dataset EGAD00001011285

• RNA-seq of cells after injection into immunodeficient mice

  This dataset includes 73 samples profiled by high-throughput Illumina sequencing, in bam format, aligned to GRCh37. Normal human CD34+ cord blood (CB), bone marrow (BM), or post-natal thymus (PNT) cells were transduced with various combinations of T-ALL oncogenes, cultured in vitro on OP9-DL1 feeders for up to 25 days, and then transplanted into immunodeficient NSG or NRG mice. The samples were collected after development of frank leukemia in recipient mice.

  Dataset EGAD00001009751

• Single-cell ATAC-sequencing of rhabdomyosarcoma tumour tissue (2025-09-30)

  This study investigates high-risk rhabdomyosarcoma (RMS) using multiple single-cell and spatial genomic technologies. We generated and analysed single-cell and single-nucleus RNA-sequencing, chromatin accessibility, and spatial transcriptomics data from primary tumours and validation samples. These datasets characterise cellular diversity within rhabdomyosarcoma and identify cell states associated with aggressive disease. The data support research into tumour biology, risk stratification, and therapeutic target discovery. This repository houses the single-cell ATAC sequencing of RMS tumours data. . This dataset contains all the data available for this study on 2025-09-30.

  Dataset EGAD00001015711

• Clinical and biomarker dataset

  Clinical & biomarker data from IMagyn050: treatment arm, treatment approach, outcome of surgery, ECOG PS, PD-L1 status, race, age, disease stage, progression free survival (investigator assessed), overall survival, histology, tumor mutation burden and status, genomic loss of heterozygosity, microsatellite status, BRCA1/2 mutation status, tissue of origin. Mutation status based on FoundationOne NGS for the following genes is also being provided: TP53, BRCA1, CCNE1, MYC, NF1, PIK3CA, RAD21, TERC, PRKCI, KRAS, RB1, BRCA2, ARID1A, AKT2, PTEN, KDM5A, NOTCH3, FGF12, ERBB2, CDK12, EMSY, WHSC1L1, BCL2L1, CDKN2A, GNAS, ARFRP1, ZNF217, SOX2, CCND2, FGF6, FGF23, LYN, MUTYH, AURKA, FGFR1, MCL1, MLL2, MYCL1, ZNF703, BRAF, MAP2K4, CREBBP, TSC2

  Dataset EGAD00001009797

• sWGS of OV04 PDX samples for ACN rascal study

  This dataset contains 148 .bam files of shallow WGS data (~0.1X) from OV04 PDX samples. Sequencing reads were aligned to the 1000 Genomes Project GRCh37-derived reference genome using the BWA aligner (v.0.07.17; CRUK-CI alignment pipeline).

  Dataset EGAD00001008119

• WGS data for ATLAS paper (123 patients)

  WGS data of multi-region samples from PLANET 123 Patient cohort

  Dataset EGAD00001009858

• Tracking early lung cancer metastatic dissemination in TRACERx using ctDNA dataset

  Whole-exome sequencing of tumour regions and deep targeted sequencing of plasma samples.

  Dataset EGAD00001010031

• BLUEPRINT release August 2016, RNA-Seq for CD14-positive, CD16-negative classical monocyte, on genome GRCh38

  RNA-Seq data for 8 CD14-positive, CD16-negative classical monocyte sample(s). 8 run(s), 8 experiment(s), 8 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_rnaseq_analysis_crg_20160816

  Dataset EGAD00001002308

• BLUEPRINT release August 2016, ChIP-Seq for CD3-positive, CD4-positive, CD8-positive, double positive thymocyte, on genome GRCh38

  ChIP-Seq data for 3 CD3-positive, CD4-positive, CD8-positive, double positive thymocyte sample(s). 11 run(s), 11 experiment(s), 11 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_chipseq_analysis_ebi_20160816

  Dataset EGAD00001002445