22938 results for "ega"

in 35.66 milliseconds.

• Biological and Therapeutic Implications of a Unique Subtype of NPM1 Mutated AML (ATACseq Data)

  This dataset contains 18 ATACseq reads, in fastq format. Samples were collected from fresh bone marrow and peripheral blood sample from AML patients.

  Dataset EGAD00001006670

• RNA sequencing of PTCL-NOS

  This dataset contains raw .fastq files of a paired-end RNA-seq experiment on 15 PTCL-NOS samples. Samples were prepared with Truseq stranded mRNA library kit.

  Dataset EGAD00001006925

• IMpower133 processed RNA-seq data for genes utilized for cluster assignments

  This dataset contains log2(TPM + 1) for 271 tumor samples profiled by RNA-seq for the subset of genes used for validation of the NMF cluster assignments.

  Dataset EGAD00001006928

• Bulk RNAseq fastq files

  RNAseq FASTq files from 15 samples from patients with ovarian cancer, 5 samples for each of the 3 tumor immune phenotypes (Infiltrated, Excluded and Desert).

  Dataset EGAD00001006975

• Reliable detection of somatic mutations in single DNA molecules from sperm

  Nanoseq data from sperm from 2 individuals, including technical replicates from one individual (10 total sequences). 8 additional samples and 2 matched normals to call mutations in NanoSeq data (dataset EGAD00001006459).

  Dataset EGAD00001007028

• HV31 - Illumina PCR-free sequencing

  Illumina PCR-free sequencing data for individual HV31 generated using DNA from peripheral blood mononuclear cells, to a sequencing depth of ~44×. Sequencing was performed at the Wellcome Centre for Human Genetics on the Illumina Novaseq platform.

  Dataset EGAD00001007042

• A98282A

  Whole genome sequencing for single cells for library A98282A 1198 cells; filetype=bam

  Dataset EGAD00001007129

• ADAPTeR Study: RNAseq data from ccRCC patients

  ADAPTeR study RNAseq from multi-region samples taken pre and post nivolumab.

  Dataset EGAD00001008163

• Comprehensive Transcriptional Analysis of Early Stage Urothelial Carcinoma using whole transcriptome sequencing

  The expression profile and sequence variants of 476 early stage urothelial carcinoma were studied using whole transcriptome sequencing. RNA-Seq libraries were prepared by Ribo-Zero treatment of total-RNA followed by library preparation using ScriptSeq (both Epicentre/Illumina). RNA-Seq libraries were paired-end sequenced (2x 101 bp) on Illumina HiSeq 2000 and the resulting fastq files were processed using tools from the Genome Analysis Toolkit (GATK and from the Tuxedo suite. Access to the sequence data (mapped and un-mapped bam and vcf files), containing person identifying information, needs signature on a controlled access form, and can be accessed at The European Genome-phenome Archive (EGA) following request. An expression matrice of FPKM values are available without restriction at ArrayExpress (E-MTAB-4321).

  Study EGAS00001001236

• WTCCC case-control study for Autoimmune Thyroid Disease

  WTCCC genome-wide case-control association study for Autoimmune Thyroid Disease (ATD) using the 1958 British Birth Cohort collection as controls.

  Study EGAS00000000020

• Transcriptomic analysis of peripheral blood dendritic cells and monocytes from patients with familial chilblain lupus and hetereozygous mutations in TREX1

  Study EGAS00001006215

• Professors Colin Palmer and Ewan Pearson, from University of Dundee, are both members of the Access Group panel for the GoDARTS bioresource, which provided the data for the current study. The current Study used genotypes (EGAD00010000282) generated by the WTCCC2 (EGAS00000000121), on which both Colin and Ewan are also DAC panel members.

  Dac EGAC00001000504

• Whole Exome Sequencing for Characterization of Disease Causing Mutations in two Pakistani Families Suffering from Autosomal Recessive Ocular Disorders.

  Whole Exome Sequencing for Characterization of Disease Causing Mutations in two Pakistani Families Suffering from Autosomal Recessive Ocular Disorders.

  Dataset EGAD00001000024

• Identification of SPEN as a novel cancer gene and FGFR2 as a potential therapeutic target in adenoid cystic carcinoma

  Identification of SPEN as a novel cancer gene and FGFR2 as a potential therapeutic target in adenoid cystic carcinoma

  Dataset EGAD00001000175

• Monotherapy Breast Cancer

  These samples are from locally advanced breast cancers that have been treated with epirubicin monotherapy before surgery. We will sequence some samples from patients with good response to the therapy and some with poor response to the therapy.

  Dataset EGAD00001000349

• Targeted gene fusion sequencing (Fus-seq) in mesothelioma

  This is a small pilot data set to test the feasibility of cDNA exomes across 1200 cancer cell line panel. cDNA exomes or Fus-seq is further explained in this studies Abstract.

  Dataset EGAD00001000361

• Signatures of mismatch repair deficiency in cancer genomes

  DNA replication errors occurring in mismatch repair (MMR) deficient cells persist as mismatch mutations and predispose to a range of tumors. Here, we sequenced the first whole-genomes from MMR-deficient endometrial tumors.

  Dataset EGAD00001000641

• Somatic mitochondrial DNA mutations primary tumour samples

  Dataset EGAD00001001014

• egpg-G-1

  Illumina Omni 2.5M SNPchip data (build37) of Ethiopian samples from the Pagani et al. 2015 AJHG paper (doi: http://dx.doi.org/10.1016/j. ajhg.2015.04.019)

  Dataset EGAD00010001221

• egyptgp-G-1

  Illumina Omni 2.5M SNPchip data (build37) of Egyptian samples from the Pagani et al. 2015 AJHG paper (doi: http://dx.doi.org/10.1016/j. ajhg.2015.04.019)

  Dataset EGAD00010001223

• Clean sequence of LUAD in young never-smoker

  we conducted whole genome sequencing (WGS) to characterize the genomic alterations of 36 never-smoker Chinese patients with lung adenocarcinomas (LUADs). This dataset is containing clean fastq files of 36 never-smoker Chinese patients with lung adenocarcinomas (LUADs)

  Dataset EGAD00001003890

• Dataset SNP tumours

  This dataset contains 30 idat files each from 15 SNP array runs on patient colitis-associated colorectal cancer tumours. All phenotypes are cancer. See Baker et al. 2018 Supplementary Table 2 for patient details of 12 tumours used in the analyses in the publication.

  Dataset EGAD00010001587

• ICGC breast cancer sequencing project SNP6 data

  Affymetrix SNP6.0 breast cancer genome sequencing data

  Dataset EGAD00010000915

• COLONOMICS Whole Exome Sequencing

  This dataset consists of Illumina HiSeq 2000 Whole Exome Sequencing of 84 colorectal samples: 42 Tumor tissue samples and 42 Normal tissue samples (adjacent to tumor sites). 2x75bp paired-end sequencing reads: 2 fastq files per sample

  Dataset EGAD00001004826

• KASP1-22

  234 samples genotyped at 15 loci LGC Genomics, Hoddesden, UK using the PCR-based KASP assay (Semagn,e tal (2014). Single nucleotide polymorphism genotyping using Kompetitive Allele Specific PCR (KASP): overview of the technology and its application in crop improvement. Mol Breeding 33, 1–14.)

  Dataset EGAD00010001905

• SNPArray_Thai

  The compressed file contains plink format file for the Affymetrix Human Origins SNP array data of 452 individuals generated and analyzed in Kutanan, Liu et al 2021 study of 33 ethnolinguistic groups in Thailand and Laos.

  Dataset EGAD00010002285

• Siberia.Pakendorf

  The tar archive contains a) the txt file with the genotypes, b) illumina annotation file with info on SNPs, c) sample info file unfiltered illumina data, autosomes only data from Pugach et al MBE 2016 The Complex Admixture History and Recent Southern Origins of Siberian Populations

  Dataset EGAD00010002304

• Dataset for WGS and RNA melanoma samples

  This dataset contains WGS and RNA sequencing data for 4 melanoma samples. Sequencing was performed on Illumina Novaseq 6000 and Illumina HiSeq X. The sequencing was always paired.

  Dataset EGAD50000000093

• Tumor reactive γδ T cells contribute to a complete response to PD-1 blockade in a Merkel cell carcinoma patient

  Single cell RNA and TCR sequencing of γδ T cells FACS sorted from peripheral blood of two Merkel cell carcinoma patients

  Dataset EGAD50000000137

• Redefined indel taxonomy reveals insights into mutational signatures

  Deposited here are whole-genome sequencing bam files from the experimental isogenic cell lines used in the study "Redefined indel taxonomy reveals insights into mutational signatures, Koh, Gene (2023)".

  Dataset EGAD50000000209

• Whole genome sequencing data of high-grade serous ovarian cancer samples (set 9 part 3)

  Whole genome sequencing data of 25 high-grade serous carcinoma (HGSC) patients (65 samples) sequenced with Illumina Novoseq 6000

  Dataset EGAD50000000211

• Small‑scale mutations are infrequent as mechanisms of resistance in post‑PARP inhibitor tumour samples in high grade serous ovarian cancer

  These are 28 targeted exome sequencing fastq files (tumour and germline) generated from ovarian cancer samples which had been exposed to PARP inhibitors, for the described project.

  Dataset EGAD50000000206

• Servicio Hematología_Hospital Universitario de Salamanca_Spain

  Data obtained from Diffuse large B-cell Lymphoma cases from the Haematology Service at the University Hospital of Salamanca. The study was approved by the local Institutional Review Board, and written informed consent, following the Declaration of Helsinki, was obtained from all patients before sample collection.

  Dac EGAC50000000155

• WGS of human colorectal cancer organoid exposed to genotoxic pks+ E. coli

  Organoid cultures were exposed to different E.Coli strains and a dye control. In total 25 organoid cultures were whole-genome sequenced using the Novaseq6000 platforms. The data is deposited as .bam format.

  Dataset EGAD50000000304

• A neoadjuvant, phase II trial demonstrates efficacy and tolerability of Talimogene laherparepvec in cutaneous basal cell carcinoma (NeoBCC trial)

  This dataset is related to the NeoBCC trial and includes 12 human tissue samples

  Dataset EGAD50000000371

• Cityscape Source Tables

  Source data of clinical study data corresponding to figures reported in the paper titled: Anti-TIGIT antibody improves PD-L1 blockade through myeloid and Treg cells. PMID: 38418879 DOI: 10.1038/s41586-024-07121-9

  Dataset EGAD50000000366

• GO30103 Source Tables

  Source data of clinical study data corresponding to figures reported in the paper titled: Anti-TIGIT antibody improves PD-L1 blockade through myeloid and Treg cells. PMID: 38418879 DOI: 10.1038/s41586-024-07121-9

  Dataset EGAD50000000367

• OAK GO28915 Source Table

  Source data of clinical study data corresponding to figures reported in the paper titled: Anti-TIGIT antibody improves PD-L1 blockade through myeloid and Treg cells. PMID: 38418879 DOI: 10.1038/s41586-024-07121-9

  Dataset EGAD50000000368

• RNA sequencing of Non-Small Cell Lung Cancer and adjacent normal tissue (ICON)

  RNA sequencing was performed on 108 NSCLC tumor samples and their paired adjacent normal tissues (n=21) to identify associations with clinical and immune characteristics.

  Dataset EGAD50000000361

• Peripheral blood DNA methylation data from CD patients prior to and during ustekinumab treatment from AmsterdamUMC

  Longitudinal DNA methylation discovery data as obtained using the Illumina HumanMethylation EPIC BeadChip array (V1) on peripheral blood from CD patients at the AmsterdamUMC prior to and during ustekinumab treatment

  Dataset EGAD00010002649

• Peripheral blood DNA methylation data from CD patients prior to ustekinumab treatment from John Radcliffe Hospital

  DNA methylation validation data as obtained using the Illumina HumanMethylation EPIC BeadChip array (V1) on peripheral blood from CD patients at the John Radcliffe Hospital, Oxford, UK prior to ustekinumab treatment

  Dataset EGAD00010002650

• Peripheral blood DNA methylation data from CD patients prior to and during vedolizumab treatment from AmsterdamUMC

  Longitudinal DNA methylation discovery data as obtained using the Illumina HumanMethylation EPIC BeadChip array (V1) on peripheral blood from CD patients at the AmsterdamUMC prior to and during vedolizumab treatment

  Dataset EGAD00010002651

• Peripheral blood DNA methylation data from CD patients prior to vedolizumab treatment from John Radcliffe Hospital

  DNA methylation validation data as obtained using the Illumina HumanMethylation EPIC BeadChip array (V1) on peripheral blood from CD patients at the John Radcliffe Hospital, Oxford, UK prior to vedolizumab treatment

  Dataset EGAD00010002652

• CRC cell line ATAC-seq

  ATAC-Seq data for C32, CACO2, CL11, HT29, SW403, SW480, SW948 MSS CRC cell lines, and HCEC-1CT normal colon cell line

  Dataset EGAD50000000296

• RNASeq of PAX4 KO vs WT in 7 stages of differentiation from human iPSCs to BLC

  Transcriptomes were profiled along with the differentiation from human induced pluripotent stem cell (iPSC) to beta-like cell (BLC) with PAX4 knocked out or not.

  Dataset EGAD00001008582

• WGS of 125 cord blood hematopoietic stem and progenitor cells

  This dataset contains 125 BAM files of cord blood hematopoietic stem and progenitor cell DNA, sequenced with Illumina Novaseq 6000, and 125 files with the variant calling performed to the sequencing data.

  Dataset EGAD50000000417

• HeH_SNParry

  This dataset included 110 samples with high hyperdiploid acute lymphoblastic leukemia that were genotyped using Affymetrix SNP Array or Illumina's BeadArray platform.

  Dataset EGAD00010002456

• DupiAERD

  Dataset contains bulk RNA sequencing reads from 44 NERD patients under dupilumab therapy before and after aspirin provocation at baseline and after 24 weeks of treatment. Dataset is a multiplexed .bam file containing all sequencing reads with tagged identifiers.

  Dataset EGAD50000000565

• scRNA-seq of monochorionic dizygotic twin chimera PBMC

  Single cell RNA-seq of PBMC of monochorionic dizygotic twin chimeras. 10x chromium v3.1 was used to generate barcoded scRNA library.

  Study EGAS50000000097

• Adipose tissue macrophage dysfunction is associated with a breach of vascular integrity in NASH

  We report single-cell RNA sequencing data from myeloid cells of the human visceral adipose tissue in non-alcoholic fatty liver disease patients

  Dataset EGAD50000000615

• CRC cell line MPRA

  Massively Parallel Reporter Assays (MPRA) of colorectal cell lines HCEC-1CT (normal colon) and HT29 and SW403 (MSS cancer). Probes identified using the CRC GWAS.

  Dataset EGAD50000000596

• 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

  Study EGAS50000000385

• CRC Patient-derived-organoids Whole Genome Sequencing

  Whole Genome Sequencing raw paired-ends reads for 20 matched colorectal patient-derived-organoids (normal and tumor). Tumor samples were obtained from patients treated at Niguarda Cancer Center, (Milano, Italy) and Candiolo Cancer Institute (Candiolo, Turin, Italy).

  Dataset EGAD50000000617

• Dac for "Altered enhancer-promoter interaction leads to MNX1 expression in pediatric acute myeloid leukemia with t(7;12)(q36;p13)"

  Dac for the data of the manuscript "Altered enhancer-promoter interaction leads to MNX1 expression in pediatric acute myeloid leukemia with t(7;12)(q36;p13)" for Prof. Christoph Plass c.plass@dkfz.de

  Dac EGAC50000000072

• Whole Genome - HAP-1 clones

  Whole genome sequencing on HAP-1 clones wild-type or knockout for MBD4 and/or TDG. Libraries were prepared using the Kapa HyperPrep kit (Roche, 07962363001). Paired-end libraries (2 x 100 bp) were sequenced on a NovaSeq 6000 instrument (Illumina).

  Dataset EGAD50000000765

• MATCH-molecular driver

  Patients were biopsied at progression on molecular targeted agents and WES and/or WTS were performed to identify resistance mechanisms. 271 underwent one or sequential tissue biopsies.

  Dataset EGAD50000000697

• Low-coverage whole genome sequencing of plasma from BRCA-mutant breast cancer patients

  Plasma samples from patients with breast cancer (stage IV) who had confirmed BRCA mutations were subjected to low-coverage whole-genome sequencing This dataset contains raw fastq files from 6 breast cancer plasma samples.

  Dataset EGAD50000000810

• WES patients with colorectal polyposis

  Twenty-seven patients were included and subjected to germline WES using NovaSeq 6000 platform. After filtering out variants for sequencing quality, variant allele fraction frequency, and population frequency, variants were manually prioritized by the ACMG criteria.

  Dataset EGAD50000000842

• BAM files from whole-exome sequencing of 5 agressive B-cell lymphoma tumour samples

  This dataset contains BAM files from whole-exome sequencing (WES) of 5 agressive B-cell lymphoma tumour samples for cases 2, 3, 4 and 5. For case 2, non-tumor whole-exome sequencing is also available.

  Dataset EGAD50000000803

• Moroccan Genome Project: Sequencing Data from 109 Whole Genomes of Moroccan Individuals

  This study is the first phase of the Moroccan Genome Project, which included the complete sequencing of 109 genomes from the Kingdom of Morocco. The sequencing was performing using the Illumina NovaSeq6000 platform, with a mean coverage of 30X.

  Dac EGAC50000000353

• CSF and PBMC scRNAseq RRMS patients at diagnostic n=5

  To get insights about immune cells infiltrating cells the CSF of RRMS patients (n=5), we proceed to 10X scRNAseq of paired CSF and blood circulating cells (about 20000 cells each) sampled at diagnostic.

  Dataset EGAD50000000445

• TMT_proteomics_CUD

  CUD samples: TMT-proteomics using Orbitrap FusionTM LumosTM TribridTM Mass Spectrometer, TMT10plex (N=8 sample batch) or TMT16plex (2x N=16 sample batches) Isobaric Label Reagent (Thermo Fisher Scientific, Waltham, MA, USA), experiment type: bottom-up proteomics; data-dependent acquisition.

  Dataset EGAD00010002703

• TMT_proteomics_Ctrl

  Ctrl samples: TMT-proteomics using Orbitrap FusionTM LumosTM TribridTM Mass Spectrometer, TMT10plex (N=8 sample batch) or TMT16plex (2x N=16 sample batches) Isobaric Label Reagent (Thermo Fisher Scientific, Waltham, MA, USA), experiment type: bottom-up proteomics; data-dependent acquisition.

  Dataset EGAD00010002702

• Mucosal Melanoma transcriptomes

  This is an RNA sequencing dataset of 101 mucosal melanoma tumors. The original corresponding study is titled "Diversity of the immune microenvironment and response to checkpoint inhibitor immunotherapy in mucosal melanoma" by J.L. Vos et al., published in JCI Insight.

  Dataset EGAD50000000892

• Chemotherapy induces myeloid-driven spatial T-cell exhaustion in ovarian cancer

  Gene expression profiles of single cells from 26 chemo-naïve and IDS tumor tissue and ascites samples from 17 HGSC patients

  Study EGAS50000000607

• WGS of ecDNA neuroblastoma cell lines

  ecDNA reconstruction for MYCN-amplified neuroblastoma cell lines using shallow long-read whole-genome sequencing (MinION platform, WGS mean-coverage 5-10X).

  Study EGAS50000000349

• Genetic architecture of disease in Greenland is shaped by demographic history, fine-structure, and selection - WGS data

  This file set has 448 Greenlandic individuals sequenced using Illumina 150 Paired end sequencing and has an average sequencing depth of 35X. The data is unfiltered, in VCF format, and covers 19.751.308 variants.

  Dataset EGAD50000000933

• CRC organoid RNA-seq data access committee

  This DAC is responsible for granting access to RNA-seq data (paired-end FASTQ files) from 10 patient-derived colorectal cancer organoid patients. The data was ad hoc generated as part of the development of NovumRNA, a non-canonical tumor-specific antigen prediction pipeline.

  Dac EGAC50000000406

• DAC Dr. PORTEU – Gustave Roussy

  Targeting Heterochromatin Eliminates Malignant Stem Cells in Chronic Myelomonocytic Leukemia Through Reactivation of Retroelements and Innate Immune pathways Data Access Committee Members (Name, Email, Job Title): Principal Investigator PORTEU Françoise (FRANCOISE.PORTEU@gustaveroussy.fr) Head of Bioinformatics platform DELOGER Marc (Marc.DELOGER@gustaveroussy.fr) Data Protection Officer BECHET Clara (Clara.BECHET@gustaveroussy.fr)

  Dac EGAC50000000252

• Duplex sequencing

  We performed duplex sequencing on buccal mucosa samples (20, 28, and 254 mm^2 swabs) and esophageal samples (10 mm^2) obtained from 10 subjects.

  Study EGAS50000000717

• NanoSeq

  We performed NanoSeq on buccal mucosal samples. We used 28 mm^2 swab DNA as samples and 254 mm^2 swab DNA as controls.

  Study EGAS50000000718

• Duplex sequencing of 26 genes

  Buccal samples and paired esophageal epithelium were obtained using the three sizes of swabs and endoscopic biopsy, respectively. Forty samples from 10 subjects were analyzed via duplex sequencing. This dataset contains bam files that were mapped to the GRCh37 reference genome.

  Dataset EGAD50000000998

• Single-cell whole genome sequencing data of Pediatric B-cell Acute Lymphoblastic Leukemia

  Single-cell whole genome sequencing data of Minimal Residual Disease cells in Pediatric B-cell Acute Lymphoblastic Leukemia

  Study EGAS50000000696

• Transcriptome - Uveal Melanomas MPI

  Total RNA sequencing on 4 uveal melanoma samples. Libraries were prepared using the TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Gold. Paired-end libraries (2 x 75 bp) were sequenced on HiSeq 4000 instrument (Illumina).

  Dataset EGAD50000001138

• Changes in CRISPR/Cas9 Outcomes depending on the usage of Pifithrin-alpha

  Study of the effects of Pifithrin-alpha in the context of genetic-engineering in primary human T cells.

  Study EGAS50000000656

• BipEx_Timpson_Bristol

  "BipEx_EGAS00001006274_Timpson_Bristol Controls Exomes. This research project was a collaboration between University of Bristol, UK and the Stanley Center at the Broad Institute. In this project we sequenced and analyzed the whole exomes of 2,981 Control samples from collaborators in UK. Genomic DNA from each sample was sequenced to a mean depth of 20x."

  Dac EGAC50000000144

• PETAL trial Whole Exome Sequencing (WES)

  Associated with Molecular profiling of DLBCL patients treated in the PETAL trial. Whole Exome Sequencing (WES) of 224 Samples (162 Tumor + 62 Normal). WES was used for Molecular Profiling by simultaneous screening of mutations. Data is Complementary to sWGS.

  Dataset EGAD50000001172

• WGS data of 100 Breast Cancer patients from SV Based ctDNA Detection study

  Whole Genome Sequencing data of 100 Breast Cancer patients from "Ultrasensitive Detection and Monitoring of Circulating Tumor DNA using Structural Variants in Early-Stage Breast Cancer" study.

  Dataset EGAD50000001175

• Acetalax and bisacodyl triple-negative breast cancer RNA-Seq

  Analysis of gene expression in triple negative breast cancer xenografts exhibiting good or bad response upon acetalax and bisacodyl treament.

  Study EGAS50000000618

• RNAseq data of metastatic breast cancer samples

  Paired-end RNA sequencing data from 28 metastatic breast cancer samples. Sequencing was performed on the Illumina NovSeq 6000 and HiSeq 4000 using TruSeq Stranded mRNA Kit.

  Dataset EGAD50000000818

• DAC for "Establishment and characterization of circulating tumor cells-derived organoids from metastatic breast cancer patients."

  This is the DAC for the study "Establishment and characterization of circulating tumor cells-derived organoids from metastatic breast cancer patients." of Andreas Trumpp (a.trumpp@dkfz.de), Roberto Würth (r.wuerth@dkfz.de) and Martin Sprick (Martin.Sprick@hi-stem.de).

  Dac EGAC50000000371

• Exome-sequencing on early oral squamous cell carcinoma with clear margins

  Whole exome sequencing (WES) on early oral squamous cell carcinoma (OSCC) with clear margins, and on resection margins, 86 patients with a median follow-up of 58 months (range 30.4-83 months). Raw data (fastq format).

  Dataset EGAD50000001209

• B cell single cell sequencing (RNA + VDJ) - Autoproliferation

  10X 3' (RNA) and 10X 5' (VDJ) samples of B cells (non-proliferating/hi and autoproliferating/Dim) for healthy donor and Multiple sclerosis patients used in the paper.

  Dataset EGAD50000001237

• Methylome and transcriptome of memory B cells - Autoproliferation

  Methylome and the corresponding transcriptome of autoproliferating/Dim B cells and resting/hi B cells in Multiple sclerosis patients

  Dataset EGAD50000001236

• Short-read RNA-seq of doxycycline-inducible DUX4 human myoblast cell lines

  The dataset includes the short-read RNA sequencing data of DUX4i myoblasts (Clone-5 and Clone-7) with and without 16-hour DOX-treatment (n=1 in each condition).

  Dataset EGAD50000000719

• ChIP-seq in KMS11 and TKO cells

  Histone chIP-seq in t(4;14) Myeloma cell line KMS11 and KMS11 cells with knock-out of translocated NSD2 allele (KMS11 TKO).

  Study EGAS50000000077

• Paired-end RNA-seq FASTQ files from amniotic fluid samples

  Paired-end RNA-seq FASTQ files from amniotic fluid samples of 49 extreme premature births, affected and unaffected by the fetal inflammatory response.

  Dataset EGAD50000001260

• WGS dataset for malignant pleural and peritoneal mesothelioma

  This dataset contains Whole Genome sequencing data of pleural and peritoneal mesothelioma. The number of samples is 40. Sequencing was performed on Illumina NovaSeq 6000 and Illumina NovaSeqXPlus. The sequencing was always paired.

  Dataset EGAD50000001343

• Hematological toxicity following CAR-T cells injection dataset

  This dataset containes 44 paired of bulk RNA sequencing and 42 parired of single cell RNA sequencing issued from bone marrow aspirations obtained from patients treated with CAR-T (CD3+, CAR T+, CD34+ sorted populations).

  Dataset EGAD50000001142

• Tumor mutational landscape in individuals with CMMRD

  Whole exome sequencing data from the tumors (n=16) of individuals with constitutional mismatch repair deficiency. Data was aligned to GRCh38.

  Study EGAS50000000081

• Dataset for scRNA glioblastoma samples

  This dataset contains 5 scRNA samples of human glioblastoma samples, human cortical spheroid derived from hiPSC line 028-4 and 3 samples of mouse xenografts. Sequencing has been performed on Illumina NovaSeq 6000. Sequencing has always been paired.

  Dataset EGAD50000001117

• Dac for "Development of a fully human glioblastoma-in-brain-spheroid model for accelerated translational research"

  This is the DAC for "Development of a fully human glioblastoma-in-brain-spheroid model for accelerated translational research" of Philipp Koch (philipp.koch@zi-mannheim.de), Frank Winkler (Frank.Winkler@med.uni-heidelberg.de), Moritz Mall( m.mall@dkfz-heidelberg.de)

  Dac EGAC50000000480

• TRACERx NSCLC - whole genome sequencing for ctDNA study

  Data used in "An ultra-sensitive and specific ctDNA assay provides novel pre-operative disease stratification in early stage lung adenocarcinoma"

  Dataset EGAD50000000452

• Dataset for "HPV integration induces gene fusions" (pacBio)

  pacBio whole-genome sequencing data for "HPV integration induces gene fusions" We performed long read whole-genome sequencing on four HPV+ head and neck cancer samples using pacBio HiFi. The sequence reads were submitted in fastq format.

  Dataset EGAD50000001304

• TRIGR collaboration between University of Helsinkin and Children's Mercy Research Institute

  DAC for collaborations between by the University of Helsinki and Children's Mercy Hospital, such as the Trial to Reduce IDDM in the Genetically at Risk (TRIGR), used to study the evolving epigenomics of immune cells in type 1 diabetes at single nuclei resolution

  Dac EGAC50000000543

• The Dynamic Immune Behavior of Primary and Metastatic Ovarian Carcinoma

  Single-cell RNA-seq data of prospectively collected normal ovarian tissue sample from 1 healthy individual and tumor tissue samples with or without chemotherapy from 19 HGSOC patients.

  Dataset EGAD50000000057

• Cohort A tumor exome sequencing

  Cohort A includes glioma tumors of varied grading and pathology from male and female individuals. Tumor DNA was isolated from fresh frozen tissue.

  Study EGAS50000000949

• miRNA

  miRNA Sequencing of olfactory mucosa (OM) cells derived from cognitively healthy and individuals with AD exposed to traffic-related ultrafine particles (UFPs) for 72h in submerged cultures. The UFPs used for exposures were: A0 and A20. Exposures were compared to the corresponding blank samples.

  Dataset EGAD50000001532

• bulk RNAseq from metastatic uveal melanoma tumour biopsies

  Tumour biopsies were obtained from uveal melanoma patients (n = 35) pre and 16 days post treatment with tebentafusp. Biopsies, which were either snap frozen or put in RNA later, were analysed by bulk RNA sequencing (50 million reads per sample) using the Illumina NovaSeq system.

  Dac EGAC50000000519

• Hybrid Capture of PyBKV integration in Urothelial Carcinoma from Kidney Transplant

  Hybrid Capture of PyBKV integration in Urothelial Carcinoma from Kidney Transplant. The Panel was designed using Agilent SureDesign on SureSelect XTHS Hybrid Capture Panel. Sequencing was done on Illumina NovaSeq 6000

  Dataset EGAD50000001548

• BCR repertoir sequences from human buffy coat purified B-Cells with DIS3 and control ASO

  This dataset contains BCR sequences of buffy coat purified B-cells from 5 healthy donors. For each sample, sequences were obtained in two conditions : with control Aso and Dis Aso treatment.

  Dataset EGAD50000001601

• Methylation Array of pre- and post-5ZA-treated head and neck cancer patients refractory to anto-PD-1 therapy

  Illumina MethylationEpic Beachip data generated from tissue samples collected from head and neck cancer patients refractory to anti-PD-1 therapy, collected before and after the 5AZA treatment

  Dataset EGAD00010002718

• SDR-seq_06_BCL

  SDR-seq_BCL data access. Two follicular lymphoma (FL) primary patient samples and one germinal center subtype diffuse large B-cell lymphoma (GCB) primary patient sample. FL1 and GCB1 are sequenced in Run1. FL2 is sequenced in Run2.

  Dataset EGAD50000000551

• RNA-seq dataset for two NUP98-Rearranged Acute Myeloid Leukemia PDX samples

  This dataset includes RNA-seq of two patient-derived xenograft (PDX) samples with NUP98-Rearranged Acute Myeloid Leukemia. Bam files are provided for each sample.

  Dataset EGAD50000001564

• RNA-seq in endometrial healthy and tumor tissues

  RNA has been extracted by Rneasy mini kit from around 30mg of flash frozen tissue derived from 3 healthy and 3 tumor endometrial tissues of post-menopausal patients. Raw paired-end fastq.gz files are provided.

  Dataset EGAD50000000200

• Whole genome sequencing data of cfDNA and WBC from 5 patients with mUC

  Whole genome Illunima sequencing of cfDNA of 5 metastatic urothelial carcinoma patients. White blood cell (WBC) samples are used as patient matched germline samples (n=5). All files are in paired-end fastq format.

  Dataset EGAD50000001570

• DNA methylation and transposable element landscapes in human regulatory and conventional Tcells

  Whole genome bisulfate sequencing using tagmentation of Tcells from skin and blood.The method improved TWGBS protocol (Weichenhan et al.), Methods Mol. Biol. 2018, vol. 1708 pp.105-122) was used

  Dataset EGAD50000001022

• Clonal hematopoiesis in metastatic urothelial and renal cell carcinoma

  This study aimed to determine the prevalence and clinical relevance of clonal hematopoiesis in metastatic urothelial and renal cell carcinoma.

  Study EGAS50000000870

• DAC Study assessing the efficacy and safety of durvalumab plus olaparib plus fulvestrant in selected metastatic or locally advanced ER-positive, HER2-negative breast cancer patients.

  DAC for Study assessing the efficacy and safety of durvalumab plus olaparib plus fulvestrant in selected metastatic or locally advanced ER-positive, HER2-negative breast cancer patients.

  Dac EGAC50000000694

• Multi-modal spatial characterization of tumor-immune microenvironments identifies targetable inflammatory niches in diffuse large B-cell lymphoma

  This dataset includes NGS data of large B-cell lymphoma, including bulk RNAseq data of 71 biopsies and germline WES data of 70 biopsies.

  Dataset EGAD50000001641

• Acute Lymphoblastic Leukemia WES dataset

  This dataset includes illumina paired-end reads (fastq) of whole-exome sequencing (WES) data from three acute lymphoblastic leukemia patients. Tumor samples were obtained from patients, each with matched patient’s peripheral blood mononuclear cells (PBMCs). PBMCs are provided as a germline reference.

  Dataset EGAD50000001355

• Microarray CDX or EDX from primary tumor and metastasis

  expression analysis of FACS sorted human cells from primary tumors and distant organs micrometastases in xenografts. Patient Derived xenografts were generated transplanting tumor cells from metastatic breast cancer patients into mammary fat pad of immunocompromised mice

  Dataset EGAD00010002711

• scRNAseq sequencing reads and count matrices of murine splenocytes from diffuse large B-cell lymphoma

  Single-cell RNA-seq of 91 murine splenocytes from Bcl6tg/+ and Cd70-/-; Bcl6tg/+ diffuse large B-cell lymphoma mouse models and Cd70-/- and wild-type controls.

  Dataset EGAD00001012104

• non-malignant plasma cfRNA

  Dataset contains mRNA capture sequencing data from plasma of 125 different human donors: 88 patients with a non-malignant disease and 37 cancer-free controls. Samples were sequenced on a NovaSeq X and sequencing data is provided in FASTQ format.

  Dataset EGAD50000001806

• bulkRNAseq: Human periportal liver assembloids recapitulate periportal liver tissue in vitro

  Sample number: 40 Sample details:Total 40 samples, including hepatocyte organoids (74 samples), primary human hepatocytes (15 samples), cholangicocyte organoids (11 samples), hepatocytes cultured in monlayer (5 samples) and portal fibroblasts (3 samples).

  Dataset EGAD50000001454

• Genomic sequencing data for PNG15 and PNG16

  This study includes both long- and short-read sequencing data for PNG15 and PNG16 as well as their phased haplotype assemblies.

  Study EGAS50000001105

• cfDNA shallow Whole-Genome sequencing - expansion run

  cfDNA shallow Whole-Genome sequencing of the remaing patients with mTNBC in the TONIC trial, including 3 timepoints: baseline, week 6 and week 12. The week 6 data of the patients in the pilot run was sequenced here.

  Dataset EGAD50000001862

• Two scRNA-seq datasets from control and irradiated organoids.

  Dataset includes two scRNA-seq samples from control and irradiated organoids. Files included in the dataset are Fastq files. Sample libraries produced with Chromium X were sequenced on an Illumina NovaSeq 6000 sequencer.

  Dataset EGAD50000001933

• This data consists of iPSC derived model systems stimulated with different media.

  This data consists of iPSC derived model systems stimulated with different media (where possible from the top/bottom separately) to provide insight into which more accurately reflects the human gut environment.

  Dataset EGAD50000001918

• Methylation sequencing of CSF-derived cell free DNA

  We sequenced and enzymatically converted cell free DNA from 268 samples from 157 patients with brain tumors and 58 control CSF patients.

  Study EGAS50000001365

• Spatial transcriptomics prostate cancer

  Spatial transcriptomic characterization of human fresh frozen prostate cancer and non-malignant regions from the same patient. 100 micron thick sections were made from the biopsies, adjacent to snRNA sequencing, and subjected to 10x Genomics Visium ST analysis.

  Dataset EGAD50000001634