23248 results for "ega"

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• Methylation Array data for: Three-dimensional patient-derived models of glioblastoma retain intra-tumoral heterogeneity

  3 sets of matched patient-derived-organoids (PDOs),  -neurospheres (PDNs), and parent glioblastoma tissue (9 samples total) underwent methylation array analysis. 200ng of each sample DNA extracted via a commercial kit (Qiagen) and loaded onto the Illumina EPIC v2.0 array. Data is provided as raw red and green .idat files.

  Dataset EGAD00010002745

• FLT3 is genetically essential for ITD-mutated leukemic stem cells but dispensable for human HSCs

  bulk RNA sequencing of AML patients It contains 18 samples from primary AML patients. Half of the samples are control samples and half of the samples are FLT3-ITD knock-out (edited for the FLT3-ITD mutation). It is using Illumina high-throughput technology

  Dataset EGAD50000000636

• Whole genome sequencing data of pediatric hypodiploid B cell acute lymphoblastic leukemia

  The dataset includes FASTQ and BAM files from diagnostic and matched remission (control) bone marrow samples of one hypodiploid ALL patient (ALLT-351). Sequencing library was made using NEB Next® Ultra™ DNA Library Prep Kit. Both diagnostic (60x) and remission (30x) samples were sequenced using HiSeq X.

  Dataset EGAD50000001856

• Aligned Low pass whole genbome sequencing of cell free and tumour DNA from 5 patients with high grade serous ovarian cancer. Samples have been aligned to hg19 and bam files uploaded

  This is the aligned bam files of 5 patients, with sequential sampltes from patients comprising cfDNA and FFPE extracted tumour DNA

  Dataset EGAD50000001632

• Long-read and short-read RNA sequencing of human normal liver organoid with or without SF3B4 overexpression

  There are 2 matched short and long read RNA sequencing samples. The project aims to find alternative splicing events and resulting transcript isoforms modulated by SF3B4

  Study EGAS50000001131

• Cancer Affected Patients - Data Access Committee

  Access to the cancer cohort is made available by completing the data access agreement for review by the data access committee and will be granted to qualified investigators for appropriate use. Individuals requesting access to the data need to comply with the terms of a Data Access Agreement (DAA) and are requested to use the data only in approved and ethical ways.

  Dac EGAC50000000037

• Visium Spatial transcriptomics

  This study consists of the spatial transcriptomics data generated by : Visium CytAssist Spatial Gene Expression for FFPE (10x) for steatotic liver disease-associated hepatocellular carcinoma (SLD-HCC) (n=7) and non-SLD-HCC (n=5) The goal of this data is to compare SLD-HCC vs non-SLD-HCC as well as response to immunotherapy

  Dataset EGAD50000001506

• Whone genome DNA methylation profile

  Primary human CD4+ naive T cells were cultured in vitro and sorted based on the defined number of division steps which they have undergone. Of those populations (division 0/div4/div6) EMseq data were generated to assess the whole-genome DNA methylation profile. 2 independent experiments with 2 different donors were conducted

  Dataset EGAD50000001815

• GeoMx digital spatial profiling of NGS mRNA expression in pre-treatment biopsies from patients.

  This DAC is created to define the data controller (the person that determines the purposes for which and the means by which personal data is processed) for the following study: GeoMx digital spatial profiling of NGS mRNA expression in pre-treatment biopsies from patients with metastatic triple-negative breast cancer treated with PARP inhibitors.

  Dac EGAC50000000774

• Dynamic human admixture histories over the past ~1,300 years at the northern Himalayan frontier

  Whole-genome sequencing data from ten present-day individuals from Himachal Pradesh, India. DNA from these ten present-day individuals was converted to double-stranded libraries and sequenced on Illumina NovaSeq 6000 in 150 bp paired-end mode. The dataset consists of raw fastq and bam (hg19) files.

  Dataset EGAD50000001925

• singel cell RNAseq dataset for the study "Longitudinal Multi-Omics Study Reveals Molecular Drivers and Tumor Microenvironment in Extramedullary Multiple Myeloma"

  This dataset contains 16 fastq files of raw single-cell RNAsequencing data from 6 patients with Extramedullary multiple myeloma used for the study "Longitudinal Multi-Omics Study Reveals Molecular Drivers and Tumor Microenvironment in Extramedullary Multiple Myeloma"

  Dataset EGAD50000000053

• Dicer and/or ADAR1 depleted HEK293-LGP2 cells

  This dataset includes bulk RNA-sequencing data from HEK293-L cells subjected to siRNA-mediated knockdown of Dicer and/or ADAR1. In total, 12 samples are included, representing four experimental groups with triplicate biological replicates. RNA was extracted using TRIzol according to standard protocols and sequenced on an Illumina NovaSeq 6000.

  Dataset EGAD50000002044

• Resolution and methylation patterns of supernumerary marker chromosomes

  Herein we study the structure of ring and marker chromosomes in 10 carriers. The aim is to gain understanding of the formation and function of ring and marker chromosomes.

  Study EGAS50000001466

• PacBio Revio WGS on 10 carriers of ring and marker chromosomes

  Bam files containing PacBio HiFi reads from carriers of ring and marker chromosomes. The reads where genereated using the PacBio Revio platform. Each individual was sequenced to roughly 30X coverage on one flow cell per individual. The chromosome of interest is indicated in the file name.

  Dataset EGAD50000002111

• Impact of DIS3 Aso on BCR repertoir in human buffy coat purified B-Cells

  The aim is to identify difference in the BCR of Aso DIS3 treated cells compared to Control Aso. Using extracted DNA from human B-cells

  Study EGAS50000001107

• Exome data from 154 patients with childhood or adolescent cutaneous melanoma

  This dataset contains sequence data from 154 patients in Australia diagnosed with cutaneous melanoma before the age of 20. Each patient was exome sequenced on the illumina platform. Generated sequence reads were aligned against version 19 of the human genome assembly and stored in bam files made available here.

  Dataset EGAD50000001868

• WGS data of paediatric B-other B cell acute lymphoblastic leukemia (set4)

  The dataset includes FASTQ and CRAM files from diagnostic and matched remission (control) samples of two B-other ALL patients (ALLT-389, ALLK-124). Sequencing library was made using Novogene NGS DNA Library Prep Set. Both diagnostic (90x) and remission (30x) samples were sequenced using Illumina NovaSeq 6000.

  Dataset EGAD50000002159

• Multiple myeloma treated with T-cell redirecting immunotherapies

  Whole Genome Sequencing from patients with multiple myeloma treated with T-Cell redirecting therapies including chimeric antigen receptor T-cells (CAR-T) and Bispecific T-cell Engagers (TCE).

  Study EGAS50000000546

• Whole-exome sequencing of intrahepatic cholangiocarcinoma tumors with matched normal tissue from the Medical Center – University of Freiburg

  This dataset contains raw whole-exome sequencing data from 40 samples of intrahepatic cholangiocarcinoma patients, including tumor and matched normal tissue. Samples were sequenced on the NovaSeq platform. The cohort is part of a proteogenomic profiling study integrating genomic and proteomic data.

  Dataset EGAD50000001926

• Data Access Committee for Maurice Lab - UMC Utrecht

  The Data Access Committee of the Maurice lab at the Center for Molecular Medicine, University Medical Center Utrecht, is responsible for reviewing and approving requests for access to controlled human transcriptomics and genomics data generated by the lab. The DAC ensures that data access requests are consistent with informed consent, ethical approvals, and applicable legal and institutional regulations, including GDPR.

  Dac EGAC50000000876

• WGS of thymic epithelial tumors and paired normal

  Among the 20 newly sequenced cases, we conducted additional whole-genome sequencing (WGS) on five out of eight CN-type thymomas, excluding three with low tumor cell fractions (< 0.1). Libraries for WGS were prepared using the TrueSeq DNA PCR-free Prep Kit following standard Illumina protocols.

  Dataset EGAD50000001160

• Waldenström Macroglobulinemia Single-Cell Data Access Committee

  This Data Access Committee (DAC) is responsible for reviewing and approving access requests for controlled-access human single-cell sequencing data, including single-cell RNA sequencing and immune receptor profiling, generated from patients with Waldenström macroglobulinemia. The DAC ensures that all data access requests comply with the informed consent provided by study participants and are consistent with applicable ethical and regulatory requirements.

  Dac EGAC50000000863

• Whole exome sequencing data of matched pairs of primary tumour and normal frozen tissue of seven osteosarcoma patients

  This dataset contains whole exome sequencing data of matched pairs of primary tumour and normal frozen tissue of seven osteosarcoma patients. Whole exome sequencing with a minimum coverage of 100x was performed using the Illumina Novaseq6000 platform and the Agilent SureSelect Human All Exon V7 kit.

  Dataset EGAD50000002264

• Copy number profile of ctDNA in ovarian cancer patients

  This study analyzes the copy number profiles from circulating tumor DNA (ctDNA) in plasma samples withdrawn from ovarian cancer patients, in a subset of samples from the MITO16A clinical trial.

  Study EGAS00001008226

• MissionBio single cell DNA and protein seq for 2 samples

  This dataset contains MissionBio Targeted single-cell DNA and Protein sequencing data from a primary sample and a patient-derived xenograft (PDX) model, which is used to investigate the clonal evolution in the FOXF1/FENDRR ALL subtype. All the 2 samples are in bam file type.

  Dataset EGAD50000001793