22939 results for "ega"

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• Analysis of transcriptomic landscape of iPSC-derived neurons in Williams Syndrome

  To analyse the transcriptomic changes in iPSC-derived neuronal cells derived from individuals with Williams syndrome vs. controls at different stages of neuronal maturation. This was done to better understand how the deletion responsible for WS alters neuronal development thereby resulting in the characteristic WS phenotype

  Study EGAS50000001214

• ovarian cancer sample exome seq

  Tissue samples were collected from 18 ovarian cancer patients. After mechanical and enzymatic dissociation, a part of these tissues underwent growth factoromics analysis. For four cases, single-cell sequencing analysis was conducted under conditions with or without estradiol. Additionally, the remains of the tissues were frozen and subsequently subjected to exome sequencing on 16 of these samples. Sixteen cases were diagnosed as HGSOC, while two samples were clear cell or mucinous type (Extended Data Table 1). All cases were grade 3, and none had received neoadjuvant chemotherapy.

  Dataset EGAD50000002057

• RNA-seq data for proximal and distal human LHBT UZH (CH)

  This dataset contains bulk RNA-seq data from 15 patients who underwent rotator cuff repair surgery, yielding paired proximal and distal samples of the long head of the biceps tendon (30 samples total). The submission includes 90 files, consisting of R1 and R2 FASTQ files for each sample as well asprocessed .TXT files containing gene-level counts generated after genome alignment. Raw sequencing reads were generated on an Illumina platform, aligned to the human reference genome GRCh38.p13, and quantified at the gene level.

  Dataset EGAD50000002095

• WGS of clonal organoids, bulk-tumor tissues, and matched blood samples derived from metastatic colorectal cancer patients

  This dataset consists of WGS fastq files from 58 clonal organoids and 18 fresh-frozen (FT) bulk-tissue samples from surgically resected primary and metastatic tumors before and after anticancer therapies in 6 patients with matched blood control samples from each patient. After DNA extraction from each sample using DNeasy Blood and Tissue Kit (Qiagen), library preparation was done using TruSeq DNA PCR-free kit. Then, paired-end fastq files were generated using Illumina NovaSeq 6000.

  Dataset EGAD50000001493

• Perioperative nivolumab or nivolumab plus ipilimumab in resectable diffuse pleural mesothelioma: Primary phase 2 trial results with ctDNA residual disease analyses

  This data set includes sequence files from whole genome sequencing of tumor (n=28), normal (n=28), and blood (n=113) specimens from a phase 2 clinical trial of neoadjuvant nivolumab and nivolumab/ipilimumab in resectable diffuse pleural mesothelioma (NCT03918252).

  Study EGAS50000001195

• NAR-GAB 2025 deposit data

  Paired-end whole-exome sequencing data derived from Illumina hybrid-capture experiments (Agilent SureSelect Human All Exon kits). Six human probands with rare diseases; one sample per subject. Sequencing reads from each individual were processed into analysis-ready gVCF files following standard best-practice pipelines, including alignment, duplicate marking, base quality calibration, and variant calling. All gVCF files are encrypted using Crypt4GH and are available under controlled access through our DAC in accordance with a strict DUO-based policy.

  Dataset EGAD50000002100

• BCC HHI-ICI combination therapy

  Data of advanced basal cell carcinoma patients receiving hedgehog-inhibitor and immune checkpoint-inhibitor combination treatment. The single-cell RNA-sequencing data was generated via the Parse Biosciences platform from PBMC samples of 10 patients at 4 four timepoints each. The spatial transcriptomics dataset was generated using the 10x Visium platform (+CITE-seq) and contains altogether 10 biopsies at different timepoints during treatment from 3 patients. The processed matrices with the spatial images can be downloaded from: https://zenodo.org/records/17814765

  Dataset EGAD50000002134

• RRBS of 58 pleural mesothelioma samples (Paired-end)

  The dataset contains RRBS data (bam files) for 58 pleural mesothelioma samples. The samples were sequenced on NovaSeq6000 (Illumina, San Diego, CA) in paired-end 150bp mode. RRBS raw reads were trimmed for adaptor sequences using trim galore (v. 0.6.5) (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) and filtered for low-quality sequences using fastQC (v. 0.11.8) (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). High quality trimmed reads were mapped to the Human reference genome (UCSC genome assembly GRCh38/hg38) using Bismark (v. 0.22.3) with default parameters.

  Dataset EGAD50000002129

• RNA-sequencing of 82 pleural mesothelioma samples

  The dataset contains RNA-sequencing data (bam files) for 82 pleural mesothelioma samples. All the samples were sequenced on an Illumina NovaSeq 600 sequencer in paired-end mode, generating 100 nt length reads, to obtain an average of 60 million clusters for RNA. Demultiplexing was performed using Illumina bcl2fastq2. Fastq quality was assessed using fastQC (v. 0.11.8) (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and low-quality reads were discarded. Sequence reads were aligned to Human reference genome (UCSC genome assembly GRCh38/hg38) using STAR (v. 2.7.0b).

  Dataset EGAD50000002131

• Metagenomic data of patients with bipolar disorder or schizoprhenia spectrum disorder

  Metagenomic data of stool samples from 111 patients with either bipolar disorder or schizophrenia spectrum disorder. Data includes fq.gz files, mostly 1 forward and 1 reverse read per sample. Samples analysed in multiple lanes have 4 (paired) fastq files, which will have the same patient ID (example: 048_1 and 048_2, or 088_L1 and 088_L2. DNA was extracted from using the QIAamp Fast DNA Stool Mini Kit (Qiagen) following the manufacturer’s instructions. Shotgun metagenomic sequencing was carried out using llumina Novaseq 6000.

  Dataset EGAD50000001414

• Bell_activation_timecourse

  We purified human naive and memory B cells from PBMCs. We stimulated them with IgM cross-linker providing BCR stimulation, multimeric CD40L that engages costimulatory receptor CD40 on the B cell, and cytokines IL-2 and IL-21. To comprehensively characterise activation dynamics of naive and memory B cells, we performed single-cell RNA sequencing (scRNA-seq) and B cell receptor sequencing (BCR-seq) in resting cells (day 0), before the first division (day 1), at the time of the first division (day 3) and following the full B cell differentiation (day 6)

  Dataset EGAD50000002115

• Whole-exome sequencing and RNA-seq of paired normal-tumour samples from MMR-proficient early-onset colorectal cancer patients

  This dataset contains fastq files obtained from paired samples of normal colonic mucosa and tumour tissue, collected from 19 patients diagnosed with MMR-proficient colorectal cancer at an age of 50 years or younger. It includes both whole-exome sequencing and RNA-seq data, generated on the Illumina HiSeq 3000 platform. Additionally, the dataset includes phenotypic information from the patients.

  Dataset EGAD50000001844

• TTFields Glioblastoma Data Access Committee, Charité – Universitätsmedizin Berlin

  This Data Access Committee is responsible for reviewing and approving data access requests for genomic and associated clinical data from patients with glioblastoma, IDH wildtype, treated with surgery, standard chemoradiotherapy and Tumor Treating Fields at Charité – Universitätsmedizin Berlin. The DAC ensures that any data use is consistent with the patients’ informed consent, the study’s ethical approval and applicable data protection regulations. Approved applicants may use the data only for biomedical research on brain tumours and related methods, must not attempt re-identification of participants, and may not share the data with unauthorized third parties

  Dac EGAC50000000843

• Fragmentomics analyses of urinary cfDNA for urologic cancers

  This dataset contains sequencing data of human urinary cell-free DNA. Whole-genome sequencing (WGS) and whole-genome bisulfite sequencing (WGBS) was performed after DNA extraction from the urine samples. All samples were pair-end sequencing on Illumina system and were aligned to human genome GRCh37 (hg19). WGS and WGBS reads were aligned by SOAP2 and Methyl-Pipe, respectively. The dataset includes samples from healthy subjects, haematuria (non-cancer), and patients of bladder, kidney, or prostate cancer. Pair-end FASTQ files were provided for all the samples mentioned above.

  Dataset EGAD50000002068

• Shallow Whole-Genome Sequencing of Plasma ctDNA in Relapsed/Refractory Germ Cell Tumors

  This dataset comprises shallow whole-genome sequencing data (~3× coverage) of circulating tumor DNA extracted from baseline and on-treatment plasma samples of patients with relapsed or refractory germ cell tumors treated with salvage high-dose chemotherapy. Libraries were generated from 20 ng of cfDNA using the KAPA Hyper Prep protocol with unique dual indexing and sequenced on an Illumina NovaSeq 6000 platform to enable genome-wide copy number and biomarker analyses associated with treatment response and clinical outcome.

  Dataset EGAD50000002183

• WGS data of paediatric B-other B cell acute lymphoblastic leukemia (set3)

  The dataset includes FASTQ and BAM/CRAM files from diagnostic and matched remission (control) samples of 10 B-other ALL patients (ALLT-369,ALLT-378, ALLK-109, ALLK-110, ALLK-115, ALLT-391, ALLK-101, ALLK-113, ALLK-123, ALLT-393). Sequencing library was made using PCR free-based WGS library preparation (PCR-), using NEBNext® Ultra™ II DNA Library Prep Kit. Both diagnostic (90x) and remission (30x) samples were sequenced using Illumina NovaSeq 6000.

  Dataset EGAD50000002158

• Hybrid untargeted and targeted RNA sequencing facilitates genotype-phenotype associations at single-cell resolution

  Raw sequencing data for the manuscript "Hybrid untargeted and targeted RNA sequencing facilitates genotype-phenotype associations at single-cell resolution". It includes PacBio long-read scRNA-seq, illumina short-read scRNA-seq and Twist-based targeted scRNA-seq datasets for two adrenal samples.

  Study EGAS50000001537

• RNA sequencing of BCP-LBL and EM B-ALL patients samples

  In order to perform comprehensive transcriptomics and gene fusion analyses of a cohort of BCP-LBL and extramedullary (EM) manifestations of B-ALL patients, we performed RNA sequencing of 16 tissue samples from BCP-LBL and EM B-ALL patients. Because the material was available as FFPE, and had a relative low quality, we used a capture-based approach, where NGS libraries obtained from total RNA were captured in 4-plex, using a whole exome capture panel.

  Dataset EGAD50000002047

• PHRT study of longitudinal sampling in ovarian cancer

  High-grade serous ovarian cancer presents significant challenges due to its poor prognosis and high heterogeneity, both of which complicate treatment responses. This project aims to understand intra-patient tumor evolution by investigating different sampling sites (primary and metastatic) at the time of diagnosis and during disease recurrence.

  Study EGAS50000001424

• A single-cell atlas of the early COPD lung

  Single cell atlas of the human airways from 10 patients suffering of early stage Chronic Obstructive Pulmonary Disease and 12 healthy age matched volunteers. This dataset was sequenced by 10X Genomics 3’ RNA-seq profiling. It is composed of more than 400 000 cells coming from 119 samples total. Sampling was performed by brushings and biopsies from the nose to the 6 th division of the airways.

  Dataset EGAD50000001001

• Transcriptomics for LUNG-NSCLC2 cohort

  The goal of IMMUcan is to understand how the immune system interacts with tumors and how therapeutic interventions influence this interaction. This cohort includes patients with non-small cell lung cancer who had surgical resection. This is a subcohort of the EORTC SPECTAlung study. This dataset contains transcriptomics data processed with the STAR pipeline. Two sequencing kits were employed: Roche KAPA for high-quality RNA samples and Takara SMART-Seq Stranded for samples with limited RNA quantities.

  Dataset EGAD50000002236

• snRNA-seq data of 11 regionally sampled GBM tissue for 4 patients

  This dataset contains snRNA-seq data of 11 regionally sampled GBM tissue (peritumoral region, tumor edge, and tumor core). Regionally sampled GBM patient tissue was dissociated and nuclei were processed in an unbiased manner without any sorting procedure. Nuclei were dissociated from frozen tissue using Chromium Nuclei Isolation Kit. Nuclei barcoding, cDNA preparation, and library construction were performed following the Evercode WT or WT mini User Manual, by combinatorial barcoding to assign a unique barcode to each cell.

  Dataset EGAD50000000778

• A clinically and genomically annotated Early onset colorectal cancer and late onset colorectal cancer

  This study aimed to identify genomic characteristics of early-onset colorectal cancer (EOCRC) compared to late-onset cases. Whole-genome sequencing (WGS) was performed on EOCRC and late-onset colorectal cancer (LOCRC) tissues and blood samples to analyze their genomic profiles.

  Study EGAS50000000544

• RNA sequencing of untreated head and neck cancer patient-derived xenografts (PDXs) and matched patient tumor tissue.

  RNA sequencing was performed on untreated patient tumor tissue and matched patient-derived xenograft (PDX) models of primary head and neck squamous cell carcinoma (HNSCC). The aim of this analysis was to characterize the transcriptional landscape of the tumors in the in vivo setting.

  Study EGAS50000001595

• Enzymatic methylation sequencing of rectal mucus from patients suspected to have colorectal cancer

  This dataset contains comprises enzymatic methylation sequencing (EM-Seq) data generated from 208 rectal mucus samples from patients suspected to have colorectal cancer and healthy controls. Targeted CpG sites were enriched using a panel of genes implicated in colorectal cancer, and libraries were prepared with NEBNext EM-Seq prior to Illumina sequencing. Sequencing was performed on the Illumina NovaSeq6000 platform, producing paired-end FASTQ files. These data support analyses of DNA methylation patterns in CRC detection and progression

  Dataset EGAD50000001871

• Single nucleus mRNA sequencing of immune cells from diverse CNS regions in human health and diseases

  CNS nuclei were isolated from frozen specimen, stained with anti-NeuN and anti-Olig2, FACS purified (DAPI+NeuN-Olig2-), and analyzed with single nucleus RNA-seq. One batch of samples was also labelled with CMO and allows distinguishing indivudal samples within the analysis. A combined seurat object was generated to include all the analyses and samples were integrated using Harmony integration.

  Dataset EGAD50000001835

• Transcriptome analysis of human iPSC-derived microglia in a novel human 3D cortical tissue model

  scRNA-seq analysis of human iPSC-derived microglia in a novel, human in vitro 3D cortical tissue model. Samples include three distinct conditions (each as biological duplicates): wild-type microglia extracted from cultures after 1 month (WT_1mo) and 3 months (WT_3mo) of culturing, as well as knock-in microglia extracted from cultures carrying three familial AD mutations in the APP gene (Swedish, Iberian, Arctic; introduced by CRISPR/Cas9-mediated knock-in) after 3 months of culturing (KI_3mo).

  Dataset EGAD50000000677

• scRNA-seq of a 3D human cortical tissue model from human iPSCs exploring 2D versus 3D co-culturing

  Single-cell RNA-seq analysis of human iPSC-derived microglia/astrocytes/neurons in a novel, human in vitro 3D cortical tissue model, as well as 2D co-cultures for comparison. Samples include distinct conditions as described in the Study section. The dataset was generated using the BD Rhapsody technology and sequenced paired-end with Illumina NovaSeq2000. Information on the multiplexing of samples is reported in the Analyses section.

  Dataset EGAD50000002021

• Targeted Next-Generation Sequencing Data of IDH1 Exon 4 in Intrahepatic Cholangiocarcinoma Samples

  This dataset contains targeted next-generation sequencing data from 76 FFPE tumor tissues focusing on IDH1 exon 4 and codon 132. Genomic DNA was isolated using the QIAamp DNA FFPE Tissue Kit and sequenced on the Illumina MiSeq platform with 200x minimum coverage. The results are provided as encrypted somatic variant call files (VCF) generated through the Nextera XT library preparation protocol. This collection represents the specific somatic mutation profiles of the intrahepatic cholangiocarcinoma cohort for controlled access.

  Dataset EGAD50000002345

• Whole-exome sequencing (WES) analysis of untreated head and neck cancer patient-derived xenografts (PDXs) matched patient tumor tissue and normal mucosa tissue.

  WES analysis was performed on untreated patient tumor/normal mucosa tissue and matched patient-derived xenograft (PDX) models of primary head and neck squamous cell carcinoma (HNSCC) to investigate the preservation of tumor-specific genomic alterations in the in vivo context.

  Study EGAS50000001622

• CEITEC DAC

  A CEITEC Data Access Committee (DAC) is a body of one or more named individuals who are responsible for data release to external requesters. The members of DAC are selected members of research groups and their respective leaders. Multiple datasets may be affiliated to a single DAC. DAC continues communication with requester to understand the purpose of use, i.e. research setting the dataset is envisioned for by requester, to identify if data sharing is possible directly under current conditions for the dataset, or actions such as re-consenting is needed and desirable to accommodate the proposed research setting/data use.

  Dac EGAC50000000049

• Spatiotemporal genomic architecture informs precision oncology in glioblsatoma

  We characterized genomic and expression profiles across 127 multi-sector or longitudinal specimens from 52 glioma patients. We showed that, while samples from nearby geographical location shared similar genomic alterations (clonal or subclonal) and expression signatures, multifocal tumors were seeded from individual clones.

  Study EGAS00001001880

• Resolving_the_Genetic_Architecture_of_Aseptic_Loosening_After_Total_Hip_Replacement

  This is a genome-wide association scan of aseptic loosening after total hip replacement in a Norwegian population. 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 please see http://www.sanger.ac.uk/datasharing/

  Study EGAS00001001883

• Microinjection_of_hIPSC_derived_intestinal_organoids_with_Salmonella_Typhimurium

  To generate an RNA-Seq dataset for organoids apically stimulated with Salmonella Typhimurium.These data are 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/

  Study EGAS00001001253

• Assessment of genomic copy number alterations in breast cancer

  The aim of this study was to assess genomic copy number alterations in a panel of breast cancer cell lines. These data were used to identify common aberrations associated with breast cancer, and also to identify aberrations associated with response to therapeutic compounds.

  Study EGAS00001000585

• ESGI___Molecular_diagnosis_for_mitochondrial_disorders_

  The MITOEXME project aims to improve protocols for molecular diagnosis of patients with OXPHOS disorders with a focus on a next generation sequencing methods and to increase the knowledge of pahtophysiological mechanisms by identification of new targets and cellular studies. In this project we will sequence the exomes fo 120 patients.

  Study EGAS00001000164

• HipSci_RNASEQ_PID

  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 sub-study we perform RNAseq on iPS lines from Platelet and bleeding disorders patients

  Study EGAS00001001990

• Comparison of HCC cell lines and primary HCCs

  There are concerns about whether cancer cell lines could faithfully represent the matched primary cancer cells. Comparison of the HCC cell lines and primary HCCs demonstrated that, during long-term in vitro culture, cell lines retain the genetic landscape of the matched primary HCCs.

  Study EGAS00001001678

• Radiotherapy_induced_Sarcoma_exome

  Whole exome library making will be performed on genomic DNA derived from radiotherapy induced sarcoma samples and matched normal DNA from the same patients. Next Generation sequencing will be performed on the resulting libraries and mapped to build 37 of the human reference genome to facilitate the identification of mutations

  Study EGAS00001000194

• An efficient and comprehensive strategy for genetic diagnostics of polycystic kidney disease

  We established and validated sequence capture based NGS testing approach for all genes known for cystic and polycystic kidney disease including PKD1. This setup overcomes the complication of unspecific capture of pseudogenes by applying a mapping algorithm efficiently and specifically aligning reads to the PKD1 locus.

  Study EGAS00001001003

• Exomes of High-risk Prostate cancer

  DNA extracted from tumoral tissue of 39 patients was used for exome sequencing. As a comparison, DNA extracted from blood was used as a non-tumoral control. DNA was captured using the EZ SeqCap v3 exome kit from Roche and sequenced using an Illumina HiSeq instrument.

  Study EGAS00001001015

• Succession Of Transiently Active Tumour-Initiating Cell Clones inHuman Pancreatic Cancer

  To elucidate whether newly acquired genetic alterations during serial transplantation of patient derived primary pancreatic cancer cultures contribute to the observed clonal dynamics in vivo, all coding genes of two patient derived primary cultures and derived genetically marked serial xenografts (1°/2°/3°) were sequenced.

  Study EGAS00001000882

• WGS-Lung Cancer sample 30 pair

  This study includes 30 paired samples of Korean Lung Cancer paitients. 30 Lung Cancer samples are paired with each normal(Saliva derived for control) sequencing data.The results of this WGS study were analyzed by Mutect and GATK for ranking germline variants and cancer variants to make mutational profile matrix.

  Study EGAS00001001474

• Whole genome sequencing and whole exome sequencing of DIPG tumors and matched normal tissue

  Diffuse Intrinsic Pontine Glioma (DIPG) is a fatal brain cancer that arises in the brainstem of children with no effective treatment. To understand what drives DIPGs we integrated whole-genome-sequencing with methylation, expression and copy-number profiling.

  Study EGAS00001000575

• An exome sequencing pilot study of HIV elite-long term non progressors and rapid progressors

  A pilot study examining genetic determinants associated with elite long term non progression and rapid progression using exome sequencing of individuals at the extremes of the distribution of HIV control and progression. Data can only be used for HIV related research.

  Study EGAS00001000057

• Single cell Transcriptomic Analysis of Cellular Heterogeneity in Human Colorectal Tumors

  1,591 single cells from 11 colorectal cancer patients were profiled using Fluidigm based single cell RNA-seq protocol to characterized cellular heterogeneity of colorectal cancer. 630 single cells from 7 cell lines were profiled similarly to benchmark de novo cell type identification algorithms.

  Study EGAS00001001945

• Tetralogy of Fallot Exome Trios

  Exome sequencing of 30 parent-offspring trios to >50X mean depth, where the offspring has sporadic TOF, to identify potential causal de novo mutations. We will use the exome plus design for pulldown that incorporates ~6.8Mb of additional regulatory sequences in addition to the ~50Mb GENCODE exome.

  Study EGAS00001000071

• Breast_Cancer_Somatic_Genetics_Study_

  We propose to definitively characterise the somatic genetics of ER+ve, HER2-ve 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.

  Study EGAS00001000195

• ENGAGE___Amendment__500_genes_exon_sequencing_

  The ENGAGE project is a FP7 funded EU project aiming to combine genetic and phenotype information from European population based cohorts. In this sub-project we aim to do whole exome sequencing of individuals selected from Health 2000 and FINRISK cohorts. Individuals have been selected based on their metabolic trait phenotypes

  Study EGAS00001000137

• Radiotherapy_induced_sarcoma

  Whole genome library making will be performed on genomic DNA derived from radiotherapy induced sarcoma samples and matched normal DNA from the same patients. Next Generation sequencing will be performed on the resulting libraries and mapped to build 37 of the human reference genome to facilitate the identification of mutations

  Study EGAS00001000138