22940 results for "ega"

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• Sequencing data for oesophageal and related samples - Ng, Contino et al (WGS)

  Data supporting "Interplay of processes shapes structural variations undergoing selection in oesophageal adenocarcinoma" Ng, Contino et al. WGS (BAM files) 383 oesophageal adenocarcinoma samples 383 normal samples

  Dataset EGAD00001007808

• Single-cell transcriptome landscape of developing fetal gonads defines somatic cell lineage specification in humans

  Single-cell RNA-seq dataset recovering the gene expression programs of around 128,000 single cells derived from 17 fetal testes and 16 fetal ovaries from 5 to 12 postconceptional weeks.

  Dataset EGAD00001009811

• Chronic lymphocytic leukemia IGHV somatic hypermutation detection by targeted capture next-generation sequencing

  FASTQ and BAM files for 46 samples (consisting of 35 samples for patients diagnosed with CLL, 5 samples consisting of a dilution series of patient DNA, and 6 samples of cell lines and dilutions involving the cell lines) from targeted capture next-generation sequencing from the LySeq panel. Libraries were sequenced on either Illumina HiSeq 2500 (LySeq66 PoP, R1-3) or Illumina NovaSeq 6000 (LySeq66 Validation Round).

  Dataset EGAD00001009828

• GELATO clinical trial RNA-Seq data (metastatic lesions)

  RNA-Seq data of 46 matched lobular breast cancer metastatic samples obtained from 21 unique patients from GELATO clinical trial assayed at three timepoints: at baseline (directly after patient randomization), pre-atezolizumab (after induction treatment with carboplatin for two weeks) and on atezolizumab (after two cycles of atezolizumab combined with carboplatin). The included raw transcriptome sequencing data in fastq format was generated using Illumina NovaSeq 6000 from fresh frozen material.

  Dataset EGAD00001009834

• Single-nucleus Transcriptome of Down Syndrome Brains (short-read)

  29 DS and Control brain samples were prepared using the 10X Genomics Single Cell 3' v3 kit. The cDNA libraries were sequenced on an Illumina Novaseq 6000.

  Dataset EGAD00001008287

• Osteosarcoma sequencing data

  This dataset contains samples from 13 patients with osteosarcoma. 13 samples have whole exome tumor data. 12 samples have tumor RNAseq data. 3 samples have matched normal dna sequence data

  Dataset EGAD00001008117

• Single cell sequencing on whole bone marrow of NBM and AML

  To generate a cellular taxonomy of the human NBM and AML, representing both rare hematopoietic stem/progenitor cells (HSPCs) and stromal niche populations, allowing assessment of their cellular diversity and predicted intercellular signaling, we performed single cell RNA sequencing (scRNAseq) on viably frozen bone marrow (BM) aspirates from four healthy donors and 6 NPM1+ AML patients at diagnosis

  Dataset EGAD00001011057

• ATAC-seq data from primary AML samples with t(3;8)

  Open chromatin regions in the MYC super-enhancer region were investigated by ATAC-seq in t(3;8) AML. ATAC-seq was performed as described (Buenrostro et al, 2013) with a modification in the lysis buffer (0.30 M sucrose, 10 mM Tris pH 7.5, 60 mM KCl, 15 mM NaCl, 5 mM MgCl2, 0.1 mM EGTA, 0.1% NP40, 0.15 mM Spermine, 0.5 mM Spermidine, 2 mM 6AA) to reduce mitochondrial DNA contamination.

  Dataset EGAD00001007910

• WGS data from LCNEC patient derived tumor organoids (PDTOs) and matched parental tumors - SA

  The dataset includes cram files from WGS of 2 LCNEC tumors and matched PDTOs. For all tumors, cram files from WGS of matched normal tissue derived organoids from the corresponding patients is included. Analysis VCF files are also included in the dataset. The sequencing was done with a NovaSeq 6000 instrument.

  Dataset EGAD00001009990

• RNA-seq derived from metastatic Castration-Resistant Prostate Cancer

  Patients with progressive, metastatic castration-resistant prostate cancer (mCRPC) underwent metastatic tumor biopsy. 118 total samples including 14 paired samples (baseline and later progression). Various organ sites including soft tissue & bone were present. Published in DOI: 10.1200/JCO.2017.77.6880 Journal of Clinical Oncology 36, no. 24 (August 20, 2018) 2492-2503.

  Dataset EGAD00001008991

• RRBS data for solid tumors and adjacent normal tissues

  RRBS data for solid tumors and adjacent normal tissues

  Dataset EGAD00001009001

• Multiple myeloma follow-up Dataset

  77 samples collected from 35 multiple myeloma patients. Each patient provided one healthy sample and one primary tumor sample and, in some cases, also samples collected after the progression of the disease.

  Dataset EGAD00001010161

• Whole exome data from PMID27216186

  This dataset comprises complete exome data from from the study PMID27216186 (Harbst & Lauss et al, Cancer Research 2016). These data are from 49 samples (tumor and matched normal) from 8 patients representing multi-region sequencing of human melanoma. Files are in the BAM format and contain aligned and processed data used for e.g. somatic variant calling. The sequencing libraries were constructed using SureSelect target enrichment with Clinical Research Exome Panel (Agilent) and sequenced on a HiSeq2500 (Illumina).

  Dataset EGAD00001008149

• Genetic determinants of monocyte splicing are enriched for disease susceptibility loci including for COVID-19

  These data correspond to samples used in the following papers: 1. GWAS and meta-analysis identifies 49 genetic variants underlying critical Covid-19 2. Genetic determinants of monocyte splicing are enriched for disease susceptibility loci including for COVID-19. 3. Identification of Genetic Determinants of Transcriptional Response to Metformin in Primary Human Monocytes. They are the raw RNA sequencing files as used in all downstream analysis.

  Dataset EGAD00001010176

• Comparison of the antiviral immune response between individuals of Indian and European origin

  We purified peripheral blood mononuclear cells from individuals living in India (N=10) and the Netherlands (N=10) at baseline and 10-12 weeks after BCG vaccination. We compared chromatin accessibility between the two populations at baseline, as well as gene transcription profiles and cytokine production capacities upon viral stimulation with influenza and SARS-CoV-2

  Dataset EGAD00001009079

• RNAseq Iron-Treated iPSC-derived Microglia

  Iron accumulation in microglia has been observed in Alzheimer’s disease and other neurodegenerative disorders and is thought to contribute to disease progression through various mechanisms including neuroinflammation. To study the interaction between iron accumulation and inflammation, we treated human induced pluripotent stem cell-derived microglia (iPSC-MG) with an increasing concentration of iron, in combination with inflammatory stimuli such as interferon gamma and amyloid β, and performed RNA sequencing.

  Dataset EGAD00001008660

• XP patients NGS data collection from Gustave Roussy.

  This dataset is composed of NGS data from 33 XP patients studied by WGS.

  Dataset EGAD00001009693

• Colorectal cancer samples WES

  The whole exome was sequenced in two cancer-affected members (II:1 and III:1) of the family. The family subject of this study showed an autosomal dominant mode of CRC inheritance, fulfilling the Amsterdam I clinical criteria with three CRCs in two consecutive generations. The exome capture was performed using SureSelectXT Human All Exon V3 (51Mb, Agilent Technologies), and the library was sequenced on an Illumina HiSeq 2000 platform with paired-end reads of 101bp and a 50x average coverage depth.

  Dataset EGAD00001009170

• Paired-WGS Sequencing of Primary lymphomas of the central nervous system (PCNSL)

  Paired WGS samples, 24 tumor/control pairs of primary CNS lymphoma, sequenced on HiSeq X Ten using Illumina TruSeq Nano DNA for library preparation.

  Dataset EGAD00001007810

• Methylation profiling of human lung fibroblasts in COPD

  Primary lung fibroblast were isolated from well-matched control donors (no COPD, n=3) and patients with COPD (GOLD stage I-IV, n=8). Genomic DNA of cultured human lung fibroblast was isolated at passage 3, fragmented by tagmentation, and subjected to bisulfite treatment. 100 bp paired-end reads were generated from DNA libraries on Illumina HiSeq2500 platform.

  Dataset EGAD00001009406