23164 results for "ega"

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• 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

• Error-corrected targeted sequencing of rectal mucus from patients suspected to have colorectal cancer

  This dataset contains error-corrected next-generation sequencing (ecNGS) data generated from 161 rectal mucus samples. These samples belong to colorectal cancer, adenoma, and control participants. Genomic DNA was extracted and processed using a hybrid-capture panel targeting 50 colorectal cancer–associated genes, incorporating unique molecular identifiers (UMIs) for duplex consensus error correction. Libraries were sequenced on an Illumina NovaSeq 6000 (paired-end 150 bp) producing paired-end FASTQ files. These data support analyses of DNA mutations in CRC detection and progression.

  Dataset EGAD50000002032