3994 results for "*geneti*"

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• Ultra-long whole-genome and Cas9-targeted nanopore sequencing of fibroblasts: FSHD, BAMS, healthy controls

  Data from the D4Z4End2End study (Xiao et al. 2025), for genetic and epigenetic analysis of the D4Z4 macrosatellite in health and disease.

  Dataset EGAD50000001551

• MorphoITH: A Framework for Deconvolving Intra-Tumor Heterogeneity Using Tissue Morphology

  The ccRCC-ITH study WES dataset is derived from a morphology guided multi-regional sequencing dataset used to study the relationship between morphology and genetic evolution. It contains whole exome sequencing data of 18 tumor and 2 adjacent normal samples from 2 UTSW patients, who have consented to depositing their genomic data to public repository. Tumor samples come from different tumor sites, including primary tumor, thrombus and metastases. WES was performed using 75bp paired-end fragments at an average read depth > 50x on a NovaSeq 6000 platform (Illumina, San Diego, CA, USA). The raw data is in fastq format.

  Dataset EGAD50000001550

• Head and Neck Organoid Biobank cohort, Issing et. al., 2025, RNA + WES data

  This dataset contains the raw fastq files of RNA and whole exome sequencing of the head and neck organoid biobank. For RNA sequencing, 41 organoid samples collected at different timepoints as well as before and after genetic modification are included. For WES, 25 samples of early organoid cultures or matching tumor tissues are included.

  Dataset EGAD50000001733

• Genetically unique biospecimens derived from individuals with or without Type 1 Diabetes

  In this dataset, samples correspond to pools of genetically unique biospecimens derived from individuals with or without Type 1 Diabetes. Each sample alias contains all the DNA test numbers for that pool. Each experiment corresponds to scmxGEX (multiome RNA gene expression), scmxATAC (multiome ATAC sequencing), scRNA (single cell RNA sequencing), scATAC (single cell ATAC sequencing) for each pool. Runs link the appropriate fastq files to each experiment. Deconvolution using genetic information is required for single sample-based testing.

  Dataset EGAD50000001257

• Anti-MPO BCR sequences described in 'Anti-myeloperoxidase IgM B cells in anti-neutrophil cytoplasmic antibody-associated vasculitis'

  FASTA files from quality-checked Sanger Sequencing results from BCR-specific PCR products. B cells from 4 different MPO+ AAV patients were single cell sorted and processed to sequence the specific BCR, resulting in 51, 175, 12 and 3 heavy chain BCR sequences for AAV1, 2, 3, and 5 respectively. Sequence names indicate patient ID and isotype (IgG, IgM or IgA).

  Dataset EGAD50000001112

• WES of serrated polyposis syndrome

  Samples were obtained from patients diagnosed with serrated polyposis syndrome (SPS). To provide further detail, the dataset comprises two whole-exome sequencing samples from patients within the same family, uploaded in BAM file format with IDs 449758 and 449549. Exomic regions were sequenced using HiSeq2000 Platform (Illumina, San Diego, USA) and Sure SelectXT All Exon v5 kit (Agilent, Santa Clara, CA, USA) for exon enrichment. Only those potentially pathogenic germline genetic variants shared by both individuals were considered.

  Dataset EGAD50000001126

• Replication data for RNA-SEQUENCING: A RELIABLE TOOL TO UNVEIL TRANSCRIPTIONAL LANDSCAPE OF PAEDIATRIC B-OTHER ACUTE LYMPHOBLASTIC LEUKAEMIA

  This dataset contains the raw data of the RNA-seq experiments described in the paper "RNA-Sequencing: a reliable tool to unveil transcriptional landscape of pediatric B-other acute lymphoblastic leukemia" It contains the raw data from 60 pediatric patients diagnosed with B cell progenitor acute lymphoblastic leukemia lacking the main genetic alterations. RNA material was extracted from bone marrow or periphereal blood and RNA libraries were prepared using Illumina® TruSeq™ stranded mRNA kit following manufacturer's instructions and were sequenced in a NextSeq 550 using a v2 HighOutput 150 cycle kit 2x75bp. Funding: Instituto de Salud Carlos III (ISCIII), PI21/00213 

  Dataset EGAD50000000981

• Whole genome sequencing of childhood acute lymphoblastic leukaemia patients

  Whole genome sequencing of childhood acute lymphoblastic leukaemia patients. Matched diagnostic and germline samples were obtained from bone marrow aspirates and sequenced on the Illumina platform to characterise the underlying genetic features (DOI: 10.1038/s41375-022-01806-8).

  Dataset EGAD50000000975

• cytogenetically visibile inversions

  Pacbio Hifi whole genome sequencing data from six individuals carrying cytogenetically visible inversions. The HiFi data was produced on the PacBio Revio machine, using 1 flowcell per sample. The resulting data was aligned to hg19 using minimap2, and converted into bam using samtools.

  Dataset EGAD50000000635

• 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

• Indonesian Genome Diversity Project 3

  Low coverage whole genome sequences (1-3x) were collected to study human genetic history across Wallacea archipelago and West Papuan Region of Indonesia . We collected 254 newly sequenced genomes mostly from previously undocumented populations including 9 communities in Wallacea and 3 in West Papuan regions. Out of 254, there are 8 high coverage whole genome sequences were produce in the study (L4).

  Dataset EGAD50000000647

• Plasma mutation profile of precursor lesions and colorectal cancer using the Oncomine Colon cfDNA Assay

  Colorectal cancer (CRC) is the second leading cause of cancer death worldwide. Early detection of precursor lesions or early-stage cancer could hamper cancer development or improve survival rates. Liquid biopsy, which detects tumor biomarkers, such as mutations, in blood, is a promising avenue for cancer screening. To assess the presence of genetic variants in plasma cell-free tumor DNA from patients with precursor lesions and colorectal cancer using the commercial Oncomine Colon cfDNA Assay. Cell-free DNA (cfDNA) samples from the blood plasma of 52 Brazilian patients were analyzed. Eight patients did not have any significant lesions (five normal colonoscopies and three hyperplastic polyps), 24 exhibited precursor lesions (13 nonadvanced adenomas, ten advanced adenomas, and one sessile serrated lesion), and 20 patients with cancer (CRC). The mutation profile of 14 CRC-associated genes were determined by next-generation sequencing (NGS) using the Oncomine Colon cfDNA Assay in the Ion Torrent PGM/S5 sequencer.

  Dataset EGAD50000000679

• Genetic subtyping by Whole Exome Sequencing across Diffuse Large B Cell Lymphoma and Plasmablastic Lymphoma.

  Whole exome sequencing was performed from 108 Diffuse Large B Cell Lymphoma cases. A library containing whole exome regions was used to isolate the DNA for sequencing (SureSelect XT Human All Exon V6 (Agilent technologies)). Sequencing on a NovaSeq 6000 instrument (Illumina, paired end, 2x100, mean 566Gb per FlowCell) was performed.

  Dataset EGAD50000000546

• Label-free single-cell RNA Multiplexing leveraging Genetic Variability

  SNP-based demultiplexing of single-cell RNA-seq data

  Dataset EGAD50000000928

• scKaryoSeq of CRISPR-Cas9 edited primary human T cells

  To explore T cell-intrinsic driving forces of CRISPR-induced aneuploidy at the TRAC gene locus, we performed scKaryo-seq (Bolhaqueiro et al., Nature Genetics 2019). We compared the impact of the small molecule pifithrin-alpha in activated TRAC KO T cells. In a separate experiment, we determined the effect of pifithrin-alpha on non-activated T cells edited at the TRAC locus or treated with non-targeting Cas9 RNPs.

  Dataset EGAD50000000929

• 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

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

  This file set has 1478 Greenlandic individuals scored on the Illumina MEGA array (1,748,250 sites). The data is in PLINK bed/bim/fam format. The individuals originate from the B2018 population survey.

  Dataset EGAD50000000934

• IκBε deficiency accelerates disease development in chronic lymphocytic leukemia

  The NFKBIE gene, which encodes the NF-κB inhibitor IκBε, is mutated in 3-7% of patients with chronic lymphocytic leukemia (CLL). The most recurrent alteration is a 4-bp frameshift deletion associated with NF-κB activation in leukemic B cells and poor clinical outcome. To study the functional consequences of NFKBIE gene inactivation, both in vitro and in vivo, we engineered CLL B cells and CLL-prone mice to stably down-regulate NFKBIE expression and investigated its role in controlling NF-κB activity and disease expansion. We found that IκBε loss leads to NF-κB pathway activation and promotes both migration and proliferation of CLL cells in a dose-dependent manner. Importantly, NFKBIE inactivation was sufficient to induce a more rapid expansion of the CLL clone in lymphoid organs and contributed to the development of an aggressive disease with a shortened survival in both xenografts and genetically modified mice. IκBε deficiency was associated with an alteration of the MAPK pathway, also confirmed by RNA-sequencing in NFKBIE-mutated patient samples, and resistance to the BTK inhibitor ibrutinib. In summary, our work underscores the multimodal relevance of the NF-κB pathway in CLL and paves the way to translate these findings into novel therapeutic options.

  Dataset EGAD50000000754

• Long-read whole-genome sequencing-based concurrent haplotype phasing and aneuploidy profiling of single cells

  This dataset contains long-read whole-genome sequencing (lrWGS) data from 14 samples. Five lrWGS data are from single-cell (sc, sc_2, sc_3), multi-cell (mc, 10 cells), and bulk samples of HG002. The remaining nine lrWGS data are from two preimplantation genetic testing (PGT) families, including four from blood bulk DNA of the parental pairs and five from trophectoderm biopsies of two embryos from one family and three embryos from another family. The data are provided in raw FASTQ format and were generated using the PromethION device from Oxford Nanopore Technologies.

  Dataset EGAD50000000787

• A genome-wide CRISPR screen identifies CALCOCO2 as a regulator of beta cell function influencing type 2 diabetes risk

  Identification of the genes and processes mediating genetic association signals for complex diseases represents a major challenge. As many of the genetic signals for type 2 diabetes (T2D) exert their effects through pancreatic islet-cell dysfunction, we performed a genome-wide pooled CRISPR loss-of-function screen in a human pancreatic beta cell line. We assessed the regulation of insulin content as a disease-relevant readout of beta cell function and identified 580 genes influencing this phenotype. Integration with genetic and genomic data provided experimental support for 20 candidate T2D effector transcripts including the autophagy receptor CALCOCO2. Loss of CALCOCO2 was associated with distorted mitochondria, less proinsulin-containing immature granules and accumulation of autophagosomes upon inhibition of late-stage autophagy. Carriers of T2D-associated variants at the CALCOCO2 locus further displayed altered insulin secretion. Our study highlights how cellular screens can augment existing multi-omic efforts to support mechanistic understanding and provide evidence for causal effects at genome-wide association studies loci.

  Dataset EGAD50000000518

• Inferring causal genes at type 2 diabetes GWAS loci through chromosome interactions in islet cells

  Resolving causal genes for type 2 diabetes at loci implicated by genome-wide association studies (GWAS) requires integrating functional genomic data from relevant cell types. Chromatin features in endocrine cells of the pancreatic islet are particularly informative and recent studies leveraging chromosome conformation capture (3C) with Hi-C based methods have elucidated regulatory mechanisms in human islets. However, these genome-wide approaches are less sensitive and afford lower resolution than methods that target specific loci. Methods: To gauge the extent to which targeted 3C further resolves chromatin-mediated regulatory mechanisms at GWAS loci, we generated interaction profiles at 23 loci using next-generation (NG) capture-C in a human beta cell model (EndoC-βH1) and contrasted these maps with Hi-C maps in EndoC-βH1 cells and human islets and a promoter capture Hi-C map in human islets. Results: We found improvements in assay sensitivity of up to 33-fold and resolved ~3.6X more chromatin interactions. At a subset of 18 loci with 25 co-localised GWAS and eQTL signals, NG Capture-C interactions implicated effector transcripts at five additional genetic signals relative to promoter capture Hi-C through physical contact with gene promoters. Conclusions: High resolution chromatin interaction profiles at selectively targeted loci can complement genome- and promoter-wide maps.

  Dataset EGAD50000000517

• Raw NGS data of primary AML samples

  Raw NGS data of primary Acute Myeloid Leukemia samples. The libraries were obtained with Sophia Genetics Myeloid Solution kit, targeting 30 genes involved in AML.

  Dataset EGAD50000000506

• Epigenetic memory of SARS-CoV-2 mRNA vaccination in monocyte-derived macrophages

  Immune memory is key to effective antimicrobial responses, but the impact of mRNA vaccines on this process is not fully understood. Our research shows that SARS-CoV-2 mRNA vaccines alter the epigenetic profile of human macrophages, specifically enhancing histone acetylation, which is linked to immune training. Significant epigenetic changes, along with increased cytokine release, require two vaccine doses. However, these effects diminish over time but can be restored with a booster dose six months later, maintaining a strong pro-inflammatory response.

  Dataset EGAD50000000495

• Highly complex single-cell mixture of 5 individuals of high cell number

  Mixture of 5 unrelated individuals sequenced by 10x as a scATAC-seq. The dataset was then processed by Cell Ranger and deconvoluted to yield each individuals genetic profile using the De-goulash pipeline. The separation file is submitted as the processed file. The bam are submitted as unprocessed files.

  Dataset EGAD50000000480

• Highly complex single-cell mixture of 5 individuals of low cell number

  Mixture of 5 unrelated individuals sequenced by 10x as a scATAC-seq with low cell count. The dataset was then processed by Cell Ranger and deconvoluted to yield each individuals genetic profile using the De-goulash pipeline. The separation file is submitted as the processed file. The bam are submitted as unprocessed files.

  Dataset EGAD50000000479