14982 results for "cancer studies using rna-seq"

in 19.46 milliseconds.

• Genetics of Eating Disorders

  This genetic study examines Anorexia Nervosa, Bulimia Nervosa, and Binge Eating Disorder. We performed whole exome sequencing (WES) on 93 unrelated individuals with eating disorders (38 restricted-eating, 55 binge-eating) to identify novel damaging variants. Using an unbiased, data-driven approach, we prioritized candidate genes with an excessive burden of predicted damaging variants. We then empirically tested one top candidate pathway in a mouse model of binge-like eating. We identified an excess of novel damaging variants in 186 genes in the restricted-eating group and 245 genes in the binge-eating group. The list of genes significantly enriched (OR = 4.6, p

  Study phs001414

• human CMV-specific CD8+ T cells

  In this study we established a comprehensive workflow to collect multi-omics single-cell data using a commercially available micro-well based platform. This included whole transcriptome, cell surface markers (targeted sequencing-based cell surface proteomics), T cell specificities, adaptive immune receptor repertoire (AIRR) profiles and sample multiplexing. With this technique we identified novel paired T cell receptor sequences for three prominent human CMV epitopes. In addition, we review the ability of dCODE dextramers to detect antigenspecific T cells at low frequencies by estimating sensitivities and specificities when used as reagents for single-cell multi-omics.

  Study EGAS50000000633

• Mechanism of Decitabine response in MDS/AML patients

  Myelodysplastic syndrome (MDS) and acute myeloid leukemia (AML) with complex or monosomy karyotype show high prevalence of TP53 mutations (TP53m), poor response to induction chemotherapy and adverse outcome. These diseases may respond to decitabine but the mechanisms are presently unclear. This study investigates MDS/AML patients who were treated with decitabine for 10 days in a Phase II clinical trial. Serial samples were collected from patients before and at completion of decitabine treatment, morphologic remission and relapse. The samples were interrogated using single-cell transcriptomics to investigate potential interactions between leukemic and immune populations."

  Study EGAS50000000924

• Single cell transcriptomics of human kidney organoid endothelium reveals vessel growth processes and arterial maturation upon transplantation

  Human induced pluripotent stem cell-derived kidney organoids have potential for disease modeling and regenerative medicine purposes. However, they lack a functional vasculature in in vitro culture. Here, we transplanted kidney organoids at day 7+12 of differentiation in the coelomic cavity of chicken embryos. We then compared human endothelial cells from transplanted organoids to their respective untransplanted controls at d7+13 and d7+20 using scRNAseq. We demonstrate metabolic and phenotypic effect of transplantation with increased endothelial cell proliferation and differentiation to a fetal-like renal arterial/afferent arteriolar phenotype.

  Study EGAS50000001068

• GenomeAsia 100K Project: Human DNA samples collecting and whole genome sequencing of Asian populations

  The number of basal divergences, admixture, and the degrees of isolation among Indigenous North Eurasian and Native South American populations remain debated, with most insights derived from genome-wide genotyping data. This study aims to improve our understanding of the ancient dynamics and shaping of the contemporary populations of North Eurasia and the Americas. Using large-scale whole-genome sequencing of 1,537 individuals across 139 ethnic groups from these regions, we identify population structures, clarify the prehistoric migrations and the role of past environments in the diversification of human populations.

  Study JGAS000781

• Single-cell transcriptomic data from tumor samples

  Extramedullary multiple myeloma is an aggressive form of multiple myeloma where the myeloma cells escape BM microenvironment and infiltrate distant tissues.We analyse using single cell techniques, the composition and functional state of major immune cells in EMM tumor microenvironment, T and NK cells. This dataset contains the singlecell RNAseq data used in the publication. It includes scRNAseq data from tumor samples across extramedullary multiple myeloma soft tissue (EMM) (n=5; 3 additional samples in the study are under accession numbers mentioned in the publication), EMM bone marrow (EMM_BM) (n=5), and relapsed/refractory multiple myeloma (RRMM_BM) BM (n=6).

  Study EGAS50000001038

• Correction of the cytosine deamination artifacts in FFPE-based sequencing experiments

  Formalin-fixed paraffin-embedded (FFPE) samples are widely used in research and diagnostics, but cytosine deamination during fixation introduces sequencing artifacts, particularly C>T substitutions, which complicate reliable mutation detection. In this study, we systematically evaluated five computational methods and an enzymatic repair approach for FFPE artifact removal, as well as their combined application, using a custom dataset based on whole exome sequencing. Our results demonstrate that while computational strategies improve data quality, the enzymatic approach provides the most effective artifact correction. The study provides guidelines for both computational and enzymatic artifact correction strategies for reliable downstream analyses.

  Study EGAS50000001354

• Adult B-precursor acute lymphoblastic leukemia RoCK and ROI single-cell transcriptome

  Whohle Transcriptome sequencing was performed following the manufactures protocol from BD Rhapsody. Capture of BCR::ABL1 was performed using RoCK and ROI. RoCK and ROI is based on barcoded beads of the BD Rhapsody platform. For RoCKseq specific capture, TSO oligos on BD Rhapsody beads are modified with a/ multiple capture sequence(s) specific to transcripts of interest. ROIseq, on the other hand, is based on specific primers which are spiked in during library generation, directing reads to regions of interest (ROIs). Multiple scRNAseq experiments were performed on several biological samples to validate RoCK and ROI.

  Study EGAS50000001366

• Lethal malformation syndrome

  Identification of the genetic basis of rare monogenic diseases can provide insights into disease mechanisms, biological pathways and potential therapeutic targets. Exome sequencing has proven to be a powerful, efficient strategy for the identification of the genes underlying rare Mendelian disorders. The genetic defect behind the lethal malformation syndrome under study is known in some cases and has proven useful in revealing the primary underlying defect. We have six typical unrelated families with no known mutation. The aim of this study is to identify the locus associated with this lethal malformation syndrome in these families using exome sequencing.

  Study EGAS00001000061

• TSCA-LI amplicon sequencing of called variants in WXS data of DSALL.

  Targeted resequencing of samples was done with TruSeq custom amplicon low input kit (TSCA-LI, Illumina). The oligo capture probes were designed to include a prefix of 8 random nucleotides at the 5 end of each probe. The assay is designed such that each targeted locus is annealed with two probes, resulting in amplicons tagged with unique molecular identifiers (UMI) (22) of 16 bases. Raw FASTQ sequencing files were processed as following: (a) The first 8 bases were trimmed from each read and recorded with the corresponding base quality scores (BQ) in the attribute field. (b) Reads were aligned with BWA. (c) First round of PCR duplicate cleaning was performed with picard tools markDuplicates using the parameters BARCODE_TAG=BC TAGGING_POLICY=All REMOVE_DUPLICATES=true (d) Since in the previous step only duplicate reads with identical UMIs were removed, a second pass of filtering was done. Reads with identical mapping were considered unique only if their corresponding UMIs were different in at least 3 positions (i.e., UMI edit distance > 2). (e) Paired-end read pairs overlapping genomic positions were clipped to avoid overestimation of the sequencing coverage using bamUtils clipOverlap.

  Dataset EGAD00001003275