CD Genomics

Robust identification of perturbed cell types in single-cell RNA-seq data Single-cell RNA-seq experiments often aim to identify cell types that have significant transcriptional differences between two or more biological conditions. Here, authors introduce scDist, a statistical approach to identify perturbed cell types that controls for common confounders in these data. https://lnkd.in/gAJtdMSy

Progress in toxicogenomics to protect human health Toxicogenomics leverages molecular data to predict toxicological effects. In this Review, the authors summarize innovations in transcriptomics and emerging methods, such as single-cell technologies and multi-omics, that offer detailed insights into toxicological mechanisms to enhance hazard prediction and risk assessment. https://lnkd.in/gVGYd_4f

Multi-omic lineage tracing predicts the transcriptional, epigenetic and genetic determinants of cancer evolution Here, using single-cell omics and genomic barcoding, the authors identify transcriptional states and DNA accessibility profiles linked to tumour initiation and drug tolerance, highlighting the complexity of cancer. This study suggests that cancer evolution is driven by pre-encoded factors. https://lnkd.in/gZs9-9-4

Activating the dark genome to illuminate cancer vaccine targets Epigenetic therapy triggers myriad transposable elements to generate new antigens that could prime tumor cells for immunotherapy. A study of glioblastoma discovers indiscriminate activation in healthy cells as well, and presents a more selective strategy for potential therapeutic targeting. https://lnkd.in/gjNB8-xH

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Integrative genotyping of cancer and immune phenotypes by long-read sequencing Single-cell transcriptomics excel in cell subset classification and can be augmented by suitable genotype information. Here the authors devise a long-read sequencing workflow, termed nanoranger, for detection of molecular barcodes from single-cell cDNA and apply this to clonal tracking of acute myeloid leukemia and identification of complex immune phenotypes. https://lnkd.in/gE95N96g

Profiling cell identity and tissue architecture with single-cell and spatial transcriptomics Single-cell and spatial transcriptomics are transforming our understanding of cell plasticity and tissue diversity. This Review discusses technical and computational advancements and challenges in characterizing cell states and tissues during embryogenesis, tumorigenesis and immune responses, and the application of these tools to the clinic. https://lnkd.in/gRX3Ste8

🌟 Transform Your Research with CD Genomics' Single-Cell Isoform Sequencing Service! 🌟 Step into a new era of transcriptomic analysis with our state-of-the-art PacBio MAS-Seq technology. Our innovative approach captures full-length isoforms at the single-cell level, providing unparalleled insights into gene expression and splicing variations. Why Choose CD Genomics? Full-length isoform information, ensuring comprehensive coverage of exonic regions, splice junctions, and UTRs. High throughput sequencing that accelerates research timelines. Precise cell barcode and UMI detection for accurate transcript quantification. Cost-effective solutions for extensive single-cell studies. Streamlined workflows reducing time, cost, and complexity. Applications: Cancer Research: Identify isoform-specific mutations linked to tumorigenesis. Neurobiology: Explore neuronal diversity and detect isoform variations associated with neurological disorders. Plant Genomics: Elucidate complex transcriptomes in diverse species. 🔍 Our rigorous data analysis workflow ensures robust results, from data preprocessing and integration to differential expression and evolutionary trajectory analysis. https://lnkd.in/gRq-Q9dz #SingleCellSequencing #IsoformSequencing #Transcriptomics

Topoisomerase-modulated genome-wide DNA supercoiling domains colocalize with nuclear compartments and regulate human gene expression Here, the authors develop an assay to measure DNA supercoiling, revealing DNA supercoiling domains across the human genome that are modulated by topoisomerase and showing their colocalization with nuclear compartments and impact on gene expression. https://lnkd.in/gNg9R8rj