Improved protocol for single-nucleus RNA-sequencing of frozen human bladder tumor biopsies
Nucleus, 2022 AbstractThis paper provides a laboratory workflow for single-nucleus RNA-sequencing (snRNA-seq) including a protocol for gentle nuclei isolation from fresh frozen tumor biopsies, making it possible to analyze biobanked material. To develop this protocol, we used non-frozen and frozen human bladder tumors and cell lines.
Sofie S. Schmøkel +6 more
openaire +3 more sources
Identifying RNA splicing factors using IFT genes in Chlamydomonas reinhardtii [PDF]
, 2018 Intraflagellar transport moves proteins in and out of flagella/cilia and it is essential for the assembly of these organelles. Using whole-genome sequencing, we identified splice site mutations in two IFT genes,
Dutcher, Susan K. +3 more
core +2 more sources
Understanding and evaluating ambiguity in single-cell and single-nucleus RNA-sequencing
, 2023 Recently, a new modification has been proposed by Hjörleifsson and Sullivanet al. to the model used to classify the splicing status of reads (as spliced (mature), unspliced (nascent), or ambiguous) in single-cell and single-nucleus RNA-seq data. Here, we evaluate both the theoretical basis and practical implementation of the proposed method.
Dongze He, Charlotte Soneson, Rob Patro
openaire +2 more sources
Rainbow Kaposi's Sarcoma-Associated Herpesvirus Revealed Heterogenic Replication with Dynamic Gene Expression. [PDF]
, 2020 Molecular mechanisms of Kaposi's sarcoma-associated herpesvirus (KSHV) reactivation have been studied primarily by measuring the total or average activity of an infected cell population, which often consists of a mixture of both nonresponding and ...
Campbell, Mel +10 more
core
FlsnRNA-seq: protoplasting-free full-length single-nucleus RNA profiling in plants
Genome Biology, 2021 The broad application of single-cell RNA profiling in plants has been hindered by the prerequisite of protoplasting that requires digesting the cell walls from different types of plant tissues. Here, we present a protoplasting-free approach, flsnRNA-seq,
Yanping Long +9 more
doaj +1 more source
A Variable Polyglutamine Repeat Affects Subcellular Localization and Regulatory Activity of a Populus ANGUSTIFOLIA Protein. [PDF]
, 2018 Polyglutamine (polyQ) stretches have been reported to occur in proteins across many organisms including animals, fungi and plants. Expansion of these repeats has attracted much attention due their associations with numerous human diseases including ...
Barry, Kerrie +12 more
core +1 more source
Single-nuclei transcriptomics enable detection of somatic variants in patient brain tissue
Scientific Reports, 2023 Somatic variants are a major cause of human disease, including neurological disorders like focal epilepsies, but can be challenging to study due to their mosaicism in bulk tissue biopsies.
Sydney E. Townsend +6 more
doaj +1 more source
Frontiers in Molecular Neuroscience, 2023 IntroductionOligodendrocyte progenitor cells (OPCs) are vital for neuronal myelination and remyelination in the central nervous system. While the molecular mechanisms involved in OPCs’ differentiation and maturation are not completely understood, GABA is
Berenice A. Gutierrez +4 more
doaj +1 more source
The how and why of lncRNA function: An innate immune perspective. [PDF]
, 2020 Next-generation sequencing has provided a more complete picture of the composition of the human transcriptome indicating that much of the "blueprint" is a vastness of poorly understood non-protein-coding transcripts.
Carpenter, Susan +2 more
core
An unbiased genetic screen reveals the polygenic nature of the influenza virus anti-interferon response. [PDF]
, 2014 Influenza A viruses counteract the cellular innate immune response at several steps, including blocking RIG I-dependent activation of interferon (IFN) transcription, interferon (IFN)-dependent upregulation of IFN-stimulated genes (ISGs), and the activity
Asensio, VJ +7 more
core +2 more sources