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87 results for “RNA sequencing”

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  1. Wastewater sequencing reveals early cryptic SARS-CoV-2 variant transmission.

    Nature · 2022 · 609(7925): 101-108

    As SARS-CoV-2 continues to spread and evolve, detecting emerging variants early is critical for public health interventions. Inferring lineage prevalence by clinical testing is infeasible at scale, especially in areas with limited resources, participation, or testing and/or sequencing capacity, which …

    PMID 35798029 DOI ↗

  2. MECP2-related pathways are dysregulated in a cortical organoid model of myotonic dystrophy.

    Science translational medicine · 2022 · 14(651): eabn2375

    Myotonic dystrophy type 1 (DM1) is a multisystem, autosomal-dominant inherited disorder caused by CTG microsatellite repeat expansions (MREs) in the 3' untranslated region of the dystrophia myotonica-protein kinase (<i>DMPK</i>) gene. Despite its prominence as the most common adult-onset muscular dystrophy, …

    PMID 35767654 DOI ↗

  3. SARS-CoV-2 Distribution in Residential Housing Suggests Contact Deposition and Correlates with <i>Rothia</i> sp.

    mSystems · 2022 · 7(3): e0141121

    Monitoring severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) on surfaces is emerging as an important tool for identifying past exposure to individuals shedding viral RNA. Our past work demonstrated that SARS-CoV-2 reverse transcription-quantitative PCR (RT-qPCR) signals from surfaces can identify …

    PMID 35575492 DOI ↗

  4. Transcriptome-wide identification of RNA-binding protein binding sites using seCLIP-seq.

    Nature protocols · 2022 · 17(5): 1223-1265

    Discovery of interaction sites between RNA-binding proteins (RBPs) and their RNA targets plays a critical role in enabling our understanding of how these RBPs control RNA processing and regulation. Cross-linking and immunoprecipitation (CLIP) provides a generalizable, transcriptome-wide method by which …

    PMID 35322209 DOI ↗

  5. Wastewater sequencing uncovers early, cryptic SARS-CoV-2 variant transmission.

    medRxiv : the preprint server for health sciences · 2022

    As SARS-CoV-2 continues to spread and evolve, detecting emerging variants early is critical for public health interventions. Inferring lineage prevalence by clinical testing is infeasible at scale, especially in areas with limited resources, participation, or testing/sequencing capacity, which can also …

    PMID 35411350 DOI ↗

  6. Crosstalk between CRISPR-Cas9 and the human transcriptome.

    Nature communications · 2022 · 13(1): 1125

    CRISPR-Cas9 expression independent of its cognate synthetic guide RNA (gRNA) causes widespread genomic DNA damage in human cells. To investigate whether Cas9 can interact with endogenous human RNA transcripts independent of its guide, we perform eCLIP (enhanced CLIP) of Cas9 …

    PMID 35236841 DOI ↗

  7. Integrative RNA-omics Discovers GNAS Alternative Splicing as a Phenotypic Driver of Splicing Factor-Mutant Neoplasms.

    Cancer discovery · 2022 · 12(3): 836-855

    Mutations in splicing factors (SF) are the predominant class of mutations in myelodysplastic syndrome (MDS), but convergent downstream disease drivers remain elusive. To identify common direct targets of missplicing by mutant U2AF1 and SRSF2, we performed RNA sequencing and enhanced …

    PMID 34620690 DOI ↗

  8. SARS-CoV-2 Distribution in Residential Housing Suggests Contact Deposition and Correlates with <i>Rothia</i> sp.

    medRxiv : the preprint server for health sciences · 2021

    Monitoring severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) on surfaces is emerging as an important tool for identifying past exposure to individuals shedding viral RNA. Our past work has demonstrated that SARS-CoV-2 reverse transcription-quantitative PCR (RT-qPCR) signals from surfaces can …

    PMID 34909793 DOI ↗

  9. Gain-of-function cardiomyopathic mutations in RBM20 rewire splicing regulation and re-distribute ribonucleoprotein granules within processing bodies.

    Nature communications · 2021 · 12(1): 6324

    Mutations in the cardiac splicing factor RBM20 lead to malignant dilated cardiomyopathy (DCM). To understand the mechanism of RBM20-associated DCM, we engineered isogenic iPSCs with DCM-associated missense mutations in RBM20 as well as RBM20 knockout (KO) iPSCs. iPSC-derived engineered heart …

    PMID 34732726 DOI ↗

  10. Persistent mRNA localization defects and cell death in ALS neurons caused by transient cellular stress.

    Cell reports · 2021 · 36(10): 109685

    Persistent cytoplasmic aggregates containing RNA binding proteins (RBPs) are central to the pathogenesis of late-onset neurodegenerative disorders such as amyotrophic lateral sclerosis (ALS). These aggregates share components, molecular mechanisms, and cellular protein quality control pathways with stress-induced RNA granules (SGs). …

    PMID 34496257 DOI ↗

  11. Inhibition of YTHDF2 triggers proteotoxic cell death in MYC-driven breast cancer.

    Molecular cell · 2021 · 81(15): 3048-3064.e9

    RNA-binding proteins (RBPs) are critical regulators of post-transcriptional gene expression, and aberrant RBP-RNA interactions can promote cancer progression. Here, we interrogate the function of RBPs in cancer using pooled CRISPR-Cas9 screening and identify 57 RBP candidates with distinct roles in …

    PMID 34216543 DOI ↗

  12. Robust single-cell discovery of RNA targets of RNA-binding proteins and ribosomes.

    Nature methods · 2021 · 18(5): 507-519

    RNA-binding proteins (RBPs) are critical regulators of gene expression and RNA processing that are required for gene function. Yet the dynamics of RBP regulation in single cells is unknown. To address this gap in understanding, we developed STAMP (Surveying Targets …

    PMID 33963355 DOI ↗

  13. The sustained expression of Cas9 targeting toxic RNAs reverses disease phenotypes in mouse models of myotonic dystrophy type 1.

    Nature biomedical engineering · 2021 · 5(2): 157-168

    Myotonic dystrophy type I (DM1) is a multisystemic autosomal-dominant inherited human disorder that is caused by CTG microsatellite repeat expansions (MREs) in the 3' untranslated region of DMPK. Toxic RNAs expressed from such repetitive sequences can be eliminated using CRISPR-mediated …

    PMID 32929188 DOI ↗

  14. Repeat RNA expansion disorders of the nervous system: post-transcriptional mechanisms and therapeutic strategies.

    Critical reviews in biochemistry and molecular biology · 2021 · 56(1): 31-53

    Dozens of incurable neurological disorders result from expansion of short repeat sequences in both coding and non-coding regions of the transcriptome. Short repeat expansions underlie microsatellite repeat expansion (MRE) disorders including myotonic dystrophy (DM1, CUG<sub>50-3,500</sub> in <i>DMPK</i>; DM2, CCTG<sub>75-11,000</sub> in …

    PMID 33172304 DOI ↗

  15. Transcriptome-wide profiles of circular RNA and RNA-binding protein interactions reveal effects on circular RNA biogenesis and cancer pathway expression.

    Genome medicine · 2020 · 12(1): 112

    Circular RNAs (circRNAs) are stable, often highly expressed RNA transcripts with potential to modulate other regulatory RNAs. A few circRNAs have been shown to bind RNA-binding proteins (RBPs); however, little is known about the prevalence and distribution of these interactions …

    PMID 33287884 DOI ↗

  16. The <i>Thermus thermophilus</i> DEAD-box protein Hera is a general RNA binding protein and plays a key role in tRNA metabolism.

    RNA (New York, N.Y.) · 2020 · 26(11): 1557-1574

    RNA helicases catalyze the ATP-dependent destabilization of RNA duplexes. DEAD-box helicases share a helicase core that mediates ATP binding and hydrolysis, RNA binding and unwinding. Most members of this family contain domains flanking the core that can confer RNA substrate …

    PMID 32669294 DOI ↗

  17. Evaluation of Engineered CRISPR-Cas-Mediated Systems for Site-Specific RNA Editing.

    Cell reports · 2020 · 33(5): 108350

    Site-directed RNA editing approaches offer great potential to correct genetic mutations in somatic cells while avoiding permanent off-target genomic edits. Nuclease-dead RNA-targeting CRISPR-Cas systems recruit functional effectors to RNA molecules in a programmable fashion. Here, we demonstrate a Streptococcus pyogenes …

    PMID 33147453 DOI ↗

  18. Transcriptome-wide analysis of PGC-1α-binding RNAs identifies genes linked to glucagon metabolic action.

    Proceedings of the National Academy of Sciences of the United States of America · 2020 · 117(36): 22204-22213

    The peroxisome proliferator-activated receptor gamma coactivator 1-alpha (PGC-1α) is a transcriptional coactivator that controls expression of metabolic/energetic genes, programming cellular responses to nutrient and environmental adaptations such as fasting, cold, or exercise. Unlike other coactivators, PGC-1α contains protein domains involved …

    PMID 32848060 DOI ↗

  19. Heterogeneity and clonal relationships of adaptive immune cells in ulcerative colitis revealed by single-cell analyses.

    Science immunology · 2020 · 5(50)

    Inflammatory bowel disease (IBD) encompasses a spectrum of gastrointestinal disorders driven by dysregulated immune responses against gut microbiota. We integrated single-cell RNA and antigen receptor sequencing to elucidate key components, cellular states, and clonal relationships of the peripheral and gastrointestinal …

    PMID 32826341 DOI ↗

  20. A role for alternative splicing in circadian control of exocytosis and glucose homeostasis.

    Genes & development · 2020 · 34(15-16): 1089-1105

    The circadian clock is encoded by a negative transcriptional feedback loop that coordinates physiology and behavior through molecular programs that remain incompletely understood. Here, we reveal rhythmic genome-wide alternative splicing (AS) of pre-mRNAs encoding regulators of peptidergic secretion within pancreatic …

    PMID 32616519 DOI ↗

  21. Suppression of Endothelial AGO1 Promotes Adipose Tissue Browning and Improves Metabolic Dysfunction.

    Circulation · 2020 · 142(4): 365-379

    Metabolic disorders such as obesity and diabetes mellitus can cause dysfunction of endothelial cells (ECs) and vascular rarefaction in adipose tissues. However, the modulatory role of ECs in adipose tissue function is not fully understood. Other than vascular endothelial growth …

    PMID 32393053 DOI ↗

  22. Heterogenous Populations of Tissue-Resident CD8<sup>+</sup> T Cells Are Generated in Response to Infection and Malignancy.

    Immunity · 2020 · 52(5): 808-824.e7

    Tissue-resident memory CD8<sup>+</sup> T cells (Trm) provide host protection through continuous surveillance of non-lymphoid tissues. Using single-cell RNA-sequencing (scRNA-seq) and genetic reporter mice, we identified discrete lineages of intestinal antigen-specific CD8<sup>+</sup> T cells, including a Blimp1<sup>hi</sup>Id3<sup>lo</sup> tissue-resident effector cell population …

    PMID 32433949 DOI ↗

  23. Early precursors and molecular determinants of tissue-resident memory CD8<sup>+</sup> T lymphocytes revealed by single-cell RNA sequencing.

    Science immunology · 2020 · 5(47)

    During an immune response to microbial infection, CD8<sup>+</sup> T cells give rise to distinct classes of cellular progeny that coordinately mediate clearance of the pathogen and provide long-lasting protection against reinfection, including a subset of noncirculating tissue-resident memory (T<sub>RM</sub>) cells …

    PMID 32414833 DOI ↗

  24. An in vivo genome-wide CRISPR screen identifies the RNA-binding protein Staufen2 as a key regulator of myeloid leukemia.

    Nature cancer · 2020 · 1(4): 410-422

    Aggressive myeloid leukemias such as blast crisis chronic myeloid leukemia and acute myeloid leukemia remain highly lethal. Here we report a genome-wide in vivo CRISPR screen to identify new dependencies in this disease. Among these, RNA-binding proteins (RBPs) in general, …

    PMID 34109316 DOI ↗

  25. Direct RNA sequencing enables m<sup>6</sup>A detection in endogenous transcript isoforms at base-specific resolution.

    RNA (New York, N.Y.) · 2020 · 26(1): 19-28

    Direct RNA sequencing holds great promise for the de novo identification of RNA modifications at single-coordinate resolution; however, interpretation of raw sequencing output to discover modified bases remains a challenge. Using Oxford Nanopore's direct RNA sequencing technology, we developed a …

    PMID 31624092 DOI ↗

Datasets 22

GSE315443 GSE · GEO

MBNL2 dysfunction in outer radial glial cells is associated with disrupted corticogenesis in congenital myotonic dystrophy [scRNA-Seq]

GPL24676

GSE92602 GSE · GEO

Identification of islet-enriched long non-coding RNAs contributing to beta-cell failure in type 2 diabetes

Mus musculus · GPL9250

GSE114922 GSE · GEO

RNA sequencing of bone marrow CD34+ hematopoietic stem and progenitor cells from patients with myelodysplastic syndrome and healthy controls

Homo sapiens · GPL20301

GSE63816 GSE · GEO

Aberrant splicing of U12-type introns is the hallmark of ZRSR2 mutant myelodysplastic syndrome

Homo sapiens · GPL11154

GSE157072 GSE · GEO

RNA-Seq of CD8+ T cell subsets during LCMV infection III

Mus musculus · GPL17021

GSE65973 GSE · GEO

RNA sequencing of mice expressing NLS-hTDP-43

Mus musculus · GPL9250

GSE162335 GSE · GEO

Transcriptional Survey of Ileal-Anal Pouch Immune Cells from Ulcerative Colitis

Homo sapiens · GPL20301

GSE107122 GSE · GEO

Developmental emergence of adult neural stem cells as revealed by single cell transcriptional profiling

Mus musculus · GPL19057

GSE145968 GSE · GEO

CRISPR/Cas9 screening of RNA binding proteins (RBPs) that regulate RUNX1 isoform production

Homo sapiens · GPL20301

GSE109423 GSE · GEO

A transcriptome-wide divergence in protein translation scales with LIN28B expression

Mus musculus · GPL20301

GSE217735 GSE · GEO

Epigenetics CRISPRi screen in mouse neuronal progenitor cells (NPCs)

Mus musculus · GPL21626

GSE232514 GSE · GEO

Expanded repertoire of RNA-editing-based detection for RNA binding protein interactions (2)

Homo sapiens · GPL24676

GSE202202 GSE · GEO

RNA-seq in neurites and soma of primary hippocampal neurons isolated from P0 or P1 mice

Mus musculus · GPL19057

GSE131847 GSE · GEO

Molecular determinants and heterogeneity of circulating and tissue-resident memory CD8+ T lymphocytes revealed by single-cell RNA sequencing

Mus musculus · GPL21103

GSE132971 GSE · GEO

Direct RNA sequencing enables single-nucleotide m6A detection in endogenous transcript isoforms

Homo sapiens · GPL24106

GSE215252 GSE · GEO

FLARE: A fast and flexible peak-calling pipeline for identifying RNA editing foci

Homo sapiens · GPL24676

GSE73843 GSE · GEO

Transcriptome analysis of diverse cell types infected with human cytomegalovirus [array]

Homo sapiens · GPL15106

GSE213470 GSE · GEO

Gene expression profiles at the single cell level of CD8+ T cells from the spleens of LCMV-Armstrong or LCMV-Clone 13 infected mice

Mus musculus · GPL19057

GSE89405 GSE · GEO

Early transcriptional and epigenetic regulation of CD8+ T cell differentiation revealed by single-cell RNA-seq

Mus musculus · GPL17021

GSE73853 GSE · GEO

Transcriptome analysis of diverse cell types infected with human cytomegalovirus [RNA-Seq]

Homo sapiens · GPL11154

GSE147081 GSE · GEO

Single Cell RNA-Seq of CD8+ T cell subsets responding to tumor

Mus musculus · GPL21103

GSE51556 GSE · GEO

The dsRBP and inactive editor, ADR-1, utilizes dsRNA binding to regulate A-to-I RNA editing across the C. elegans transcriptome

6239 · GPL9269

Analyses 8

GSE114922 Processing Pipeline

GSE114922 · 7 steps · RNA-Seq · code_examples

Integrative RNA-omics Discovers GNAS Alternative Splicing as a Phenotypic Driver of Splicing Factor-Mutant Neoplasms. (2022)

GSE65973 Processing Pipeline

GSE65973 · 5 steps · RNA-Seq · code_examples

Aberrant NOVA1 function disrupts alternative splicing in early stages of amyotrophic lateral sclerosis. (2022)

GSE131847 Processing Pipeline

GSE131847 · 5 steps · RNA-Seq · code_examples

Early precursors and molecular determinants of tissue-resident memory CD8<sup>+</sup> T lymphocytes revealed by single-cell RNA sequencing. (2020)

GSE132971 Processing Pipeline

GSE132971 · 4 steps · RNA-Seq · code_examples

Direct RNA sequencing enables m<sup>6</sup>A detection in endogenous transcript isoforms at base-specific resolution. (2020)

GSE89036 Processing Pipeline

GSE89036 · 3 steps · ChIP-Seq · code_examples

Early transcriptional and epigenetic regulation of CD8<sup>+</sup> T cell differentiation revealed by single-cell RNA sequencing. (2017)

GSE89405 Processing Pipeline

GSE89405 · 39 steps · RNA-Seq · code_examples

Early transcriptional and epigenetic regulation of CD8<sup>+</sup> T cell differentiation revealed by single-cell RNA sequencing. (2017)

GSE95237 Processing Pipeline

GSE95237 · 3 steps · ChIP-Seq · code_examples

Early transcriptional and epigenetic regulation of CD8<sup>+</sup> T cell differentiation revealed by single-cell RNA sequencing. (2017)

GSE95238 Data Processing

GSE95238 · 3 steps · geo_data_processing

Early transcriptional and epigenetic regulation of CD8<sup>+</sup> T cell differentiation revealed by single-cell RNA sequencing. (2017)