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75 results for “transcriptomics”

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  1. Widespread RNA editing dysregulation in brains from autistic individuals.

    Nature neuroscience · 2019 · 22(1): 25-36

    Transcriptomic analyses of postmortem brains have begun to elucidate molecular abnormalities in autism spectrum disorder (ASD). However, a crucial pathway involved in synaptic development, RNA editing, has not yet been studied on a genome-wide scale. Here we profiled global patterns …

    PMID 30559470 DOI ↗

  2. A Transcriptome-wide Translational Program Defined by LIN28B Expression Level.

    Molecular cell · 2019 · 73(2): 304-313.e3

    LIN28 RNA binding proteins are dynamically expressed throughout mammalian development and during disease. However, it remains unclear how changes in LIN28 expression define patterns of post-transcriptional gene regulation. Here we show that LIN28 expression level is a key variable that …

    PMID 30527666 DOI ↗

  3. Patch-Seq Protocol to Analyze the Electrophysiology, Morphology and Transcriptome of Whole Single Neurons Derived From Human Pluripotent Stem Cells.

    Frontiers in molecular neuroscience · 2018 · 11: 261

    The human brain is composed of a complex assembly of about 171 billion heterogeneous cellular units (86 billion neurons and 85 billion non-neuronal glia cells). A comprehensive description of brain cells is necessary to understand the nervous system in health …

    PMID 30147644 DOI ↗

  4. Transcriptome-pathology correlation identifies interplay between TDP-43 and the expression of its kinase CK1E in sporadic ALS.

    Acta neuropathologica · 2018 · 136(3): 405-423

    Sporadic amyotrophic lateral sclerosis (sALS) is the most common form of ALS, however, the molecular mechanisms underlying cellular damage and motor neuron degeneration remain elusive. To identify molecular signatures of sALS we performed genome-wide expression profiling in laser capture microdissection-enriched …

    PMID 29881994 DOI ↗

  5. Advances and challenges in the detection of transcriptome-wide protein-RNA interactions.

    Wiley interdisciplinary reviews. RNA · 2018 · 9(1)

    RNA binding proteins (RBPs) play key roles in determining cellular behavior by manipulating the processing of target RNAs. Robust methods are required to detect the numerous binding sites of RBPs across the transcriptome. RNA-immunoprecipitation followed by sequencing (RIP-seq) and crosslinking …

    PMID 28853213 DOI ↗

  6. Robust, Cost-Effective Profiling of RNA Binding Protein Targets with Single-end Enhanced Crosslinking and Immunoprecipitation (seCLIP).

    Methods in molecular biology (Clifton, N.J.) · 2017 · 1648: 177-200

    Profiling of RNA binding protein targets in vivo provides critical insights into the mechanistic roles they play in regulating RNA processing. The enhanced crosslinking and immunoprecipitation (eCLIP) methodology provides a framework for robust, reproducible identification of transcriptome-wide protein-RNA interactions, with …

    PMID 28766298 DOI ↗

  7. The <i>C. elegans</i> neural editome reveals an ADAR target mRNA required for proper chemotaxis.

    eLife · 2017 · 6

    ADAR proteins alter gene expression both by catalyzing adenosine (A) to inosine (I) RNA editing and binding to regulatory elements in target RNAs. Loss of ADARs affects neuronal function in all animals studied to date. <i>Caenorhabditis elegans</i> lacking ADARs exhibit …

    PMID 28925356 DOI ↗

  8. Pseudotemporal Ordering of Single Cells Reveals Metabolic Control of Postnatal β Cell Proliferation.

    Cell metabolism · 2017 · 25(5): 1160-1175.e11

    Pancreatic β cell mass for appropriate blood glucose control is established during early postnatal life. β cell proliferative capacity declines postnatally, but the extrinsic cues and intracellular signals that cause this decline remain unknown. To obtain a high-resolution map of …

    PMID 28467932 DOI ↗

  9. Experimental and Computational Considerations in the Study of RNA-Binding Protein-RNA Interactions.

    Advances in experimental medicine and biology · 2016 · 907: 1-28

    After an RNA is transcribed, it undergoes a variety of processing steps that can change the encoded protein sequence (through alternative splicing and RNA editing), regulate the stability of the RNA, and control subcellular localization, timing, and rate of translation. …

    PMID 27256380 DOI ↗

  10. RNA-binding protein CPEB1 remodels host and viral RNA landscapes.

    Nature structural & molecular biology · 2016 · 23(12): 1101-1110

    Host and virus interactions occurring at the post-transcriptional level are critical for infection but remain poorly understood. Here, we performed comprehensive transcriptome-wide analyses revealing that human cytomegalovirus (HCMV) infection results in widespread alternative splicing (AS), shortening of 3' untranslated regions …

    PMID 27775709 DOI ↗

  11. Predicting the functional states of human iPSC-derived neurons with single-cell RNA-seq and electrophysiology.

    Molecular psychiatry · 2016 · 21(11): 1573-1588

    Human neural progenitors derived from pluripotent stem cells develop into electrophysiologically active neurons at heterogeneous rates, which can confound disease-relevant discoveries in neurology and psychiatry. By combining patch clamping, morphological and transcriptome analysis on single-human neurons in vitro, we defined …

    PMID 27698428 DOI ↗

  12. Protein-RNA Networks Regulated by Normal and ALS-Associated Mutant HNRNPA2B1 in the Nervous System.

    Neuron · 2016 · 92(4): 780-795

    HnRNPA2B1 encodes an RNA binding protein associated with neurodegeneration. However, its function in the nervous system is unclear. Transcriptome-wide crosslinking and immunoprecipitation in mouse spinal cord discover UAGG motifs enriched within ∼2,500 hnRNP A2/B1 binding sites and an unexpected role …

    PMID 27773581 DOI ↗

  13. SONAR Discovers RNA-Binding Proteins from Analysis of Large-Scale Protein-Protein Interactomes.

    Molecular cell · 2016 · 64(2): 282-293

    RNA metabolism is controlled by an expanding, yet incomplete, catalog of RNA-binding proteins (RBPs), many of which lack characterized RNA binding domains. Approaches to expand the RBP repertoire to discover non-canonical RBPs are currently needed. Here, HaloTag fusion pull down …

    PMID 27720645 DOI ↗

  14. Genomic analysis of the molecular neuropathology of tuberous sclerosis using a human stem cell model.

    Genome medicine · 2016 · 8(1): 94

    Tuberous sclerosis complex (TSC) is a genetic disease characterized by benign tumor growths in multiple organs and neurological symptoms induced by mTOR hyperfunction. Because the molecular pathology is highly complex and the etiology poorly understood, we employed a defined human …

    PMID 27655340 DOI ↗

  15. Rbfox2 function in RNA metabolism is impaired in hypoplastic left heart syndrome patient hearts.

    Scientific reports · 2016 · 6: 30896

    Hypoplastic left heart syndrome (HLHS) is a fatal congenital heart disease in which the left side of the heart is underdeveloped, impairing the systemic circulation. Underdeveloped left ventricle exerts biomechanical stress on the right ventricle that can progress into heart …

    PMID 27485310 DOI ↗

  16. Robust transcriptome-wide discovery of RNA-binding protein binding sites with enhanced CLIP (eCLIP).

    Nature methods · 2016 · 13(6): 508-14

    As RNA-binding proteins (RBPs) play essential roles in cellular physiology by interacting with target RNA molecules, binding site identification by UV crosslinking and immunoprecipitation (CLIP) of ribonucleoprotein complexes is critical to understanding RBP function. However, current CLIP protocols are technically …

    PMID 27018577 DOI ↗

  17. Dysregulation of RBFOX2 Is an Early Event in Cardiac Pathogenesis of Diabetes.

    Cell reports · 2016 · 15(10): 2200-2213

    Alternative splicing (AS) defects that adversely affect gene expression and function have been identified in diabetic hearts; however, the mechanisms responsible are largely unknown. Here, we show that the RNA-binding protein RBFOX2 contributes to transcriptome changes under diabetic conditions. RBFOX2 …

    PMID 27239029 DOI ↗

  18. Enhanced CLIP Uncovers IMP Protein-RNA Targets in Human Pluripotent Stem Cells Important for Cell Adhesion and Survival.

    Cell reports · 2016 · 15(3): 666-679

    Human pluripotent stem cells (hPSCs) require precise control of post-transcriptional RNA networks to maintain proliferation and survival. Using enhanced UV crosslinking and immunoprecipitation (eCLIP), we identify RNA targets of the IMP/IGF2BP family of RNA-binding proteins in hPSCs. At the broad …

    PMID 27068461 DOI ↗

  19. Resources for the Comprehensive Discovery of Functional RNA Elements.

    Molecular cell · 2016 · 61(6): 903-13

    Transcriptome-wide maps of RNA binding protein (RBP)-RNA interactions by immunoprecipitation (IP)-based methods such as RNA IP (RIP) and crosslinking and IP (CLIP) are key starting points for evaluating the molecular roles of the thousands of human RBPs. A significant bottleneck …

    PMID 26990993 DOI ↗

  20. The Clothes Make the mRNA: Past and Present Trends in mRNP Fashion.

    Annual review of biochemistry · 2015 · 84: 325-54

    Throughout their lifetimes, messenger RNAs (mRNAs) associate with proteins to form ribonucleoproteins (mRNPs). Since the discovery of the first mRNP component more than 40 years ago, what is known as the mRNA interactome now comprises >1,000 proteins. These proteins bind …

    PMID 25784054 DOI ↗

  21. Identification of novel long noncoding RNAs underlying vertebrate cardiovascular development.

    Circulation · 2015 · 131(14): 1278-1290

    Long noncoding RNAs (lncRNAs) have emerged as critical epigenetic regulators with important functions in development and disease. Here, we sought to identify and functionally characterize novel lncRNAs critical for vertebrate development. By relying on human pluripotent stem cell differentiation models, …

    PMID 25739401 DOI ↗

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

    Cell reports · 2014 · 6(4): 599-607

    Inadequate adenosine-to-inosine editing of noncoding regions occurs in disease but is often uncorrelated with ADAR levels, underscoring the need to study deaminase-independent control of editing. C. elegans have two ADAR proteins, ADR-2 and the theoretically catalytically inactive ADR-1. Using high-throughput …

    PMID 24508457 DOI ↗

  23. High-resolution profiling and analysis of viral and host small RNAs during human cytomegalovirus infection.

    Journal of virology · 2012 · 86(1): 226-35

    Human cytomegalovirus (HCMV) contributes its own set of microRNAs (miRNAs) during lytic infection of cells, likely fine-tuning conditions important for viral replication. To enhance our understanding of this component of the HCMV-host transcriptome, we have conducted deep-sequencing analysis of small …

    PMID 22013051 DOI ↗

  24. RNA-seq analysis of gene expression and alternative splicing by double-random priming strategy.

    Methods in molecular biology (Clifton, N.J.) · 2011 · 729: 247-55

    Transcriptome analysis by deep sequencing, more commonly known as RNA-seq is, becoming the method of choice for gene discovery and quantitative splicing detection. We published a double-random priming RNA-seq approach capable of generating strand-specific information [Li et al., Proc Natl …

    PMID 21365495 DOI ↗

  25. Determination of tag density required for digital transcriptome analysis: application to an androgen-sensitive prostate cancer model.

    Proceedings of the National Academy of Sciences of the United States of America · 2008 · 105(51): 20179-84

    High-throughput sequencing has rapidly gained popularity for transcriptome analysis in mammalian cells because of its ability to generate digital and quantitative information on annotated genes and to detect transcripts and mRNA isoforms. Here, we described a double-random priming method for …

    PMID 19088194 DOI ↗

Datasets 5

GSE198212 GSE · GEO

Remodeling of oncogenic transcriptomes by small-molecules targeting the RNA-binding protein NONO

Homo sapiens · GPL24676

GSE154778 GSE · GEO

Single-cell transcriptomics analysis of pancreatic primary tumor and metastatic biopsy tissues

Homo sapiens · GPL20301

GSE279255 GSE · GEO

Tissue-resident memory CD8 T Cell Diversity is Spatiotemporally Imprinted

Mus musculus · GPL24247

GSE279254 GSE · GEO

Tissue-resident memory CD8 T Cell Diversity is Spatiotemporally Imprinted [snRNA-Seq]

Mus musculus · GPL24247

GSE280895 GSE · GEO

Tissue-resident memory CD8 T Cell Diversity is Spatiotemporally Imprinted

Mus musculus · GPL31217

Analyses 3

GSE279255 Spatial transcriptomics Data Processing

GSE279255 · 2 steps · Spatial transcriptomics · geo_data_processing

Tissue-resident memory CD8 T cell diversity is spatiotemporally imprinted. (2025)

GSE280895 Spatial transcriptomics Data Processing

GSE280895 · 7 steps · Spatial transcriptomics · geo_data_processing

Tissue-resident memory CD8 T cell diversity is spatiotemporally imprinted. (2025)

GSE154778 Processing Pipeline

GSE154778 · 1 step · RNA-Seq · code_examples

A super-enhancer-regulated RNA-binding protein cascade drives pancreatic cancer. (2023)