RNA-seq
Assay133
Publications
102
sra_metadata
94
geo_metadata
27
abstract
15
keywords_mesh
Publications
Structural and mechanistic analysis of covalent ligands targeting the RNA-binding protein NONO.
Cell chemical biology
(2026)
PMID:41534524
sra_metadata
MBNL2 dysfunction in outer radial glial cells is associated with disrupted corticogenesis in congenital myotonic dystrophy.
Neurobiology of disease
(2026)
PMID:41644016
geo_metadata
Single-cell and isoform-specific translational profiling of the mouse brain.
Nature
(2026)
PMID:41708856
geo_metadata
abstract
Flipper: An advanced framework for identifying differential RNA binding behavior with eCLIP data.
bioRxiv : the preprint server for biology
(2026)
PMID:41959526
geo_metadata
Stratification of enterochromaffin cells by single-cell expression analysis.
bioRxiv : the preprint server for biology
(2025)
PMID:37662229
geo_metadata
sra_metadata
Tissue-resident memory CD8 T cell diversity is spatiotemporally imprinted.
Nature
(2025)
PMID:39843748
sra_metadata
LARP6 regulates the mRNA translation of fibrogenic genes in liver fibrosis.
bioRxiv : the preprint server for biology
(2025)
PMID:39868246
geo_metadata
Stratification of enterochromaffin cells by single-cell expression analysis.
eLife
(2025)
PMID:40184163
geo_metadata
sra_metadata
Identification of RBP binding sites using RNA deaminases.
Methods in enzymology
(2025)
PMID:40250958
keywords_mesh
Evaluation of novel computational methods to identify RNA-binding protein footprints from structural data.
RNA (New York, N.Y.)
(2025)
PMID:40399037
sra_metadata
Neuronal aging causes mislocalization of splicing proteins and unchecked cellular stress.
Nature neuroscience
(2025)
PMID:40456907
geo_metadata
sra_metadata
Enhancing RNA base editing on mammalian transcripts with small nuclear RNAs.
Nature chemical biology
(2025)
PMID:40968292
sra_metadata
geo_metadata
Integrative CRISPR Screening and RNA Analyses Discover an Essential Role for PUF60 Interactions with 3' Splice Sites in Cancer Progression.
Cancer research
(2025)
PMID:41411621
geo_metadata
circHIPK3 nucleates IGF2BP2 and functions as a competing endogenous RNA.
bioRxiv : the preprint server for biology
(2024)
PMID:37745562
abstract
Computational cell-cell interaction technologies drive mechanistic and biomarker discovery in the tumor microenvironment.
Current opinion in biotechnology
(2024)
PMID:38142648
abstract
Large-scale evaluation of the ability of RNA-binding proteins to activate exon inclusion.
Nature biotechnology
(2024)
PMID:38168984
geo_metadata
sra_metadata
abstract
Expanded palette of RNA base editors for comprehensive RBP-RNA interactome studies.
Nature communications
(2024)
PMID:38287010
sra_metadata
geo_metadata
Transcriptome regulation by PARP13 in basal and antiviral states in human cells.
iScience
(2024)
PMID:38495826
abstract
A phage nucleus-associated RNA-binding protein is required for jumbo phage infection.
Nucleic acids research
(2024)
PMID:38554115
sra_metadata
Protocol to process crosslinking and immunoprecipitation data into annotated binding sites.
STAR protocols
(2024)
PMID:38669139
keywords_mesh
Epistatic interactions between NMD and TRP53 control progenitor cell maintenance and brain size.
Neuron
(2024)
PMID:38697111
sra_metadata
geo_metadata
ePRINT: exonuclease assisted mapping of protein-RNA interactions.
Genome biology
(2024)
PMID:38807229
sra_metadata
Long-read Ribo-STAMP simultaneously measures transcription and translation with isoform resolution.
Genome research
(2024)
PMID:38906680
geo_metadata
sra_metadata
Zfp697 is an RNA-binding protein that regulates skeletal muscle inflammation and remodeling.
Proceedings of the National Academy of Sciences of the United States of America
(2024)
PMID:39141348
geo_metadata
sra_metadata
High-sensitivity in situ capture of endogenous RNA-protein interactions in fixed cells and primary tissues.
Nature communications
(2024)
PMID:39152130
geo_metadata
sra_metadata
Autism-associated CHD8 controls reactive gliosis and neuroinflammation via remodeling chromatin in astrocytes.
Cell reports
(2024)
PMID:39154337
geo_metadata
sra_metadata
Integrated multi-omics analysis of zinc-finger proteins uncovers roles in RNA regulation.
Molecular cell
(2024)
PMID:39303722
geo_metadata
sra_metadata
keywords_mesh
Steering research on mRNA splicing in cancer towards clinical translation.
Nature reviews. Cancer
(2024)
PMID:39384951
abstract
Localized molecular chaperone synthesis maintains neuronal dendrite proteostasis.
Nature communications
(2024)
PMID:39737952
sra_metadata
geo_metadata
An RNA-targeting CRISPR-Cas13d system alleviates disease-related phenotypes in Huntington's disease models.
Nature neuroscience
(2023)
PMID:36510111
geo_metadata
sra_metadata
Multiplexed transcriptome discovery of RNA-binding protein binding sites by antibody-barcode eCLIP.
Nature methods
(2023)
PMID:36550273
sra_metadata
geo_metadata
Early transcriptional and epigenetic divergence of CD8+ T cells responding to acute versus chronic infection.
PLoS biology
(2023)
PMID:36716323
sra_metadata
geo_metadata
RNA binding protein DDX5 restricts RORγt<sup>+</sup> T<sub>reg</sub> suppressor function to promote intestine inflammation.
Science advances
(2023)
PMID:36724232
geo_metadata
sra_metadata
Splicing factor SRSF1 deficiency in the liver triggers NASH-like pathology and cell death.
Nature communications
(2023)
PMID:36759613
sra_metadata
geo_metadata
In Vivo Screening Unveils Pervasive RNA-Binding Protein Dependencies in Leukemic Stem Cells and Identifies ELAVL1 as a Therapeutic Target.
Blood cancer discovery
(2023)
PMID:36763002
geo_metadata
sra_metadata
Remodeling oncogenic transcriptomes by small molecules targeting NONO.
Nature chemical biology
(2023)
PMID:36864190
geo_metadata
sra_metadata
Proteomic discovery of chemical probes that perturb protein complexes in human cells.
Molecular cell
(2023)
PMID:37084731
geo_metadata
sra_metadata
Pyruvate Kinase M (PKM) binds ribosomes in a poly-ADP ribosylation dependent manner to induce translational stalling.
Nucleic acids research
(2023)
PMID:37224531
sra_metadata
Skipper analysis of eCLIP datasets enables sensitive detection of constrained translation factor binding sites.
Cell genomics
(2023)
PMID:37388912
sra_metadata
A super-enhancer-regulated RNA-binding protein cascade drives pancreatic cancer.
Nature communications
(2023)
PMID:37673892
sra_metadata
geo_metadata
FLARE: a fast and flexible workflow for identifying RNA editing foci.
BMC bioinformatics
(2023)
PMID:37784060
keywords_mesh
sra_metadata
geo_metadata
abstract
Integrative RNA-omics Discovers GNAS Alternative Splicing as a Phenotypic Driver of Splicing Factor-Mutant Neoplasms.
Cancer discovery
(2022)
PMID:34620690
abstract
geo_metadata
sra_metadata
RNA binding protein DDX5 directs tuft cell specification and function to regulate microbial repertoire and disease susceptibility in the intestine.
Gut
(2022)
PMID:34853057
sra_metadata
geo_metadata
Pseudouridine synthases modify human pre-mRNA co-transcriptionally and affect pre-mRNA processing.
Molecular cell
(2022)
PMID:35051350
geo_metadata
sra_metadata
APEX Proximity Labeling of Stress Granule Proteins.
Methods in molecular biology (Clifton, N.J.)
(2022)
PMID:35171492
abstract
Discovery and functional interrogation of SARS-CoV-2 protein-RNA interactions.
bioRxiv : the preprint server for biology
(2022)
PMID:35233578
geo_metadata
sra_metadata
Identification of the global miR-130a targetome reveals a role for TBL1XR1 in hematopoietic stem cell self-renewal and t(8;21) AML.
Cell reports
(2022)
PMID:35263585
sra_metadata
geo_metadata
Discovery and functional interrogation of SARS-CoV-2 protein-RNA interactions.
Research square
(2022)
PMID:35313591
sra_metadata
geo_metadata
Antibody-Oligonucleotide Conjugation Using a SPAAC Copper-Free Method Compatible with 10× Genomics' Single-Cell RNA-Seq.
Methods in molecular biology (Clifton, N.J.)
(2022)
PMID:35344168
keywords_mesh
abstract
The Host-Microbiome Response to Hyperbaric Oxygen Therapy in Ulcerative Colitis Patients.
Cellular and molecular gastroenterology and hepatology
(2022)
PMID:35378331
abstract
The long noncoding RNA Malat1 regulates CD8+ T cell differentiation by mediating epigenetic repression.
The Journal of experimental medicine
(2022)
PMID:35593887
geo_metadata
sra_metadata
MECP2-related pathways are dysregulated in a cortical organoid model of myotonic dystrophy.
Science translational medicine
(2022)
PMID:35767654
abstract
geo_metadata
sra_metadata
Aberrant NOVA1 function disrupts alternative splicing in early stages of amyotrophic lateral sclerosis.
Acta neuropathologica
(2022)
PMID:35778567
sra_metadata
geo_metadata
The splicing factor RBM17 drives leukemic stem cell maintenance by evading nonsense-mediated decay of pro-leukemic factors.
Nature communications
(2022)
PMID:35781533
geo_metadata
Prions induce an early Arc response and a subsequent reduction in mGluR5 in the hippocampus.
Neurobiology of disease
(2022)
PMID:35905927
sra_metadata
geo_metadata
Characterization of an RNA binding protein interactome reveals a context-specific post-transcriptional landscape of MYC-amplified medulloblastoma.
Nature communications
(2022)
PMID:36473869
sra_metadata
The sustained expression of Cas9 targeting toxic RNAs reverses disease phenotypes in mouse models of myotonic dystrophy type 1.
Nature biomedical engineering
(2021)
PMID:32929188
geo_metadata
sra_metadata
A CRISPR RNA-binding protein screen reveals regulators of RUNX1 isoform generation.
Blood advances
(2021)
PMID:33656539
geo_metadata
sra_metadata
Loss of LUC7L2 and U1 snRNP subunits shifts energy metabolism from glycolysis to OXPHOS.
Molecular cell
(2021)
PMID:33852893
sra_metadata
geo_metadata
Robust single-cell discovery of RNA targets of RNA-binding proteins and ribosomes.
Nature methods
(2021)
PMID:33963355
sra_metadata
geo_metadata
Inhibition of YTHDF2 triggers proteotoxic cell death in MYC-driven breast cancer.
Molecular cell
(2021)
PMID:34216543
geo_metadata
sra_metadata
ADAR and hnRNPC deficiency synergize in activating endogenous dsRNA-induced type I IFN responses.
The Journal of experimental medicine
(2021)
PMID:34297039
geo_metadata
sra_metadata
abstract
Non-microRNA binding competitively inhibits LIN28 regulation.
Cell reports
(2021)
PMID:34380031
geo_metadata
sra_metadata
fSHAPE, fSHAPE-eCLIP, and SHAPE-eCLIP probe transcript regions that interact with specific proteins.
STAR protocols
(2021)
PMID:34485935
keywords_mesh
Persistent mRNA localization defects and cell death in ALS neurons caused by transient cellular stress.
Cell reports
(2021)
PMID:34496257
geo_metadata
abstract
sra_metadata
Gain-of-function cardiomyopathic mutations in RBM20 rewire splicing regulation and re-distribute ribonucleoprotein granules within processing bodies.
Nature communications
(2021)
PMID:34732726
geo_metadata
abstract
sra_metadata
Direct RNA sequencing enables m<sup>6</sup>A detection in endogenous transcript isoforms at base-specific resolution.
RNA (New York, N.Y.)
(2020)
PMID:31624092
abstract
sra_metadata
geo_metadata
Longitudinal assessment of tumor development using cancer avatars derived from genetically engineered pluripotent stem cells.
Nature communications
(2020)
PMID:31992716
sra_metadata
Suppression of Endothelial AGO1 Promotes Adipose Tissue Browning and Improves Metabolic Dysfunction.
Circulation
(2020)
PMID:32393053
sra_metadata
geo_metadata
Early precursors and molecular determinants of tissue-resident memory CD8<sup>+</sup> T lymphocytes revealed by single-cell RNA sequencing.
Science immunology
(2020)
PMID:32414833
geo_metadata
sra_metadata
abstract
Heterogenous Populations of Tissue-Resident CD8<sup>+</sup> T Cells Are Generated in Response to Infection and Malignancy.
Immunity
(2020)
PMID:32433949
sra_metadata
geo_metadata
A role for alternative splicing in circadian control of exocytosis and glucose homeostasis.
Genes & development
(2020)
PMID:32616519
geo_metadata
keywords_mesh
sra_metadata
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)
PMID:32669294
geo_metadata
A large-scale binding and functional map of human RNA-binding proteins.
Nature
(2020)
PMID:32728246
geo_metadata
Large-scale tethered function assays identify factors that regulate mRNA stability and translation.
Nature structural & molecular biology
(2020)
PMID:32807991
sra_metadata
geo_metadata
DDX5 promotes oncogene C3 and FABP1 expressions and drives intestinal inflammation and tumorigenesis.
Life science alliance
(2020)
PMID:32817263
sra_metadata
Heterogeneity and clonal relationships of adaptive immune cells in ulcerative colitis revealed by single-cell analyses.
Science immunology
(2020)
PMID:32826341
geo_metadata
sra_metadata
AMPK regulation of Raptor and TSC2 mediate metformin effects on transcriptional control of anabolism and inflammation.
Genes & development
(2020)
PMID:32912901
geo_metadata
sra_metadata
Context-dependent functional compensation between Ythdf m<sup>6</sup>A reader proteins.
Genes & development
(2020)
PMID:32943573
geo_metadata
Evaluation of Engineered CRISPR-Cas-Mediated Systems for Site-Specific RNA Editing.
Cell reports
(2020)
PMID:33147453
geo_metadata
sra_metadata
keywords_mesh
Zmat3 Is a Key Splicing Regulator in the p53 Tumor Suppression Program.
Molecular cell
(2020)
PMID:33157015
sra_metadata
geo_metadata
Transcriptome-wide profiles of circular RNA and RNA-binding protein interactions reveal effects on circular RNA biogenesis and cancer pathway expression.
Genome medicine
(2020)
PMID:33287884
abstract
sra_metadata
geo_metadata
An in vivo genome-wide CRISPR screen identifies the RNA-binding protein Staufen2 as a key regulator of myeloid leukemia.
Nature cancer
(2020)
PMID:34109316
geo_metadata
sra_metadata
RBP-Maps enables robust generation of splicing regulatory maps.
RNA (New York, N.Y.)
(2019)
PMID:30413564
abstract
A Transcriptome-wide Translational Program Defined by LIN28B Expression Level.
Molecular cell
(2019)
PMID:30527666
sra_metadata
geo_metadata
Widespread RNA editing dysregulation in brains from autistic individuals.
Nature neuroscience
(2019)
PMID:30559470
sra_metadata
geo_metadata
Overriding FUS autoregulation in mice triggers gain-of-toxic dysfunctions in RNA metabolism and autophagy-lysosome axis.
eLife
(2019)
PMID:30747709
sra_metadata
Glial cells maintain synapses by inhibiting an activity-dependent retrograde protease signal.
PLoS genetics
(2019)
PMID:30870413
sra_metadata
Disruption in A-to-I Editing Levels Affects C. elegans Development More Than a Complete Lack of Editing.
Cell reports
(2019)
PMID:31018137
sra_metadata
Corrigendum: Patch-Seq Protocol to Analyze the Electrophysiology, Morphology and Transcriptome of Whole Single Neurons Derived From Human Pluripotent Stem Cells.
Frontiers in molecular neuroscience
(2019)
PMID:31244603
keywords_mesh
Pervasive Chromatin-RNA Binding Protein Interactions Enable RNA-Based Regulation of Transcription.
Cell
(2019)
PMID:31251911
keywords_mesh
A protein-RNA interaction atlas of the ribosome biogenesis factor AATF.
Scientific reports
(2019)
PMID:31363146
geo_metadata
Complex Oscillatory Waves Emerging from Cortical Organoids Model Early Human Brain Network Development.
Cell stem cell
(2019)
PMID:31474560
sra_metadata
geo_metadata
The RNA Helicase DDX6 Controls Cellular Plasticity by Modulating P-Body Homeostasis.
Cell stem cell
(2019)
PMID:31588046
geo_metadata
keywords_mesh
sra_metadata
Systematic Discovery of RNA Binding Proteins that Regulate MicroRNA Levels.
Molecular cell
(2018)
PMID:29547715
geo_metadata
Transcriptome-pathology correlation identifies interplay between TDP-43 and the expression of its kinase CK1E in sporadic ALS.
Acta neuropathologica
(2018)
PMID:29881994
geo_metadata
sra_metadata
keywords_mesh
An important class of intron retention events in human erythroblasts is regulated by cryptic exons proposed to function as splicing decoys.
RNA (New York, N.Y.)
(2018)
PMID:29959282
abstract
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)
PMID:30147644
keywords_mesh
Biallelic mutations in the 3' exonuclease TOE1 cause pontocerebellar hypoplasia and uncover a role in snRNA processing.
Nature genetics
(2017)
PMID:28092684
sra_metadata
Early transcriptional and epigenetic regulation of CD8<sup>+</sup> T cell differentiation revealed by single-cell RNA sequencing.
Nature immunology
(2017)
PMID:28218746
geo_metadata
sra_metadata
iPSCORE: A Resource of 222 iPSC Lines Enabling Functional Characterization of Genetic Variation across a Variety of Cell Types.
Stem cell reports
(2017)
PMID:28410642
sra_metadata
Pseudotemporal Ordering of Single Cells Reveals Metabolic Control of Postnatal β Cell Proliferation.
Cell metabolism
(2017)
PMID:28467932
sra_metadata
geo_metadata
keywords_mesh
abstract
Single-Cell Alternative Splicing Analysis with Expedition Reveals Splicing Dynamics during Neuron Differentiation.
Molecular cell
(2017)
PMID:28673540
geo_metadata
sra_metadata
Elimination of Toxic Microsatellite Repeat Expansion RNA by RNA-Targeting Cas9.
Cell
(2017)
PMID:28803727
geo_metadata
sra_metadata
NEAT1 scaffolds RNA-binding proteins and the Microprocessor to globally enhance pri-miRNA processing.
Nature structural & molecular biology
(2017)
PMID:28846091
geo_metadata
The <i>C. elegans</i> neural editome reveals an ADAR target mRNA required for proper chemotaxis.
eLife
(2017)
PMID:28925356
sra_metadata
Short poly(A) tails are a conserved feature of highly expressed genes.
Nature structural & molecular biology
(2017)
PMID:29106412
sra_metadata
geo_metadata
PPAR-δ is repressed in Huntington's disease, is required for normal neuronal function and can be targeted therapeutically.
Nature medicine
(2016)
PMID:26642438
geo_metadata
sra_metadata
A Small RNA-Catalytic Argonaute Pathway Tunes Germline Transcript Levels to Ensure Embryonic Divisions.
Cell
(2016)
PMID:27020753
sra_metadata
Enhanced CLIP Uncovers IMP Protein-RNA Targets in Human Pluripotent Stem Cells Important for Cell Adhesion and Survival.
Cell reports
(2016)
PMID:27068461
geo_metadata
sra_metadata
Musashi-2 attenuates AHR signalling to expand human haematopoietic stem cells.
Nature
(2016)
PMID:27121842
geo_metadata
sra_metadata
Dysregulation of RBFOX2 Is an Early Event in Cardiac Pathogenesis of Diabetes.
Cell reports
(2016)
PMID:27239029
sra_metadata
Experimental and Computational Considerations in the Study of RNA-Binding Protein-RNA Interactions.
Advances in experimental medicine and biology
(2016)
PMID:27256380
keywords_mesh
Distinct and shared functions of ALS-associated proteins TDP-43, FUS and TAF15 revealed by multisystem analyses.
Nature communications
(2016)
PMID:27378374
geo_metadata
sra_metadata
Genomic analysis of the molecular neuropathology of tuberous sclerosis using a human stem cell model.
Genome medicine
(2016)
PMID:27655340
sra_metadata
abstract
geo_metadata
Predicting the functional states of human iPSC-derived neurons with single-cell RNA-seq and electrophysiology.
Molecular psychiatry
(2016)
PMID:27698428
sra_metadata
geo_metadata
Protein-RNA Networks Regulated by Normal and ALS-Associated Mutant HNRNPA2B1 in the Nervous System.
Neuron
(2016)
PMID:27773581
sra_metadata
geo_metadata
RNA-binding protein CPEB1 remodels host and viral RNA landscapes.
Nature structural & molecular biology
(2016)
PMID:27775709
geo_metadata
sra_metadata
Identification of novel long noncoding RNAs underlying vertebrate cardiovascular development.
Circulation
(2015)
PMID:25739401
abstract
sra_metadata
geo_metadata
The Ro60 autoantigen binds endogenous retroelements and regulates inflammatory gene expression.
Science (New York, N.Y.)
(2015)
PMID:26382853
sra_metadata
geo_metadata
A Gene Regulatory Network Cooperatively Controlled by Pdx1 and Sox9 Governs Lineage Allocation of Foregut Progenitor Cells.
Cell reports
(2015)
PMID:26440894
geo_metadata
sra_metadata
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)
PMID:24508457
sra_metadata
abstract
geo_metadata
The Period protein homolog LIN-42 negatively regulates microRNA biogenesis in C. elegans.
Developmental biology
(2014)
PMID:24699545
abstract
Genome-wide analysis reveals SR protein cooperation and competition in regulated splicing.
Molecular cell
(2013)
PMID:23562324
sra_metadata
Reactivation of fetal splicing programs in diabetic hearts is mediated by protein kinase C signaling.
The Journal of biological chemistry
(2013)
PMID:24151077
abstract
Differential L1 regulation in pluripotent stem cells of humans and apes.
Nature
(2013)
PMID:24153179
geo_metadata
sra_metadata
Targeted degradation of sense and antisense C9orf72 RNA foci as therapy for ALS and frontotemporal degeneration.
Proceedings of the National Academy of Sciences of the United States of America
(2013)
PMID:24170860
geo_metadata
sra_metadata
High-resolution profiling and analysis of viral and host small RNAs during human cytomegalovirus infection.
Journal of virology
(2012)
PMID:22013051
sra_metadata
Integrative genome-wide analysis reveals cooperative regulation of alternative splicing by hnRNP proteins.
Cell reports
(2012)
PMID:22574288
sra_metadata
geo_metadata
LIN28 binds messenger RNAs at GGAGA motifs and regulates splicing factor abundance.
Molecular cell
(2012)
PMID:22959275
geo_metadata
sra_metadata
Divergent roles of ALS-linked proteins FUS/TLS and TDP-43 intersect in processing long pre-mRNAs.
Nature neuroscience
(2012)
PMID:23023293
geo_metadata
sra_metadata
Long pre-mRNA depletion and RNA missplicing contribute to neuronal vulnerability from loss of TDP-43.
Nature neuroscience
(2011)
PMID:21358643
geo_metadata
sra_metadata
RNA-seq analysis of gene expression and alternative splicing by double-random priming strategy.
Methods in molecular biology (Clifton, N.J.)
(2011)
PMID:21365495
abstract