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38 results for “single cell”
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Single-cell and isoform-specific translational profiling of the mouse brain.
Nature · 2026
The brain displays the richest repertoire of post-transcriptional mechanisms regulating mRNA translation<sup>1-11</sup>. Among these, alternative splicing has been shown to drive cell-type specificity and, when disrupted, is strongly linked to neurological disorders<sup>12-17</sup>. However, genome-wide measurements of mRNA translation with isoform …
PMID 41708856 DOI ↗
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Stratification of enterochromaffin cells by single-cell expression analysis.
eLife · 2025 · 12
Dynamic interactions between gut mucosal cells and the external environment are essential to maintain gut homeostasis. Enterochromaffin (EC) cells transduce both chemical and mechanical signals and produce 5-hydroxytryptamine to mediate disparate physiological responses. However, the molecular and cellular basis for …
PMID 40184163 DOI ↗
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Tissue-resident memory CD8 T cell diversity is spatiotemporally imprinted.
Nature · 2025 · 639(8054): 483-492
Tissue-resident memory CD8 T (T<sub>RM</sub>) cells provide protection from infection at barrier sites. In the small intestine, T<sub>RM</sub> cells are found in at least two distinct subpopulations: one with higher expression of effector molecules and another with greater memory potential<sup>1</sup>. …
PMID 39843748 DOI ↗
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Stratification of enterochromaffin cells by single-cell expression analysis.
bioRxiv : the preprint server for biology · 2025
Dynamic interactions between gut mucosal cells and the external environment are essential to maintain gut homeostasis. Enterochromaffin (EC) cells transduce both chemical and mechanical signals and produce 5-hydroxytryptamine (5-HT) to mediate disparate physiological responses. However, the molecular and cellular basis …
PMID 37662229 DOI ↗
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Steering research on mRNA splicing in cancer towards clinical translation.
Nature reviews. Cancer · 2024 · 24(12): 887-905
Splicing factors are affected by recurrent somatic mutations and copy number variations in several types of haematologic and solid malignancies, which is often seen as prima facie evidence that splicing aberrations can drive cancer initiation and progression. However, numerous spliceosome …
PMID 39384951 DOI ↗
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Long-read Ribo-STAMP simultaneously measures transcription and translation with isoform resolution.
Genome research · 2024 · 34(11): 2012-2024
Transcription and translation are intertwined processes in which mRNA isoforms are crucial intermediaries. However, methodological limitations in analyzing translation at the mRNA isoform level have left gaps in our understanding of critical biological processes. To address these gaps, we developed …
PMID 38906680 DOI ↗
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ePRINT: exonuclease assisted mapping of protein-RNA interactions.
Genome biology · 2024 · 25(1): 140
RNA-binding proteins (RBPs) regulate key aspects of RNA processing including alternative splicing, mRNA degradation and localization by physically binding RNA molecules. Current methods to map these interactions, such as CLIP, rely on purifying single proteins at a time. Our new …
PMID 38807229 DOI ↗
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Bento: a toolkit for subcellular analysis of spatial transcriptomics data.
Genome biology · 2024 · 25(1): 82
The spatial organization of molecules in a cell is essential for their functions. While current methods focus on discerning tissue architecture, cell-cell interactions, and spatial expression patterns, they are limited to the multicellular scale. We present Bento, a Python toolkit …
PMID 38566187 DOI ↗
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Functional Diversity of Memory CD8 T Cells is Spatiotemporally Imprinted.
bioRxiv : the preprint server for biology · 2024
Tissue-resident memory CD8 T cells (T<sub>RM</sub>) kill infected cells and recruit additional immune cells to limit pathogen invasion at barrier sites. Small intestinal (SI) T<sub>RM</sub> cells consist of distinct subpopulations with higher expression of effector molecules or greater memory potential. …
PMID 38585842 DOI ↗
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Computational cell-cell interaction technologies drive mechanistic and biomarker discovery in the tumor microenvironment.
Current opinion in biotechnology · 2024 · 85: 103048
Complex networks of cell-cell interactions (CCIs) within the tumor microenvironment (TME) play a crucial role in cancer persistence. These communication axes represent prime targets for therapeutic intervention, but our incomplete understanding of the cellular heterogeneity and interacting partners within the …
PMID 38142648 DOI ↗
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Early transcriptional and epigenetic divergence of CD8+ T cells responding to acute versus chronic infection.
PLoS biology · 2023 · 21(1): e3001983
During a microbial infection, responding CD8+ T cells give rise to effector cells that provide acute host defense and memory cells that provide sustained protection. An alternative outcome is exhaustion, a state of T cell dysfunction that occurs in the …
PMID 36716323 DOI ↗
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The Host-Microbiome Response to Hyperbaric Oxygen Therapy in Ulcerative Colitis Patients.
Cellular and molecular gastroenterology and hepatology · 2022 · 14(1): 35-53
Hyperbaric oxygen therapy (HBOT) is a promising treatment for moderate-to-severe ulcerative colitis. However, our current understanding of the host and microbial response to HBOT remains unclear. This study examined the molecular mechanisms underpinning HBOT using a multi-omic strategy. Pre- and …
PMID 35378331 DOI ↗
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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 · 2463: 67-80
Recent advances in multimodal approaches toward single-cell analyses present valuable data points that can complement standard flow cytometry data. In particular, the overlay of cell-surface proteome data with gene expression analysis presents a necessary advancement, particularly in the field of …
PMID 35344168 DOI ↗
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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 ↗
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Pseudouridine synthases modify human pre-mRNA co-transcriptionally and affect pre-mRNA processing.
Molecular cell · 2022 · 82(3): 645-659.e9
Pseudouridine is a modified nucleotide that is prevalent in human mRNAs and is dynamically regulated. Here, we investigate when in their life cycle mRNAs become pseudouridylated to illuminate the potential regulatory functions of endogenous mRNA pseudouridylation. Using single-nucleotide resolution pseudouridine …
PMID 35051350 DOI ↗
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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 ↗
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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 ↗
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A CRISPR RNA-binding protein screen reveals regulators of RUNX1 isoform generation.
Blood advances · 2021 · 5(5): 1310-1323
The proper balance of hematopoietic stem cell (HSC) self-renewal and differentiation is critical for normal hematopoiesis and is disrupted in hematologic malignancy. Among regulators of HSC fate, transcription factors have a well-defined central role, and mutations promote malignant transformation. More …
PMID 33656539 DOI ↗
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Base editing: advances and therapeutic opportunities.
Nature reviews. Drug discovery · 2020 · 19(12): 839-859
Base editing - the introduction of single-nucleotide variants (SNVs) into DNA or RNA in living cells - is one of the most recent advances in the field of genome editing. As around half of known pathogenic genetic variants are due …
PMID 33077937 DOI ↗
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Context-dependent functional compensation between Ythdf m<sup>6</sup>A reader proteins.
Genes & development · 2020 · 34(19-20): 1373-1391
The N6-methyladenosine (m<sup>6</sup>A) modification is the most prevalent post-transcriptional mRNA modification, regulating mRNA decay and splicing. It plays a major role during normal development, differentiation, and disease progression. The modification is regulated by a set of writer, eraser, and reader …
PMID 32943573 DOI ↗
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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 ↗
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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 ↗
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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 ↗
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Principles of RNA processing from analysis of enhanced CLIP maps for 150 RNA binding proteins.
Genome biology · 2020 · 21(1): 90
A critical step in uncovering rules of RNA processing is to study the in vivo regulatory networks of RNA binding proteins (RBPs). Crosslinking and immunoprecipitation (CLIP) methods enable mapping RBP targets transcriptome-wide, but methodological differences present challenges to large-scale analysis …
PMID 32252787 DOI ↗
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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 25+
Multi-Modal Comparison of human Hepatic Stellate Cells identifies novel therapeutic targets for Metabolic Dysfunction-Associated Steatotic Liver Disease
Homo sapiens · GPL24676, GPL37309
Single cell and isoform-specific translational profiling of the mouse brain
GPL24247, GPL34475, GPL34585
Single cell and isoform-specific translational profiling of the mouse brain [ribostamp]
GPL24247
Single cell and isoform-specific translational profiling of the mouse brain [Bulk RNA-seq]
GPL24247
Single cell and isoform-specific translational profiling of the mouse brain [Ribo-STAMP]
GPL24247
Next Generation Sequencing: in vivo genome-wide CRISPR sgRNA screen in primary cancer-initiating and propagating bcCML stem cells
Mus musculus · GPL21103
Inhibition of YTHDF2 triggers proteotoxic cell death in MYC-driven breast cancer
Homo sapiens · GPL20301
Transcriptional Survey of Ileal-Anal Pouch Immune Cells from Ulcerative Colitis
Homo sapiens · GPL20301
Single-cell analysis of Crohnâs disease lesions identifies a pathogenic cellular module associated with resistance to anti-TNF therapy
Homo sapiens · GPL18573
Single-cell transcriptomics analysis of pancreatic primary tumor and metastatic biopsy tissues
Homo sapiens · GPL20301
Developmental emergence of adult neural stem cells as revealed by single cell transcriptional profiling
Mus musculus · GPL19057
Robust single-cell discovery of RNA targets of RNA binding proteins and ribosomes [STAMP_pacbio]
Homo sapiens · GPL28352
Robust single-cell discovery of RNA targets of RNA binding proteins and ribosomes [NP]
Homo sapiens · GPL24106
Pseudotemporal ordering of single cells reveals metabolic control of postnatal beta cell proliferation
Mus musculus · GPL17021
Robust single-cell discovery of RNA targets of RNA binding proteins and ribosomes [scRNA-seq]
Homo sapiens · GPL24676
Epistatic interactions between NMD and TRP53 control progenitor cell maintenance and brain size (scRNA-seq)
Mus musculus · GPL21103
Robust single-cell discovery of RNA targets of RNA binding proteins and ribosomes [RNA-seq]
Homo sapiens · GPL20301
MECP2-related pathways are dysregulated in a cortical organoid model of Myotonic dystrophy [scRNA-Seq]
Homo sapiens · GPL24676
Robust single-cell discovery of RNA targets of RNA binding proteins and ribosomes [tia1_eclip]
Homo sapiens · GPL16791
Robust single-cell discovery of RNA targets of RNA binding proteins and ribosomes
Homo sapiens · GPL16791
Molecular determinants and heterogeneity of circulating and tissue-resident memory CD8+ T lymphocytes revealed by single-cell RNA sequencing
Mus musculus · GPL21103
Single-cell alternative splicing analysis with Expedition reveals splicing dynamics during neuron differentiation
Homo sapiens · GPL11154
Nested oscillatory dynamics in cortical organoids model early human brain network development
Homo sapiens · GPL20301
Showing first 25 dataset results.
Analyses 10
GSE275091 · 1 step · RNA-Seq · code_examples
Single-cell and isoform-specific translational profiling of the mouse brain. (2026)
GSE275133 · 2 steps · RNA-Seq · code_examples
Single-cell and isoform-specific translational profiling of the mouse brain. (2026)
GSE276504 · 1 step · geo_data_processing
Single-cell and isoform-specific translational profiling of the mouse brain. (2026)
GSE314176 · 1 step · geo_data_processing
Single-cell and isoform-specific translational profiling of the mouse brain. (2026)
GSE107122 · 4 steps · RNA-Seq · code_examples
Epistatic interactions between NMD and TRP53 control progenitor cell maintenance and brain size. (2024)
GSE213469 · 2 steps · ATAC-seq · code_examples
Early transcriptional and epigenetic divergence of CD8+ T cells responding to acute versus chronic infection. (2023)
GSE213470 · 2 steps · RNA-Seq · code_examples
Early transcriptional and epigenetic divergence of CD8+ T cells responding to acute versus chronic infection. (2023)
GSE147081 · 5 steps · RNA-Seq · code_examples
Heterogenous Populations of Tissue-Resident CD8<sup>+</sup> T Cells Are Generated in Response to Infection and Malignancy. (2020)
GSE68618 · 11 steps · ChIP-Seq · code_examples
Pseudotemporal Ordering of Single Cells Reveals Metabolic Control of Postnatal β Cell Proliferation. (2017)
GSE86479 · 2 steps · RNA-Seq · code_examples
Pseudotemporal Ordering of Single Cells Reveals Metabolic Control of Postnatal β Cell Proliferation. (2017)