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52 results for “differentiation”
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Longitudinal assessment of tumor development using cancer avatars derived from genetically engineered pluripotent stem cells.
Nature communications · 2020 · 11(1): 550
Many cellular models aimed at elucidating cancer biology do not recapitulate pathobiology including tumor heterogeneity, an inherent feature of cancer that underlies treatment resistance. Here we introduce a cancer modeling paradigm using genetically engineered human pluripotent stem cells (hiPSCs) that …
PMID 31992716 DOI ↗
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The RNA Helicase DDX6 Controls Cellular Plasticity by Modulating P-Body Homeostasis.
Cell stem cell · 2019 · 25(5): 622-638.e13
Post-transcriptional mechanisms have the potential to influence complex changes in gene expression, yet their role in cell fate transitions remains largely unexplored. Here, we show that suppression of the RNA helicase DDX6 endows human and mouse primed embryonic stem cells …
PMID 31588046 DOI ↗
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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 · 24(9): 1255-1265
During terminal erythropoiesis, the splicing machinery in differentiating erythroblasts executes a robust intron retention (IR) program that impacts expression of hundreds of genes. We studied IR mechanisms in the <i>SF3B1</i> splicing factor gene, which expresses ∼50% of its transcripts in …
PMID 29959282 DOI ↗
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Single-Cell Alternative Splicing Analysis with Expedition Reveals Splicing Dynamics during Neuron Differentiation.
Molecular cell · 2017 · 67(1): 148-161.e5
Alternative splicing (AS) generates isoform diversity for cellular identity and homeostasis in multicellular life. Although AS variation has been observed among single cells, little is known about the biological or evolutionary significance of such variation. We developed Expedition, a computational …
PMID 28673540 DOI ↗
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Early transcriptional and epigenetic regulation of CD8<sup>+</sup> T cell differentiation revealed by single-cell RNA sequencing.
Nature immunology · 2017 · 18(4): 422-432
During microbial infection, responding CD8<sup>+</sup> T lymphocytes differentiate into heterogeneous subsets that together provide immediate and durable protection. To elucidate the dynamic transcriptional changes that underlie this process, we applied a single-cell RNA-sequencing approach and analyzed individual CD8<sup>+</sup> T lymphocytes …
PMID 28218746 DOI ↗
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High-Throughput and Cost-Effective Characterization of Induced Pluripotent Stem Cells.
Stem cell reports · 2017 · 8(4): 1101-1111
Reprogramming somatic cells to induced pluripotent stem cells (iPSCs) offers the possibility of studying the molecular mechanisms underlying human diseases in cell types difficult to extract from living patients, such as neurons and cardiomyocytes. To date, studies have been published …
PMID 28410643 DOI ↗
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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 ↗
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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 ↗
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The Calcineurin Variant CnAβ1 Controls Mouse Embryonic Stem Cell Differentiation by Directing mTORC2 Membrane Localization and Activation.
Cell chemical biology · 2016 · 23(11): 1372-1382
Embryonic stem cells (ESC) have the potential to generate all the cell lineages that form the body. However, the molecular mechanisms underlying ESC differentiation and especially the role of alternative splicing in this process remain poorly understood. Here, we show …
PMID 27746127 DOI ↗
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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 ↗
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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 ↗
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A Gene Regulatory Network Cooperatively Controlled by Pdx1 and Sox9 Governs Lineage Allocation of Foregut Progenitor Cells.
Cell reports · 2015 · 13(2): 326-36
The generation of pancreas, liver, and intestine from a common pool of progenitors in the foregut endoderm requires the establishment of organ boundaries. How dorsal foregut progenitors activate pancreatic genes and evade the intestinal lineage choice remains unclear. Here, we …
PMID 26440894 DOI ↗
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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 ↗
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Regulation of asymmetric division and CD8+ T lymphocyte fate specification by protein kinase Cζ and protein kinase Cλ/ι.
Journal of immunology (Baltimore, Md. : 1950) · 2015 · 194(5): 2249-59
During an immune response against a microbial pathogen, activated naive T lymphocytes give rise to effector cells that provide acute host defense and memory cells that provide long-lived immunity. It has been shown that T lymphocytes can undergo asymmetric division, …
PMID 25617472 DOI ↗
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Human cytomegalovirus infection of human embryonic stem cell-derived primitive neural stem cells is restricted at several steps but leads to the persistence of viral DNA.
Journal of virology · 2014 · 88(8): 4021-39
Congenital human cytomegalovirus (HCMV) infection is a major cause of central nervous system structural anomalies and sensory impairments. It is likely that the stage of fetal development, as well as the state of differentiation of susceptible cells at the time …
PMID 24453373 DOI ↗
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Functional genomic analysis of the let-7 regulatory network in Caenorhabditis elegans.
PLoS genetics · 2013 · 9(3): e1003353
The let-7 microRNA (miRNA) regulates cellular differentiation across many animal species. Loss of let-7 activity causes abnormal development in Caenorhabditis elegans and unchecked cellular proliferation in human cells, which contributes to tumorigenesis. These defects are due to improper expression of …
PMID 23516374 DOI ↗
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Reactivation of fetal splicing programs in diabetic hearts is mediated by protein kinase C signaling.
The Journal of biological chemistry · 2013 · 288(49): 35372-86
Diabetic cardiomyopathy is one of the complications of diabetes that eventually leads to heart failure and death. Aberrant activation of PKC signaling contributes to diabetic cardiomyopathy by mechanisms that are poorly understood. Previous reports indicate that PKC is implicated in …
PMID 24151077 DOI ↗
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Differential L1 regulation in pluripotent stem cells of humans and apes.
Nature · 2013 · 503(7477): 525-529
Identifying cellular and molecular differences between human and non-human primates (NHPs) is essential to the basic understanding of the evolution and diversity of our own species. Until now, preserved tissues have been the main source for most comparative studies between …
PMID 24153179 DOI ↗
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Coordinate Nodal and BMP inhibition directs Baf60c-dependent cardiomyocyte commitment.
Genes & development · 2013 · 27(21): 2332-44
A critical but molecularly uncharacterized step in heart formation and regeneration is the process that commits progenitor cells to differentiate into cardiomyocytes. Here, we show that the endoderm-derived dual Nodal/bone morphogenetic protein (BMP) antagonist Cerberus-1 (Cer1) in embryonic stem cell …
PMID 24186978 DOI ↗
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Retrotransposon long interspersed nucleotide element-1 (LINE-1) is activated during salamander limb regeneration.
Development, growth & differentiation · 2012 · 54(7): 673-85
Salamanders possess an extraordinary capacity for tissue and organ regeneration when compared to mammals. In our effort to characterize the unique transcriptional fingerprint emerging during the early phase of salamander limb regeneration, we identified transcriptional activation of some germline-specific genes …
PMID 22913491 DOI ↗
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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 ↗
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Alternative splicing in stem cell self-renewal and diferentiation.
Advances in experimental medicine and biology · 2010 · 695: 92-104
This chapter provides a review of recent advances in understanding the importance of alternative pre-messenger RNA splicing in stem cell biology. The majority of transcribed pre-mRNAs undergo RNA splicing where introns are excised and exons are juxtaposed to form mature …
PMID 21222201 DOI ↗
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A distinct microRNA signature for definitive endoderm derived from human embryonic stem cells.
Stem cells and development · 2010 · 19(6): 797-807
Human embryonic stem cells (hESCs) have the potential to differentiate into many adult cell types, and they are being explored as a resource for cell replacement therapies for multiple diseases. In order to optimize in vitro differentiation protocols, it will …
PMID 19807270 DOI ↗
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Deep sequencing identifies new and regulated microRNAs in Schmidtea mediterranea.
RNA (New York, N.Y.) · 2009 · 15(8): 1483-91
MicroRNAs (miRNAs) play important roles in directing the differentiation of cells down a variety of cell lineage pathways. The planarian Schmidtea mediterranea can regenerate all lost body tissue after amputation due to a population of pluripotent somatic stem cells called …
PMID 19553344 DOI ↗
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An RNA code for the FOX2 splicing regulator revealed by mapping RNA-protein interactions in stem cells.
Nature structural & molecular biology · 2009 · 16(2): 130-7
The elucidation of a code for regulated splicing has been a long-standing goal in understanding the control of post-transcriptional gene expression events that are crucial for cell survival, differentiation and development. We decoded functional RNA elements in vivo by constructing …
PMID 19136955 DOI ↗
Datasets 25+
Zfp697/ZNF697 is an RNA-binding protein that modulates TGF-β1 2 signaling and hepatic inflammation in liver disease
Mus musculus · GPL30172
Epigenetic landscapes reveal transcription factors that regulate CD8+ T cell differentiation
GPL17021
MBNL2 dysfunction in outer radial glial cells is associated with disrupted corticogenesis in congenital myotonic dystrophy [scRNA-Seq]
GPL24676
Densely interconnected transcriptional circuits control cell states in human hematopoiesis
Homo sapiens · GPL4685
Aberrant splicing of U12-type introns is the hallmark of ZRSR2 mutant myelodysplastic syndrome
Homo sapiens · GPL11154
Definition of a Small Core Transcriptional Circuit Regulated by AML1-ETO [ChIP-seq, Cut&Run]
Homo sapiens · GPL24676
Definition of a Small Core Transcriptional Circuit Regulated by AML1-ETO [RNA-seq]
Homo sapiens · GPL18573
The transcription factors ZEB2 and T-bet cooperate to program cytotoxic T cell terminal differentiation
Mus musculus · GPL17543
Genome-wide maps of chromatin state and chromatin accessibility in CD8 T cell subsets
Mus musculus · GPL17021
In vivo CRISPR screening unveils RNA binding protein dependencies for leukemic stem cells and identifies ELAVL1 as a potential therapeutic target [eCLIPseq]
Mus musculus · GPL21103
In vivo CRISPR screening unveils RNA binding protein dependencies for leukemic stem cells and identifies ELAVL1 as a potential therapeutic target [RNA-seq]
Mus musculus · GPL18480
Exonuclease assisted mapping of protein-RNA interactions (ePRINT)
Homo sapiens · GPL30173
Mitochondrial double-stranded RNA triggers chronic stress in aged neurons
Homo sapiens · GPL24676, GPL30173
Tissue-resident memory CD8 T Cell Diversity is Spatiotemporally Imprinted
Mus musculus · GPL24247
The RNA helicase DDX6 regulates self-renewal and differentiation of human and mouse stem cells [polysome RNA-seq]
Homo sapiens · GPL20301
The RNA helicase DDX6 regulates self-renewal and differentiation of human and mouse stem cells [RRBS]
Homo sapiens · GPL16791
The long noncoding RNA Malat1 regulates CD8+ T cell differentiation by mediating epigenetic repression (ChIP-Seq)
Mus musculus · GPL21103
CRISPR/Cas9 screening of RNA binding proteins (RBPs) that regulate RUNX1 isoform production
Homo sapiens · GPL20301
The RNA helicase DDX6 regulates self-renewal and differentiation of human and mouse stem cells [ATAC-Seq]
Homo sapiens · GPL11154
Tissue-resident memory CD8 T Cell Diversity is Spatiotemporally Imprinted [snRNA-Seq]
Mus musculus · GPL24247
The RNA helicase DDX6 regulates self-renewal and differentiation of human and mouse stem cells [CLIP-Seq]
Homo sapiens · GPL20301
RBM17 Mediates Evasion of Pro-Leukemic Factors from Splicing-coupled NMD to Enforce Leukemic Stem Cell Maintenance
Homo sapiens · GPL20301
Global Identification of the miR-130a targetome in human HSPC Reveals a Novel Role for TBL1XR1 in Hematopoietic Stem Cell Self-Renewal and t(8;21) AML [CUT&RUN]
Homo sapiens · GPL18573
Showing first 25 dataset results.
Analyses 25
GSE157072 · 3 steps · RNA-Seq · code_examples
The long noncoding RNA Malat1 regulates CD8+ T cell differentiation by mediating epigenetic repression. (2022)
GSE203086 · 10 steps · RNA-Seq · code_examples
The long noncoding RNA Malat1 regulates CD8+ T cell differentiation by mediating epigenetic repression. (2022)
GSE203089 · 19 steps · OTHER · code_examples
The long noncoding RNA Malat1 regulates CD8+ T cell differentiation by mediating epigenetic repression. (2022)
GSE203090 · 3 steps · ChIP-Seq · code_examples
The long noncoding RNA Malat1 regulates CD8+ T cell differentiation by mediating epigenetic repression. (2022)
GSE203091 · 6 steps · OTHER · code_examples
The long noncoding RNA Malat1 regulates CD8+ T cell differentiation by mediating epigenetic repression. (2022)
GSE203092 · 10 steps · GSE · code_examples
The long noncoding RNA Malat1 regulates CD8+ T cell differentiation by mediating epigenetic repression. (2022)
GSE72408 · 1 step · GSE · code_examples
The long noncoding RNA Malat1 regulates CD8+ T cell differentiation by mediating epigenetic repression. (2022)
GSE112383 · 3 steps · RNA-Seq · code_examples
The RNA Helicase DDX6 Controls Cellular Plasticity by Modulating P-Body Homeostasis. (2019)
GSE112439 · 4 steps · Bisulfite-Seq · code_examples
The RNA Helicase DDX6 Controls Cellular Plasticity by Modulating P-Body Homeostasis. (2019)
GSE112479 · 3 steps · GSE · code_examples
The RNA Helicase DDX6 Controls Cellular Plasticity by Modulating P-Body Homeostasis. (2019)
GSE112782 · 5 steps · RIP-Seq · code_examples
The RNA Helicase DDX6 Controls Cellular Plasticity by Modulating P-Body Homeostasis. (2019)
GSE124071 · 3 steps · ATAC-seq · code_examples
The RNA Helicase DDX6 Controls Cellular Plasticity by Modulating P-Body Homeostasis. (2019)
GSE124072 · 3 steps · RNA-Seq · code_examples
The RNA Helicase DDX6 Controls Cellular Plasticity by Modulating P-Body Homeostasis. (2019)
GSE125808 · 4 steps · RNA-Seq · code_examples
The RNA Helicase DDX6 Controls Cellular Plasticity by Modulating P-Body Homeostasis. (2019)
GSE125954 · 4 steps · ChIP-Seq · code_examples
The RNA Helicase DDX6 Controls Cellular Plasticity by Modulating P-Body Homeostasis. (2019)
GSE134164 · 3 steps · RNA-Seq · code_examples
The RNA Helicase DDX6 Controls Cellular Plasticity by Modulating P-Body Homeostasis. (2019)
GSE85908 · 11 steps · RNA-Seq · code_examples
Single-Cell Alternative Splicing Analysis with Expedition Reveals Splicing Dynamics during Neuron Differentiation. (2017)
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 · 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 · 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 · 3 steps · geo_data_processing
Early transcriptional and epigenetic regulation of CD8<sup>+</sup> T cell differentiation revealed by single-cell RNA sequencing. (2017)
GSE16678 · 7 steps · GSE · code_examples
A distinct microRNA signature for definitive endoderm derived from human embryonic stem cells. (2010)
GSE16681 · 1 step · GSE · code_examples
A distinct microRNA signature for definitive endoderm derived from human embryonic stem cells. (2010)
GSE16687 · 7 steps · GSE · code_examples
A distinct microRNA signature for definitive endoderm derived from human embryonic stem cells. (2010)
GSE16689 · 7 steps · GSE · code_examples
A distinct microRNA signature for definitive endoderm derived from human embryonic stem cells. (2010)