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64 results for “Modeling”
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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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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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PPAR-δ is repressed in Huntington's disease, is required for normal neuronal function and can be targeted therapeutically.
Nature medicine · 2016 · 22(1): 37-45
Huntington's disease (HD) is a progressive neurodegenerative disorder caused by a CAG trinucleotide repeat expansion in the huntingtin (HTT) gene, which encodes a polyglutamine tract in the HTT protein. We found that peroxisome proliferator-activated receptor delta (PPAR-δ) interacts with HTT …
PMID 26642438 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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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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Genome-wide analysis reveals SR protein cooperation and competition in regulated splicing.
Molecular cell · 2013 · 50(2): 223-35
SR proteins are well-characterized RNA binding proteins that promote exon inclusion by binding to exonic splicing enhancers (ESEs). However, it has been unclear whether regulatory rules deduced on model genes apply generally to activities of SR proteins in the cell. …
PMID 23562324 DOI ↗
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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 ↗
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A model for neural development and treatment of Rett syndrome using human induced pluripotent stem cells.
Cell · 2010 · 143(4): 527-39
Autism spectrum disorders (ASD) are complex neurodevelopmental diseases in which different combinations of genetic mutations may contribute to the phenotype. Using Rett syndrome (RTT) as an ASD genetic model, we developed a culture system using induced pluripotent stem cells (iPSCs) …
PMID 21074045 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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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 ↗
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Multiple layers of molecular controls modulate self-renewal and neuronal lineage specification of embryonic stem cells.
Human molecular genetics · 2008 · 17(R1): R67-75
Elucidating the molecular changes that arise during neural differentiation and fate specification is crucial for building accurate in vitro models of neurodegenerative diseases using human embryonic stem cells (hESCs). Here we review the importance of hESCs and derived progenitors in …
PMID 18632700 DOI ↗
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RNA sequence analysis defines Dicer's role in mouse embryonic stem cells.
Proceedings of the National Academy of Sciences of the United States of America · 2007 · 104(46): 18097-102
Short RNA expression was analyzed from Dicer-positive and Dicer-knockout mouse embryonic [corrected] stem (ES) cells, using high-throughput pyrosequencing. A correlation of miRNA quantification with sequencing frequency estimates that there are 110,000 miRNAs per ES cell, the majority of which can …
PMID 17989215 DOI ↗
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Alternative splicing events identified in human embryonic stem cells and neural progenitors.
PLoS computational biology · 2007 · 3(10): 1951-67
Human embryonic stem cells (hESCs) and neural progenitor (NP) cells are excellent models for recapitulating early neuronal development in vitro, and are key to establishing strategies for the treatment of degenerative disorders. While much effort had been undertaken to analyze …
PMID 17967047 DOI ↗
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The EJC factor eIF4AIII modulates synaptic strength and neuronal protein expression.
Cell · 2007 · 130(1): 179-91
Proper neuronal function and several forms of synaptic plasticity are highly dependent on precise control of mRNA translation, particularly in dendrites. We find that eIF4AIII, a core exon junction complex (EJC) component loaded onto mRNAs by pre-mRNA splicing, is associated …
PMID 17632064 DOI ↗
Datasets 16
Next Generation Sequencing: in vivo genome-wide CRISPR sgRNA screen in primary cancer-initiating and propagating bcCML stem cells
Mus musculus · GPL21103
Remodeling of oncogenic transcriptomes by small-molecules targeting the RNA-binding protein NONO
Homo sapiens · GPL24676
Refined molecular taxonomy and treatment remodeling of pancreatic cancer using single-cell resolution
Homo sapiens · GPL20301
Remodeling oncogenic transcriptomes by small molecules targeting NONO
Homo sapiens · GPL20301
Zfp697 is an RNA-binding protein that regulates skeletal muscle inflammation and remodeling (Zfp697 transduced primary mouse myotubes ChIP-Seq)
Mus musculus · GPL21626
Autism-associated CHD8 controls reactive gliosis and neuroinflammation via remodeling chromatin in astrocytes [bulk RNA-seq]
Mus musculus · GPL24247
Autism-associated CHD8 controls reactive gliosis and neuroinflammation via remodeling chromatin in astrocytes [ATAC-seq]
Mus musculus · GPL24247
Cancer avatars derived from genetically engineered pluripotent stem cells allow for longitudinal assessment of tumor development
Homo sapiens · GPL20301
Modeling the Neuropathology of Tuberous Sclerosis with Human Stem Cells Reveals a Role for Inflammation and Angiogenic Growth Factors [Treatment]
Homo sapiens · GPL16791
Zfp697 is an RNA-binding protein that regulates skeletal muscle inflammation and remodeling (Zfp697 skeletal muscle knockout RNA-Seq of unloading-reloading protocol)
Mus musculus · GPL24247
Modeling the Neuropathology of Tuberous Sclerosis with Human Stem Cells Reveals a Role for Inflammation and Angiogenic Growth Factors
Homo sapiens · GPL16791
Autism-associated CHD8 controls reactive gliosis and neuroinflammation via remodeling chromatin in astrocytes [Microglia RNA-seq]
Mus musculus · GPL24247
Cancer avatars derived from genetically engineered pluripotent stem cells allow for longitudinal assessment of tumor development
Homo sapiens · GPL24676
Zfp697 is an RNA-binding protein that regulates skeletal muscle inflammation and remodeling (Zfp697 transduced primary mouse myotubes RNA-Seq)
Mus musculus · GPL17021
Modeling the Neuropathology of Tuberous Sclerosis with Human Stem Cells Reveals a Role for Inflammation and Angiogenic Growth Factors [Cell Model]
Homo sapiens · GPL16791
Analyses 20
GSE114820 · 4 steps · RNA-Seq · code_examples
Zfp697 is an RNA-binding protein that regulates skeletal muscle inflammation and remodeling. (2024)
GSE143437 · 7 steps · RNA-Seq · code_examples
Zfp697 is an RNA-binding protein that regulates skeletal muscle inflammation and remodeling. (2024)
GSE145480 · 11 steps · RNA-Seq · code_examples
Zfp697 is an RNA-binding protein that regulates skeletal muscle inflammation and remodeling. (2024)
GSE147127 · 5 steps · RNA-Seq · code_examples
Zfp697 is an RNA-binding protein that regulates skeletal muscle inflammation and remodeling. (2024)
GSE210263 · 10 steps · RNA-Seq · code_examples
Zfp697 is an RNA-binding protein that regulates skeletal muscle inflammation and remodeling. (2024)
GSE237099 · 3 steps · RNA-Seq · code_examples
Zfp697 is an RNA-binding protein that regulates skeletal muscle inflammation and remodeling. (2024)
GSE271650 · 5 steps · RNA-Seq · code_examples
Autism-associated CHD8 controls reactive gliosis and neuroinflammation via remodeling chromatin in astrocytes. (2024)
GSE271651 · 8 steps · RNA-Seq · code_examples
Autism-associated CHD8 controls reactive gliosis and neuroinflammation via remodeling chromatin in astrocytes. (2024)
GSE271652 · 5 steps · ATAC-seq · code_examples
Autism-associated CHD8 controls reactive gliosis and neuroinflammation via remodeling chromatin in astrocytes. (2024)
GSE273092 · 3 steps · RNA-Seq · code_examples
Zfp697 is an RNA-binding protein that regulates skeletal muscle inflammation and remodeling. (2024)
GSE273093 · 3 steps · RNA-Seq · code_examples
Zfp697 is an RNA-binding protein that regulates skeletal muscle inflammation and remodeling. (2024)
GSE273094 · 3 steps · ChIP-Seq · code_examples
Zfp697 is an RNA-binding protein that regulates skeletal muscle inflammation and remodeling. (2024)
GSE198212 · 7 steps · RIP-Seq · code_examples
Remodeling oncogenic transcriptomes by small molecules targeting NONO. (2023)
GSE198419 · 7 steps · RNA-Seq · code_examples
Remodeling oncogenic transcriptomes by small molecules targeting NONO. (2023)
GSE202051 · 5 steps · RNA-Seq · code_examples
A super-enhancer-regulated RNA-binding protein cascade drives pancreatic cancer. (2023)
GSE222216 · 4 steps · RNA-Seq · code_examples
Remodeling oncogenic transcriptomes by small molecules targeting NONO. (2023)
GSE222217 · 7 steps · GSE · code_examples
Remodeling oncogenic transcriptomes by small molecules targeting NONO. (2023)
GSE78959 · 3 steps · RNA-Seq · code_examples
Genomic analysis of the molecular neuropathology of tuberous sclerosis using a human stem cell model. (2016)
GSE78960 · 3 steps · RNA-Seq · code_examples
Genomic analysis of the molecular neuropathology of tuberous sclerosis using a human stem cell model. (2016)
GSE78961 · 3 steps · GSE · code_examples
Genomic analysis of the molecular neuropathology of tuberous sclerosis using a human stem cell model. (2016)