Search publications
87 results for “RNA sequencing”
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Integrative genome-wide analysis reveals cooperative regulation of alternative splicing by hnRNP proteins.
Cell reports · 2012 · 1(2): 167-78
Understanding how RNA binding proteins control the splicing code is fundamental to human biology and disease. Here, we present a comprehensive study to elucidate how heterogeneous nuclear ribonucleoparticle (hnRNP) proteins, among the most abundant RNA binding proteins, coordinate to regulate …
PMID 22574288 DOI ↗
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Comprehensive identification of miRNA target sites in live animals.
Methods in molecular biology (Clifton, N.J.) · 2011 · 732: 169-85
MicroRNAs (miRNAs) are small RNA molecules that posttranscriptionally regulate the expression of protein-coding genes. The mature miRNAs are loaded into Argonaute-containing protein complexes (miRISC, miRNA Induced S ilencing Complex), and guide these complexes to the 3' UTR of targeted mRNA …
PMID 21431713 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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Long pre-mRNA depletion and RNA missplicing contribute to neuronal vulnerability from loss of TDP-43.
Nature neuroscience · 2011 · 14(4): 459-68
We used cross-linking and immunoprecipitation coupled with high-throughput sequencing to identify binding sites in 6,304 genes as the brain RNA targets for TDP-43, an RNA binding protein that, when mutated, causes amyotrophic lateral sclerosis. Massively parallel sequencing and splicing-sensitive junction …
PMID 21358643 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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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 ↗
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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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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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Inference of splicing regulatory activities by sequence neighborhood analysis.
PLoS genetics · 2006 · 2(11): e191
Sequence-specific recognition of nucleic-acid motifs is critical to many cellular processes. We have developed a new and general method called Neighborhood Inference (NI) that predicts sequences with activity in regulating a biochemical process based on the local density of known …
PMID 17121466 DOI ↗
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Identification and analysis of alternative splicing events conserved in human and mouse.
Proceedings of the National Academy of Sciences of the United States of America · 2005 · 102(8): 2850-5
Alternative pre-mRNA splicing affects a majority of human genes and plays important roles in development and disease. Alternative splicing (AS) events conserved since the divergence of human and mouse are likely of primary biological importance, but relatively few of such …
PMID 15708978 DOI ↗
Datasets 22
MBNL2 dysfunction in outer radial glial cells is associated with disrupted corticogenesis in congenital myotonic dystrophy [scRNA-Seq]
GPL24676
Identification of islet-enriched long non-coding RNAs contributing to beta-cell failure in type 2 diabetes
Mus musculus · GPL9250
RNA sequencing of bone marrow CD34+ hematopoietic stem and progenitor cells from patients with myelodysplastic syndrome and healthy controls
Homo sapiens · GPL20301
Aberrant splicing of U12-type introns is the hallmark of ZRSR2 mutant myelodysplastic syndrome
Homo sapiens · GPL11154
RNA-Seq of CD8+ T cell subsets during LCMV infection III
Mus musculus · GPL17021
Transcriptional Survey of Ileal-Anal Pouch Immune Cells from Ulcerative Colitis
Homo sapiens · GPL20301
Developmental emergence of adult neural stem cells as revealed by single cell transcriptional profiling
Mus musculus · GPL19057
CRISPR/Cas9 screening of RNA binding proteins (RBPs) that regulate RUNX1 isoform production
Homo sapiens · GPL20301
A transcriptome-wide divergence in protein translation scales with LIN28B expression
Mus musculus · GPL20301
Epigenetics CRISPRi screen in mouse neuronal progenitor cells (NPCs)
Mus musculus · GPL21626
Expanded repertoire of RNA-editing-based detection for RNA binding protein interactions (2)
Homo sapiens · GPL24676
RNA-seq in neurites and soma of primary hippocampal neurons isolated from P0 or P1 mice
Mus musculus · GPL19057
Molecular determinants and heterogeneity of circulating and tissue-resident memory CD8+ T lymphocytes revealed by single-cell RNA sequencing
Mus musculus · GPL21103
Direct RNA sequencing enables single-nucleotide m6A detection in endogenous transcript isoforms
Homo sapiens · GPL24106
FLARE: A fast and flexible peak-calling pipeline for identifying RNA editing foci
Homo sapiens · GPL24676
Transcriptome analysis of diverse cell types infected with human cytomegalovirus [array]
Homo sapiens · GPL15106
Gene expression profiles at the single cell level of CD8+ T cells from the spleens of LCMV-Armstrong or LCMV-Clone 13 infected mice
Mus musculus · GPL19057
Early transcriptional and epigenetic regulation of CD8+ T cell differentiation revealed by single-cell RNA-seq
Mus musculus · GPL17021
Transcriptome analysis of diverse cell types infected with human cytomegalovirus [RNA-Seq]
Homo sapiens · GPL11154
Single Cell RNA-Seq of CD8+ T cell subsets responding to tumor
Mus musculus · GPL21103
The dsRBP and inactive editor, ADR-1, utilizes dsRNA binding to regulate A-to-I RNA editing across the C. elegans transcriptome
6239 · GPL9269
Analyses 8
GSE114922 · 7 steps · RNA-Seq · code_examples
Integrative RNA-omics Discovers GNAS Alternative Splicing as a Phenotypic Driver of Splicing Factor-Mutant Neoplasms. (2022)
GSE65973 · 5 steps · RNA-Seq · code_examples
Aberrant NOVA1 function disrupts alternative splicing in early stages of amyotrophic lateral sclerosis. (2022)
GSE131847 · 5 steps · RNA-Seq · code_examples
Early precursors and molecular determinants of tissue-resident memory CD8<sup>+</sup> T lymphocytes revealed by single-cell RNA sequencing. (2020)
GSE132971 · 4 steps · RNA-Seq · code_examples
Direct RNA sequencing enables m<sup>6</sup>A detection in endogenous transcript isoforms at base-specific resolution. (2020)
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)