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1.
Nucleic Acids Res ; 48(W1): W300-W306, 2020 07 02.
Article in English | MEDLINE | ID: mdl-32286627

ABSTRACT

The rMAPS2 (RNA Map Analysis and Plotting Server 2) web server, freely available at http://rmaps.cecsresearch.org/, has provided the high-throughput sequencing data research community with curated tools for the identification of RNA binding protein sites. rMAPS2 analyzes differential alternative splicing or CLIP peak data obtained from high-throughput sequencing data analysis tools like MISO, rMATS, Piranha, PIPE-CLIP and PARalyzer, and then, graphically displays enriched RNA-binding protein target sites. The initial release of rMAPS focused only on the most common alternative splicing event, skipped exon or exon skipping. However, there was a high demand for the analysis of other major types of alternative splicing events, especially for retained intron events since this is the most common type of alternative splicing in plants, such as Arabidopsis thaliana. Here, we expanded the implementation of rMAPS2 to facilitate analyses for all five major types of alternative splicing events: skipped exon, mutually exclusive exons, alternative 5' splice site, alternative 3' splice site and retained intron. In addition, by employing multi-threading, rMAPS2 has vastly improved the user experience with significant reductions in running time, ∼3.5 min for the analysis of all five major alternative splicing types at once.


Subject(s)
Alternative Splicing , RNA-Binding Proteins/metabolism , Software , Animals , Arabidopsis/genetics , Binding Sites , Cattle , Exons , Humans , Introns , Mice , Nucleotide Motifs , RNA/chemistry , RNA/metabolism , RNA Splice Sites , Rats , Sequence Analysis, RNA
2.
Cell Rep ; 24(6): 1653-1666.e7, 2018 08 07.
Article in English | MEDLINE | ID: mdl-30089273

ABSTRACT

The mammary gland consists of cells with gene expression patterns reflecting their cellular origins, function, and spatiotemporal context. However, knowledge of developmental kinetics and mechanisms of lineage specification is lacking. We address this significant knowledge gap by generating a single-cell transcriptome atlas encompassing embryonic, postnatal, and adult mouse mammary development. From these data, we map the chronology of transcriptionally and epigenetically distinct cell states and distinguish fetal mammary stem cells (fMaSCs) from their precursors and progeny. fMaSCs show balanced co-expression of factors associated with discrete adult lineages and a metabolic gene signature that subsides during maturation but reemerges in some human breast cancers and metastases. These data provide a useful resource for illuminating mammary cell heterogeneity, the kinetics of differentiation, and developmental correlates of tumorigenesis.


Subject(s)
Mammary Glands, Animal/growth & development , Animals , Cell Differentiation/physiology , Female , Humans , Mammary Glands, Animal/cytology , Mice , Stem Cells/metabolism , Transcriptome
3.
Stem Cell Rev Rep ; 7(3): 532-43, 2011 Sep.
Article in English | MEDLINE | ID: mdl-21298405

ABSTRACT

Endothelial cells (ECs) represent the major component of the embryonic pancreatic niche and play a key role in the differentiation of insulin-producing ß cells in vivo. However, it is unknown if ECs promote such differentiation in vitro. We investigated whether interaction of ECs with mouse embryoid bodies (EBs) in culture promotes differentiation of pancreatic progenitors and insulin-producing cells and the mechanisms involved. We developed a co-culture system of mouse EBs and human microvascular ECs (HMECs). An increase in the expression of the pancreatic markers PDX-1, Ngn3, Nkx6.1, proinsulin, GLUT-2, and Ptf1a was observed at the interface between EBs and ECs (EB-EC). No expression of these markers was found at the periphery of EBs cultured without ECs or those co-cultured with mouse embryonic fibroblasts (MEFs). At EB-EC interface, proinsulin and Nkx6.1 positive cells co-expressed phospho-Smad1/5/8 (pSmad1/5/8). Therefore, EBs were treated with HMEC conditioned media (HMEC-CM) suspecting soluble factors involved in bone morphogenetic protein (BMP) pathway activation. Upregulation of PDX-1, Ngn3, Nkx6.1, insulin-1, insulin-2, amylin, SUR1, GKS, and amylase as well as down-regulation of SST were detected in treated EBs. In addition, higher expression of BMP-2/-4 and their receptor (BMPR1A) were also found in these EBs. Recombinant human BMP-2 (rhBMP-2) mimicked the effects of the HMEC-CM on EBs. Noggin (NOG), a BMP antagonist, partially inhibited these effects. These results indicate that the differentiation of EBs to pancreatic progenitors and insulin-producing cells can be enhanced by ECs in vitro and that BMP pathway activation is central to this process.


Subject(s)
Bone Morphogenetic Proteins/metabolism , Cell Differentiation/physiology , Embryonic Stem Cells/physiology , Endothelial Cells/physiology , Insulin-Secreting Cells/physiology , Pancreas/cytology , Signal Transduction/physiology , Animals , Biomarkers/metabolism , Cells, Cultured , Coculture Techniques , Embryoid Bodies/cytology , Embryoid Bodies/physiology , Embryonic Stem Cells/cytology , Endothelial Cells/cytology , Humans , Insulin/metabolism , Insulin-Secreting Cells/cytology , Mice , Stem Cells/cytology , Stem Cells/physiology
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