scholarly journals Gene Profiling of Bone around Orthodontic Mini-Implants by RNA-Sequencing Analysis

2015 ◽  
Vol 2015 ◽  
pp. 1-14 ◽  
Author(s):  
Kyung-Yen Nahm ◽  
Jung Sun Heo ◽  
Jae-Hyung Lee ◽  
Dong-Yeol Lee ◽  
Kyu-Rhim Chung ◽  
...  
Keyword(s):  
Bone Formation ◽  
Rna Sequencing ◽  
Cell Fate ◽  
Reduction Process ◽  
Gene Profiling ◽  
Sequencing Analysis ◽  
Rna Seq ◽  
Mini Implants ◽  
Oxidation Reduction ◽  
The Times

This study aimed to evaluate the genes that were expressed in the healing bones around SLA-treated titanium orthodontic mini-implants in a beagle at early (1-week) and late (4-week) stages with RNA-sequencing (RNA-Seq). Samples from sites of surgical defects were used as controls. Total RNA was extracted from the tissue around the implants, and an RNA-Seq analysis was performed with Illumina TruSeq. In the 1-week group, genes in the gene ontology (GO) categories of cell growth and the extracellular matrix (ECM) were upregulated, while genes in the categories of the oxidation-reduction process, intermediate filaments, and structural molecule activity were downregulated. In the 4-week group, the genes upregulated included ECM binding, stem cell fate specification, and intramembranous ossification, while genes in the oxidation-reduction process category were downregulated. GO analysis revealed an upregulation of genes that were related to significant mechanisms, including those with roles in cell proliferation, the ECM, growth factors, and osteogenic-related pathways, which are associated with bone formation. From these results, implant-induced bone formation progressed considerably during the times examined in this study. The upregulation or downregulation of selected genes was confirmed with real-time reverse transcription polymerase chain reaction. The RNA-Seq strategy was useful for defining the biological responses to orthodontic mini-implants and identifying the specific genetic networks for targeted evaluations of successful peri-implant bone remodeling.

scholarly journals Deep RNA sequencing analysis of syncytialization-related genes during BeWo cell fusion

Reproduction ◽  
2017 ◽  
Vol 153 (1) ◽  
pp. 35-48 ◽  
Author(s):  
Ru Zheng ◽  
Yue Li ◽  
Huiying Sun ◽  
Xiaoyin Lu ◽  
Bao-Fa Sun ◽  
...  
Keyword(s):  
Rna Sequencing ◽  
Cell Fate ◽  
Cell Fusion ◽  
Mapk Pathway ◽  
Differentially Expressed ◽  
Cell Junction ◽  
Bewo Cell ◽  
Sequencing Analysis ◽  
Rna Seq ◽  
Bewo Cells

The syncytiotrophoblast (STB) plays a key role in maintaining the function of the placenta during human pregnancy. However, the molecular network that orchestrates STB development remains elusive. The aim of this study was to obtain broad and deep insight into human STB formation via transcriptomics. We adopted RNA sequencing (RNA-Seq) to investigate genes and isoforms involved in forskolin (FSK)-induced fusion of BeWo cells. BeWo cells were treated with 50 μM FSK or dimethyl sulfoxide (DMSO) as a vehicle control for 24 and 48 h, and the mRNAs at 0, 24 and 48 h were sequenced. We detected 28,633 expressed genes and identified 1902 differentially expressed genes (DEGs) after FSK treatment for 24 and 48 h. Among the 1902 DEGs, 461 were increased and 395 were decreased at 24 h, whereas 879 were upregulated and 763 were downregulated at 48 h. When the 856 DEGs identified at 24 h were traced individually at 48 h, they separated into 6 dynamic patterns via a K-means algorithm, and most were enriched in down–even and up–even patterns. Moreover, the gene ontology (GO) terms syncytium formation, cell junction assembly, cell fate commitment, calcium ion transport, regulation of epithelial cell differentiation and cell morphogenesis involved in differentiation were clustered, and the MAPK pathway was most significantly regulated. Analyses of alternative splicing isoforms detected 123,200 isoforms, of which 1376 were differentially expressed. The present deep analysis of the RNA-Seq data of BeWo cell fusion provides important clues for understanding the mechanisms underlying human STB formation.

scholarly journals Comprehensive Analysis of lncRNAs and circRNAs Reveals the Metabolic Specialization in Oxidative and Glycolytic Skeletal Muscles

2019 ◽  
Vol 20 (12) ◽  
pp. 2855 ◽  
Author(s):  
Linyuan Shen ◽  
Mailin Gan ◽  
Qianzi Tang ◽  
Guoqing Tang ◽  
Yanzhi Jiang ◽  
...  
Keyword(s):  
Meat Quality ◽  
Skeletal Muscles ◽  
Target Genes ◽  
Fiber Type ◽  
Muscle Metabolism ◽  
Reduction Process ◽  
Differentially Expressed ◽  
Rna Seq ◽  
Oxidation Reduction ◽  
Regulatory Analysis

The biochemical and functional differences between oxidative and glycolytic muscles could affect human muscle health and animal meat quality. However, present understanding of the epigenetic regulation with respect to lncRNAs and circRNAs is rudimentary. Here, porcine oxidative and glycolytic skeletal muscles, which were at the growth curve inflection point, were sampled to survey variant global expression of lncRNAs and circRNAs using RNA-seq. A total of 4046 lncRNAs were identified, including 911 differentially expressed lncRNAs (p < 0.05). The cis-regulatory analysis identified target genes that were enriched for specific GO terms and pathways (p < 0.05), including the oxidation-reduction process, glycolytic process, and fatty acid metabolic. All these were closely related to different phenotypes between oxidative and glycolytic muscles. Additionally, 810 circRNAs were identified, of which 137 were differentially expressed (p < 0.05). Interestingly, some circRNA-miRNA-mRNA networks were found, which were closely linked to muscle fiber-type switching and mitochondria biogenesis in muscles. Furthermore, 44.69%, 39.19%, and 54.01% of differentially expressed mRNAs, lncRNAs, and circRNAs respectively were significantly enriched in pig quantitative trait loci (QTL) regions for growth and meat quality traits. This study reveals a mass of candidate lncRNAs and circRNAs involved in muscle physiological functions, which may improve understanding of muscle metabolism and development from an epigenetic perspective.

Identification of Differentially Expressed and Spliced Genes with RNA Sequencing Analysis of CLL Specimens

Blood ◽  
2012 ◽  
Vol 120 (21) ◽  
pp. 4582-4582
Author(s):  
Wei Liao ◽  
Gwen Jordaan ◽  
Artur Jaroszewicz ◽  
Matteo Pellegrini ◽  
Sanjai Sharma
Keyword(s):  
B Cells ◽  
Rna Sequencing ◽  
Differentially Expressed Genes ◽  
Fold Change ◽  
Differentially Expressed ◽  
Pcr Analysis ◽  
Sequencing Analysis ◽  
Rna Seq ◽  
Mrna Isoforms ◽  
Core Set

Abstract Abstract 4582 High throughput sequencing of cellular mRNA provides a comprehensive analysis of the transcriptome. Besides identifying differentially expressed genes in different cell types, it also provides information of mRNA isoforms and splicing alterations. We have analyzed two CLL specimens and a normal peripheral blood B cells mRNA by this approach and performed data analysis to identify differentially expressed and spliced genes. The result showed CLLs specimens express approximately 40% more transcripts compared to normal B cells. The FPKM data (fragment per kilobase of exon per million) revealed a higher transcript expression on chromosome 12 in CLL#1 indicating the presence of trisomy 12, which was confirmed by fluorescent in-situ hybridization assay. With a two-fold change in FPKM as a cutoff and a p value cutoff of 0.05 as compared to the normal B cell control, 415 genes and 174 genes in CLL#1 and 676 and 235 genes in CLL#2 were up and downregulated or differentially expressed. In these two CLL specimens, 45% to 75% of differentially expressed genes are common to both the CLL specimens indicating that genetically disparate CLL specimens have a high percentage of a core set of genes that are potentially important for CLL biology. Selected differentially expressed genes with increased expression (selectin P ligand, SELPLG, and adhesion molecule interacts with CXADR antigen 1, AMICA) and decreased (Fos, Jun, CD69 and Rhob) expression based on the FPKM from RNA-sequencing data were also analyzed in additional CLL specimens by real time PCR analysis. The expression data from RNA-seq closely matches the fold-change in expression as measured by RT-PCR analysis and confirms the validity of the RNA-seq analysis. Interestingly, Fos was identified as one of the most downregulated gene in CLL. Using the Cufflinks and Cuffdiff software, the splicing patterns of genes in CLL specimens and normal B cells were analyzed. Approximately, 1100 to 1250 genes in the two CLL specimens were significantly differentially spliced as compared to normal B cells. In this analysis as well, there is a core set of 800 common genes which are differentially spliced in the two CLL specimens. The RNA-sequencing analysis accurately identifies differentially expressed novel genes and splicing variations that will help us understand the biology of CLL. Disclosures: No relevant conflicts of interest to declare.

scholarly journals RNA-sequencing analysis of the effect of luteolin on methamphetamine-induced hepatotoxicity in rats: a preliminary study

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e8529
Author(s):  
Dong Qu ◽  
Kaikai Zhang ◽  
Lijian Chen ◽  
Qi Wang ◽  
Huijun Wang
Keyword(s):  
Fatty Acid ◽  
Rna Sequencing ◽  
Biochemical Analysis ◽  
Fatty Acid Synthase ◽  
Sequencing Analysis ◽  
Protective Effects ◽  
Rna Seq ◽  
Oral Gavage ◽  
Fatty Acid Binding ◽  
Preliminary Study

In this study, RNA-sequencing (RNA-seq) was utilized to investigate the effects of luteolin on hepatotoxicity caused by methamphetamine (METH). The rats in METH group were administrated with METH (15 mg/kg, two times per day) via intraperitoneal (i.p.) injections for four consecutive days. The rats in luteolin + METH group were firstly administrated with luteolin (100 mg/kg, once a day) by oral gavage for 3 days before METH treatment. Lueolin attenuated the hepatotoxicity induced by METH via histopathological and biochemical analysis. The results of RNA-seq showed that luteolin could regulate 497 differentially expressed genes (DEGs), and the selected DEGs were mainly enriched in eight pathways, according to KEGG analysis. Furthermore, qRT-PCR was utilized to verify the results of RNA-seq. Six genes were selected as follows: liver enriched antimicrobial peptide 2 (Leap2), fatty acid synthase (Fasn), fatty acid binding protein 5 (Fabp5), patatin like phospholipase domain containing 3 (Pnpla3), myelin basic protein (Mbp) and calmodulin 3 (Calm3). Though because of the design flaws, the luteolin group has not been included, this study demonstrated that luteolin might exert hepato-protective effects from METH via modulation of oxidative phosphorylation, cytochrome P450 and certain signaling pathways.

scholarly journals Myrislignan Induces Redox Imbalance and Activates Autophagy in Toxoplasma gondii

2021 ◽  
Vol 11 ◽  
Author(s):  
Jili Zhang ◽  
Jia Chen ◽  
Kun Lv ◽  
Bing Li ◽  
Biqing Yan ◽  
...  
Keyword(s):  
Toxoplasma Gondii ◽  
Reduction Process ◽  
New Drugs ◽  
Sequencing Analysis ◽  
Oxidation Reduction ◽  
Transmission Electron ◽  
Important Health ◽  
Deep Sequencing Analysis

Toxoplasma gondii (T. gondii) is an important health problem in human and animals, and the highlighting side effects of launched therapeutic chemicals cannot be ignored. Thus, it is urgent to develop new drugs to against the infection. Myrislignan originated from nutmeg exhibited excellent anti-T. gondii activity in vitro and in vivo, and was able to destroy mitochondrial function. However, the exact mechanism of action is still unknown. In this study, combining RNAs deep-sequencing analysis and surface plasmon resonance (SPR) analysis, the differentially expressed genes (DEGs) and high affinity proteins suggested that myrislignan may affect the oxidation-reduction process of T. gondii. Furthermore, the upregulating ROS activity after myrislignan incubation verified that myrislignan destroyed the oxidant-antioxidant homeostasis of tachyzoites. Transmission electron microscopy (TEM) indicated that myrislignan induced the formation of autophagosome-like double-membrane structure. Moreover, monodansyl cadaverine (MDC) staining and western blot further illustrated autophagosome formation. Myrislignan treatment induced a significant reduction in T. gondii by flow cytometry analysis. Together, these findings demonstrated that myrislignan can induce the oxidation-reduction in T. gondii, lead to the autophagy, and cause the death of T. gondii.

scholarly journals RNA-sequencing analysis of high glucose-treated monocytes reveals novel transcriptome signatures and associated epigenetic profiles

2013 ◽  
Vol 45 (7) ◽  
pp. 287-299 ◽  
Author(s):  
Feng Miao ◽  
Zhuo Chen ◽  
Lingxiao Zhang ◽  
Jinhui Wang ◽  
Harry Gao ◽  
...  
Keyword(s):  
Rna Sequencing ◽  
High Glucose ◽  
Sequencing Analysis ◽  
Rna Seq ◽  
Blood Monocytes ◽  
Motif Analysis ◽  
Interferon Stimulated Genes ◽  
Normal Glucose ◽  
Upregulated Genes

We performed high throughput transcriptomic profiling with RNA sequencing (RNA-Seq) to uncover network responses in human THP-1 monocytes treated with high glucose (HG). Our data analyses revealed that interferon (IFN) signaling, pattern recognition receptors, and activated interferon regulatory factors (IRFs) were enriched among the HG-upregulated genes. Motif analysis identified an HG-responsive IRF-mediated network in which interferon-stimulated genes (ISGs) were enriched. Notably, this network showed strong overlap with a recently discovered IRF7-driven network relevant to Type 1 diabetes. We next examined if the HG-regulated genes possessed any characteristic chromatin features in the basal state by profiling 15 active and repressive chromatin marks under normal glucose conditions using chromatin immunoprecipitation linked to promoter microarrays. Composite profiles revealed higher histone H3 lysine-9-acetylation levels around the promoters of HG-upregulated genes compared with all RefSeq promoters. Interestingly, within the HG-upregulated genes, active chromatin marks were enriched not only at high CpG content promoters, but surprisingly also at low CpG content promoters. Similar results were obtained with peripheral blood monocytes exposed to HG. These new results reveal a novel mechanism by which HG can exercise IFN-α-like effects in monocytes by upregulating a set of ISGs poised for activation with multiple chromatin marks.

scholarly journals O-GlcNAcylation of Sox2 at threonine 258 regulates the self-renewal and early cell fate of embryonic stem cells

2021 ◽  
Author(s):  
Dong Keon Kim ◽  
Jang-Seok Lee ◽  
Eun Young Lee ◽  
Hansol Jang ◽  
Suji Han ◽  
...  
Keyword(s):  
Stem Cells ◽  
Embryonic Stem Cells ◽  
Rna Sequencing ◽  
Cell Fate ◽  
Embryonic Stem ◽  
Cartilage Tissue ◽  
Sequencing Analysis ◽  
Post Translational Modification ◽  
Self Renewal ◽  
Cell Fate Decisions

AbstractSox2 is a core transcription factor in embryonic stem cells (ESCs), and O-GlcNAcylation is a type of post-translational modification of nuclear-cytoplasmic proteins. Although both factors play important roles in the maintenance and differentiation of ESCs and the serine 248 (S248) and threonine 258 (T258) residues of Sox2 are modified by O-GlcNAcylation, the function of Sox2 O-GlcNAcylation is unclear. Here, we show that O-GlcNAcylation of Sox2 at T258 regulates mouse ESC self-renewal and early cell fate. ESCs in which wild-type Sox2 was replaced with the Sox2 T258A mutant exhibited reduced self-renewal, whereas ESCs with the Sox2 S248A point mutation did not. ESCs with the Sox2 T258A mutation heterologously introduced using the CRISPR/Cas9 system, designated E14-Sox2TA/WT, also exhibited reduced self-renewal. RNA sequencing analysis under self-renewal conditions showed that upregulated expression of early differentiation genes, rather than a downregulated expression of self-renewal genes, was responsible for the reduced self-renewal of E14-Sox2TA/WT cells. There was a significant decrease in ectodermal tissue and a marked increase in cartilage tissue in E14-Sox2TA/WT-derived teratomas compared with normal E14 ESC-derived teratomas. RNA sequencing of teratomas revealed that genes related to brain development had generally downregulated expression in the E14-Sox2TA/WT-derived teratomas. Our findings using the Sox2 T258A mutant suggest that Sox2 T258 O-GlcNAc has a positive effect on ESC self-renewal and plays an important role in the proper development of ectodermal lineage cells. Overall, our study directly links O-GlcNAcylation and early cell fate decisions.

scholarly journals Single-Cell RNA Sequencing Analysis Reveals Sequential Cell Fate Transition during Human Spermatogenesis

2018 ◽  
Vol 23 (4) ◽  
pp. 599-614.e4 ◽  
Author(s):  
Mei Wang ◽  
Xixi Liu ◽  
Gang Chang ◽  
Yidong Chen ◽  
Geng An ◽  
...  
Keyword(s):  
Single Cell ◽  
Rna Sequencing ◽  
Cell Fate ◽  
Sequencing Analysis ◽  
Single Cell Rna Sequencing ◽  
Human Spermatogenesis

scholarly journals how_are_we_stranded_here: Quick determination of RNA-Seq strandedness

2021 ◽  
Author(s):  
Beth Signal ◽  
Tim Kahlke
Keyword(s):  
Quality Control ◽  
Rna Sequencing ◽  
Published Data ◽  
Sequencing Analysis ◽  
Rna Seq ◽  
Sequencing Data ◽  
Sequence Quality ◽  
Quick Determination

ABSTRACTQuality control checks are the first step in RNA-Sequencing analysis, which enable the identification of common issues that occur in the sequenced reads. Checks for sequence quality, contamination, and complexity are commonplace, and allow users to implement steps downstream which can account for these issues. Strand-specificity of reads is frequently overlooked and is often unavailable even in published data, yet when unknown or incorrectly specified can have detrimental effects on the reproducibility and accuracy of downstream analyses. We present how_are_we_stranded_here, a Python library that helps to quickly infer strandedness of paired-end RNA-Sequencing data.

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