scholarly journals Comparative transcriptome analysis of rumen papillae in suckling and weaned Japanese Black calves using RNA sequencing

2018 ◽  
Vol 96 (6) ◽  
pp. 2226-2237 ◽  
Author(s):  
Koki Nishihara ◽  
Daichi Kato ◽  
Yutaka Suzuki ◽  
Dahye Kim ◽  
Misato Nakano ◽  
...  
Keyword(s):  
Rna Sequencing ◽  
Transcriptome Analysis ◽  
Comparative Transcriptome ◽  
Comparative Transcriptome Analysis

scholarly journals Comparative transcriptome analysis reveals sesquiterpenoid biosynthesis among 1-, 2- and 3-year old Atractylodes chinensis

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Jianhua Zhao ◽  
Chengzhen Sun ◽  
Fengyu Shi ◽  
Shanshan Ma ◽  
Jinshuang Zheng ◽  
...  
Keyword(s):  
Rna Sequencing ◽  
Transcriptome Analysis ◽  
Molecular Mechanisms ◽  
Expression Patterns ◽  
Pcr Analysis ◽  
Squalene Epoxidase ◽  
Sequencing Analysis ◽  
Comparative Transcriptome ◽  
Comparative Transcriptome Analysis ◽  
Qrt Pcr

Abstract Background Atractylodes chinensis (DC.) Koidz is a well-known medicinal plant containing the major bioactive compound, atractylodin, a sesquiterpenoid. High-performance liquid chromatography (HPLC) analysis demonstrated that atractylodin was most abundant in 3-year old A. chinensis rhizome, compared with those from 1- and 2-year old rhizomes, however, the molecular mechanisms underlying accumulation of atractylodin in rhizomes are poorly understood. Results In this study, we characterized the transcriptomes from rhizomes of 1-, 2- and 3-year old (Y1, Y2 and Y3, respectively) A. chinensis, to identify differentially expressed genes (DEGs). We identified 240, 169 and 131 unigenes encoding the enzyme genes in the mevalonate (MVA), methylerythritol phosphate (MEP), sesquiterpenoid and triterpenoid biosynthetic pathways, respectively. To confirm the reliability of the RNA sequencing analysis, eleven key gene encoding factors involved in the sesquiterpenoid and triterpenoid biosynthetic pathway, as well as in pigment, amino acid, hormone and transcription factor functions, were selected for quantitative real time PCR (qRT-PCR) analysis. The results demonstrated similar expression patterns to those determined by RNA sequencing, with a Pearson’s correlation coefficient of 0.9 between qRT-PCR and RNA-seq data. Differential gene expression analysis of rhizomes from different ages revealed 52 genes related to sesquiterpenoid and triterpenoid biosynthesis. Among these, seven DEGs were identified in Y1 vs Y2, Y1 vs Y3 and Y2 vs Y3, of which five encoded four key enzymes, squalene/phytoene synthase (SS), squalene-hopene cyclase (SHC), squalene epoxidase (SE) and dammarenediol II synthase (DS). These four enzymes directly related to squalene biosynthesis and subsequent catalytic action. To validate the result of these seven DEGs, qRT-PCR was performed and indicated most of them displayed lower relative expression in 3-year old rhizome, similar to transcriptomic analysis. Conclusion The enzymes SS, SHC, SE and DS down-regulated expression in 3-year old rhizome. This data corresponded to the higher content of sesquiterpenoid in 3-year old rhizome, and confirmed by qRT-PCR. The results of comparative transcriptome analysis and identified key enzyme genes laid a solid foundation for investigation of production sesquiterpenoid in A. chinensis.

scholarly journals Comparative transcriptome analysis of hESC- and iPSC-derived lentoid bodies

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Muhammad Ali ◽  
Firoz Kabir ◽  
Jason J. Thomson ◽  
Yinghong Ma ◽  
Caihong Qiu ◽  
...  
Keyword(s):  
Stem Cells ◽  
Rna Sequencing ◽  
Transcriptome Analysis ◽  
Pluripotent Stem Cells ◽  
Embryonic Stem ◽  
Comparative Transcriptome ◽  
Rna Seq ◽  
Peripheral Blood Mononuclear ◽  
Report Generation ◽  
Comparative Transcriptome Analysis

AbstractThe ocular lens serves as an excellent system to investigate the intricate details of development and differentiation. Generation of lentoid bodies or lens-like structures using pluripotent stem cells is important for understanding the processes critical for lens morphogenesis and the mechanism of cataractogenesis. We previously reported the generation of peripheral blood mononuclear cell (PBMC)-originated, induced pluripotent stem cells (iPSCs). Here, we report generation of lentoid bodies from human embryonic stem cells (hESCs) and (PBMC)-originated, iPSCs employing the “fried egg” method with brief modifications. The ultrastructure analysis of hESC- and iPSC-derived lentoid bodies identified closely packed lens epithelial- and differentiating fiber-like cells. In addition, we performed RNA sequencing (RNA-Seq) based transcriptome profiling of hESC- and iPSC-derived lentoid bodies at differentiation day 25. Next-generation RNA sequencing (RNA-Seq) of hESC- and iPSC-derived lentoid bodies detected expression (≥0.659 RPKM) of 13,975 and 14,003 genes, respectively. Comparative transcriptome analysis of hESC- and iPSC-derived lentoid bodies revealed 13,563 (>96%) genes common in both datasets. Among the genes common in both transcriptome datasets, 12,856 (~95%) exhibited a quantitatively similar expression profile. Next, we compared the mouse lens epithelial and fiber cell transcriptomes with hESC- and iPSC-derived lentoid bodies transcriptomes and identified > 96% overlap with lentoid body transcriptomes. In conclusion, we report first-time comparative transcriptome analysis of hESC- and iPSC-derived lentoid bodies at differentiation day 25.

Sign in / Sign up

Export Citation Format

Share Document