RNA-Seq transcriptome analysis of Spirodela dormancy without reproduction

Mercury is one of the detrimental toxicants that can be found in the environment and exists naturally in different forms; inorganic and organic. Human exposure to inorganic mercury, such as mercury chloride, occurs through air pollution, absorption of food or water, and personal care products. This study aimed to investigate the effect of HgCl2 on cell viability, cell cycle, apoptotic pathway, and alters of the transcriptome profiles in human non-small cell lung cancer cells, H1299. Our data show that HgCl2 treatment causes inhibition of cell growth via cell cycle arrest at G0/G1- and S-phase. In addition, HgCl2 induces apoptotic cell death through the caspase-3-independent pathway. Comprehensive transcriptome analysis using RNA-seq indicated that cellular nitrogen compound metabolic process, cellular metabolism, and translation for biological processes-related gene sets were significantly up- and downregulated by HgCl2 treatment. Interestingly, comparative gene expression patterns by RNA-seq indicated that mitochondrial ribosomal proteins were markedly altered by low-dose of HgCl2 treatment. Altogether, these data show that HgCl2 induces apoptotic cell death through the dysfunction of mitochondria.

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184 Whole-transcriptome analysis by RNA-Seq for genetic diagnosis of Mendelian skin disorders in the context of consanguinity

Journal of Investigative Dermatology ◽

10.1016/j.jid.2021.02.204 ◽

2021 ◽

Vol 141 (5) ◽

pp. S32

Author(s):

L. Youssefian ◽

A. Saeidian ◽

P. Fortina ◽

A. South ◽

J. Uitto ◽

...

Keyword(s):

Transcriptome Analysis ◽

Genetic Diagnosis ◽

Rna Seq ◽

Skin Disorders ◽

Whole Transcriptome Analysis ◽

Whole Transcriptome

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De novo RNA-Seq based transcriptome analysis of Papiliotrema laurentii strain RY1 under nitrogen starvation

Gene ◽

10.1016/j.gene.2017.12.014 ◽

2018 ◽

Vol 645 ◽

pp. 146-156 ◽

Cited By ~ 5

Author(s):

Soumyadev Sarkar ◽

Somnath Chakravorty ◽

Avishek Mukherjee ◽

Debanjana Bhattacharya ◽

Semantee Bhattacharya ◽

...

Keyword(s):

Transcriptome Analysis ◽

Nitrogen Starvation ◽

De Novo ◽

Rna Seq

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Transcriptome Analysis Based on RNA-Seq in Understanding Pathogenic Mechanisms of Diseases and the Immune System of Fish: A Comprehensive Review

International Journal of Molecular Sciences ◽

10.3390/ijms19010245 ◽

2018 ◽

Vol 19 (1) ◽

pp. 245 ◽

Cited By ~ 39

Author(s):

Arun Sudhagar ◽

Gokhlesh Kumar ◽

Mansour El-Matbouli

Keyword(s):

Immune System ◽

Transcriptome Analysis ◽

Rna Seq ◽

Comprehensive Review ◽

Pathogenic Mechanisms

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De Novo Transcriptome Analysis of Medicinally Important Plantago ovata Using RNA-Seq

PLoS ONE ◽

10.1371/journal.pone.0150273 ◽

2016 ◽

Vol 11 (3) ◽

pp. e0150273 ◽

Cited By ~ 14

Author(s):

Shivanjali Kotwal ◽

Sanjana Kaul ◽

Pooja Sharma ◽

Mehak Gupta ◽

Rama Shankar ◽

...

Keyword(s):

Transcriptome Analysis ◽

De Novo ◽

Rna Seq ◽

Plantago Ovata ◽

De Novo Transcriptome

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Time-Course Transcriptome Analysis Reveals Resistance Genes of Panax ginseng Induced by Cylindrocarpon destructans Infection Using RNA-Seq

PLoS ONE ◽

10.1371/journal.pone.0149408 ◽

2016 ◽

Vol 11 (2) ◽

pp. e0149408 ◽

Cited By ~ 7

Author(s):

Yuan Gao ◽

Xiaoli He ◽

Bin Wu ◽

Qiliang Long ◽

Tianwei Shao ◽

...

Keyword(s):

Panax Ginseng ◽

Resistance Genes ◽

Transcriptome Analysis ◽

Time Course ◽

Rna Seq ◽

Cylindrocarpon Destructans

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De novo gonad transcriptome analysis of the common littoral shrimp Palaemon serratus: novel insights into sex-related genes

BMC Genomics ◽

10.1186/s12864-019-6157-4 ◽

2019 ◽

Vol 20 (1) ◽

Cited By ~ 3

Author(s):

Inés González-Castellano ◽

Chiara Manfrin ◽

Alberto Pallavicini ◽

Andrés Martínez-Lage

Keyword(s):

Transcriptome Analysis ◽

De Novo ◽

Expression Patterns ◽

Gonadal Development ◽

Differentially Expressed ◽

Rna Seq ◽

Illumina Hiseq ◽

Specific Expression ◽

Development Processes ◽

The Common

Abstract Background The common littoral shrimp Palaemon serratus is an economically important decapod resource in some European communities. Aquaculture practices prevent the genetic deterioration of wild stocks caused by overfishing and at the same time enhance the production. The biotechnological manipulation of sex-related genes has the proved potential to improve the aquaculture production but the scarcity of genomic data about P. serratus hinders these applications. RNA-Seq analysis has been performed on ovary and testis samples to generate a reference gonadal transcriptome. Differential expression analyses were conducted between three ovary and three testis samples sequenced by Illumina HiSeq 4000 PE100 to reveal sex-related genes with sex-biased or sex-specific expression patterns. Results A total of 224.5 and 281.1 million paired-end reads were produced from ovary and testis samples, respectively. De novo assembly of ovary and testis trimmed reads yielded a transcriptome with 39,186 transcripts. The 29.57% of the transcriptome retrieved at least one annotation and 11,087 differentially expressed genes (DEGs) were detected between ovary and testis replicates. Six thousand two hundred seven genes were up-regulated in ovaries meanwhile 4880 genes were up-regulated in testes. Candidate genes to be involved in sexual development and gonadal development processes were retrieved from the transcriptome. These sex-related genes were discussed taking into account whether they were up-regulated in ovary, up-regulated in testis or not differentially expressed between gonads and in the framework of previous findings in other crustacean species. Conclusions This is the first transcriptome analysis of P. serratus gonads using RNA-Seq technology. Interesting findings about sex-related genes from an evolutionary perspective (such as Dmrt1) and for putative future aquaculture applications (Iag or vitellogenesis genes) are reported here. We provide a valuable dataset that will facilitate further research into the reproductive biology of this shrimp.

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Whole Transcriptome Analysis of Hypertension Induced Cardiac Injury Using Deep Sequencing

Cellular Physiology and Biochemistry ◽

10.1159/000438659 ◽

2016 ◽

Vol 38 (2) ◽

pp. 670-682 ◽

Cited By ~ 4

Author(s):

Tao-Tao Li ◽

Xiao-Yan Li ◽

Li-Xin Jia ◽

Jing Zhang ◽

Wen-Mei Zhang ◽

...

Keyword(s):

Transcriptome Analysis ◽

Cell Activation ◽

Critical Role ◽

Cardiac Injury ◽

Interaction Network ◽

Receptor Interaction ◽

Rna Seq ◽

Cardiac Inflammation ◽

Molecular Events ◽

Focal Adhesion Protein

Background/Aims: Hypertension plays a critical role in the cardiac inflammation and injury. However, the mechanism of how hypertension causes the cardiac injury at a molecular level remains to be elucidated. Methods: RNA-Seq has been demonstrated to be an effective approach for transcriptome analysis, which is essential to reveal the molecular constituents of cells and tissues. In this study, we investigated the global molecular events associated with the mechanism of hypertension induced cardiac injury using RNA-Seq analysis. Results: Our results showed that totally 1,801 genes with different expression variations were identified after Ang II infusion at 1, 3 and 7 days. Go analysis showed that the top 5 high enrichment Go terms were response to stress, response to wounding, cellular component organization, cell activation and defense response. KEGG pathway analysis revealed the top 5 significantly overrepresented pathways were associated with ECM-receptor interaction, focal adhesion, protein digestion and absorption, phagosome and asthma. Moreover, protein-protein interaction network analysis indicated that ubiquitin C may play a key role in the processes of hypertension-induced cardiac injury. Conclusion: Our study provides a comprehensive understanding of the transcriptome events in hypertension-induced cardiac pathology.

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