Research Article

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03/20/2015
Differentially expressed genes; Macrobrachium nipponense; Ovary; Reproduction-related genes; Testis

This study utilized high-throughput RNA sequencing technology to identify reproduction- and development-related genes of Macrobrachium nipponense by analyzing gene expression profiles of testis and ovary. More than 20 million 1 x 51-bp reads were obtained by Illumina sequencing, generating more than 7.7 and 11.7 million clean reads in the testis and ovary library, respectively. ... more

H. Qiao; Y.W. Xiong; S.F. Jiang; H.T. Fu; S.M. Sun; S.B. Jin; Y.S. Gong; W.Y. Zhang
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Co-expression network; Differentially expressed genes; Hepatitis C; Pathway

We predicted potential genes and identified pathways associated with hepatitis C. The gene expression profiles of GSE40184 from blood samples and GSE38597 from liver biopsy samples were downloaded from the GEO database. Differentially expressed genes (DEGs) were recognized using the Limma Package. The Pearson correlation test was used to construct the co-expression network of DEGs. Gene ... more

Y. Tang; Q. Tang; C. Dong; X. Li; Z. Zhang; F. An
03/11/2013
Differentially expressed genes; Regulation network; Testicular seminoma

Testicular seminoma has become the most common solid malignancy in young men, especially in the 20s group. We obtained the gene expression profile of human testicular seminoma cells from NCBI, identified the differentially expressed genes of testicular seminoma cells of different stages, and constructed the regulation networks of different stages of testicular seminoma using ... more

J.J. Sha; Y.H. Dong; D.M. Liu; J.J. Bo; Y.R. Huang; Z. Li; P. Ping
10/07/2013
CMAP; Differentially expressed genes; Pulmonary hypoxia-related diseases; Similar drugs

Exposure of humans to low levels of environmental oxygen results in alveolar hypoxia and normally causes chronic pulmonary hypertension and morphological alterations of precapillary pulmonary vessels. In this study, the microarray dataset GSE11341 was used to identify potential differentially expressed genes related with human lung microvascular endothelial cell hypoxia. In addition, gene ... more

L. Zhou; L.M. Wang; H.M. Song; Y.Q. Shen; W.J. Xu; J.H. Xu; Y. Liu; W.W. Yan; J.F. Jiang
06/01/2015
Differentially expressed genes; Epstein-Barr virus-positive nasopharyngeal carcinoma; Target genes; Typical miRNAs

This study aims to identify the crucial miRNAs in Epstein-Barr virus-positive nasopharyngeal carcinoma (NPC) and their target genes. Gene expression profile data (GSE12452) that included 31 NPC and 10 normal nasopharyngeal tissue specimens were downloaded. Differentially expressed genes (DEGs) were identified using significance analysis of microarrays. The underlying function of DEGs was ... more

L.H. Zhu; X.T. Miao; N.Y. Wang
03/19/2014
Gall fly; Illumina sequencing; Procecidochares utilis; Simple sequence repeat (SSR) marker; Transcriptome

Procecidochares utilis is a tephritid gall fly, which is known to be an effective biological agent that can be used to control the notoriously widespread crofton weed Eupatorium adenophorum. Despite its importance, genetic resources for P. utilis remain scarce. In this study, 1.2 Gb sequences were generated using Illumina paired-end sequencing technology. De ... more

X. Gao; J.Y. Zhu; S. Ma; Z. Zhang; C. Xiao; Q. Li; Z.Y. Li; G.X. Wu
03/20/2015
Expressed sequence tag; Illumina sequencing; Odontobutis potamophila; Single nucleotide polymorphism validation

Transcriptome sequencing technology has been applied in the development and discovery of single nucleotide polymorphism (SNP) markers in fish. In this study, a panel of 120 expressed sequence tag (EST)-derived SNPs was selected by several selection filters from the resultant EST library of Odontobutis potamophila using Illumina Sequencing. In total, 37 SNPs from 120 putative SNPs ... more

H.W. Zhang; S.W. Yin; L.J. Zhang; X.Y. Hou; Y.Y. Wang; G.S. Zhang
01/30/2015
Genome-wide analysis; KT/HAK/KUP family; Potassium transporter; Prunus persica

The KT/HAK/KUP family members encoding high-affinity potassium (K+) transporters mediate K+ transport across the plasma membranes of plant cells to maintain plant normal growth and metabolic activities. In this paper, we identified 16 potassium transporter genes in the peach (Prunus persica) using the Hidden Markov model scanning strategy and searching the ... more

Z.Z. Song; R.J. Ma; M.L. Yu
12/23/2016
Fruit; Gene expression profiling; Gene Expression Regulation, Plant; Mutation; Prunus persica; Transcriptome

Fruit ripening is a complex developmental process, the details of which remain largely unknown in fleshy fruits. In this paper, the fruit flesh of two peach varieties, "Zhongyou9" (a nectarine; Prunus persica L. Batsch) and its mutant "Hongyu", was analyzed by RNA-seq technology during two stages of ripening at 20-day intervals. One hundred and eighty significant upregulated and two hundred ... more

H.F. Pan; Y. Sheng; Z.H. Gao; H.L. Chen; Y.J. Qi; X.K. Yi; G.H. Qin; J.Y. Zhang
05/25/2017
Acclimatization; Cold-Shock Response; Flowers; Genes, Essential; Genes, Plant; Genetic markers; Genotype; Genotyping Techniques; Plant breeding; Polymerase chain reaction; Prunus persica; Reference Standards

Selecting and validating reference genes are the first steps in studying gene expression by reverse transcriptase-quantitative polymerase chain reaction (RT-qPCR). The present study aimed to evaluate the stability of five reference genes for the purpose of normalization when studying gene expression in various cultivars of Prunus persica with different chilling requirements. Flower bud tissues ... more

N. Marini; C.B. Bevilacqua; M.V. Büttow; M.C.B. Raseira; S. Bonow

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