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pcr array analysis reveals a novel expression profile of ferroptosis-related genes in idiopathic pulmonary fibrosis

BMC PULMONARY MEDICINE 2025年第1期25卷 1-17页

作者： Shen, Chenyou Wang, Wei Wei, Dong Yang, Xusheng Jiang, Cheng Sheng, Yating Chen, Yuan Sun, Jie Li, Xiaoshan Li, Guirong Ye, Shugao Chen, Jingyu Nanjing Med Univ Affiliated Wuxi Peoples Hosp Wuxi Peoples Hosp Lung Transplant CtrWuxi Med Ctr 299 Qingyang Rd Wuxi 214023 Jiangsu Peoples R China Nanjing Med Univ Wuxi Peoples Hosp Affiliated Wuxi Peoples Hosp Dept Sci ResWuxi Med Ctr 299 Qingyang Rd Wuxi 214023 Jiangsu Peoples R China Nanjing Med Univ Affiliated Wuxi Peoples Hosp Nanjing Med Univ Dept Neurol Wuxi Peoples HospWuxi Med Ctr Qingyang Rd 299 Wuxi 214023 Jiangsu Peoples R China

Background Idiopathic pulmonary fibrosis (IPF) is a chronic, irreversible, and fatal disease characterized by progressive interstitial lung fibrosis. Given its insidious onset and poor outcome, there is an urgent need to elucidate the molecular mechanisms underlying IPF and identify effective therapeutic targets and diagnosis and prognosis biomarkers. Ferroptosis is an iron-dependent form of programmed cell death that occurs as lipid peroxides accumulate. Growing evidence suggests that ferroptosis is important in IPF. Methods Human ferroptosis pcr array was performed on IPF and control lung tissue. The differentially expressed ferroptosis-related genes (DE-FRGs) were identified, underwent functional enrichment analyses, protein-protein interaction network construction, and potential drug target prediction. The DE-FRGs were validated and their value as diagnostic and prognostic blood biomarkers were evaluated using the Gene Expression Omnibus dataset GSE28042. Results The array identified 13 DE-FRGs. Gene Ontology enrichment and Kyoto Encyclopedia of Genes and Genomes pathway analyses revealed that the DE-FRGs were mainly related to iron ion transport, blood microparticles, and oxidoreductase activity, and were involved in porphyrin metabolism, necroptosis, and the p53 signaling pathway in addition to ferroptosis. The 13 DE-FRGs were analyzed using the Drug-Gene Interaction Database to explore novel IPF therapeutic agents, yielding 42 potential drugs. Four DE-FRGs (BBC3, STEAP3, EPRS, SLC39A8) in the peripheral blood of IPF patients from the GSE28042 dataset demonstrated the same expression pattern as that observed in the lung tissue array. The receiver operating characteristic analysis demonstrated that the area under the curve of STEAP3 and EPRS were > 0.75. The survival analysis demonstrated that STEAP3 and EPRS were significantly different between the IPF and control groups. Conclusions The FRG expression profiles in IPF and control lung tissue were characterized

关键词： Idiopathic pulmonary fibrosis Ferroptosis pcr array Bioinformatics analysis Drug targets Biomarkers

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pcr array of Specific RNA methylation associated genes Involved in Oxidative Stress of RPE Cells

PCR array of Specific RNA methylation associated genes Invol...

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2023第二十三届国际眼科学学术会议、2023第二十三届国际视光学学术会议、2023第十届国际角膜塑形学术论坛、中国研究型医院学会眼科学与视觉科学专业委员会2023学术年会(海口站)、海南省医学会眼科学分会2023年学术年会暨第51期海南眼科论坛、2023第二十三届上海国际眼科和视光技术及设备展览会(海口站)、2023中国民营眼科医院和视光诊治中心展示推广会

作者： Ke Mao Shanghai renji hospital

Purpose Methylation is the most prevalent RNA modification within protein-coding mRNAs in *** aim of this study was to identify RNA methylation associated genes variance from human retinal pigmented epithelial(RPE) cells under oxidative *** ARPE-19 cells were cultured with ox-LDL(100 mg/L),H2O2(100uM) or serum free medium for 48 ***-specific pcr array was conducted to analyze the differentially expressed RNA methylation associated genes(DEGs) between the different *** ResultsA total of 68 RNA methylation associated genes were identified,of which 11 were upregulated(METTL14,WTAP,FTO,NSUN1,NSUN2,NSUN5,DNMT2,TET2,Prrc2a,LRPPRC and e IF3I)and 8 were downregulated(TRMT61A,METTL1,VIRMA,HAKAI,YTHDF1,ALKBH1,Rtc and Ppc) in H2O2 group compared to control *** 7 genes were upregulated(METTL14,FTO,NSUN1,NSUN2,LRPPRC ei F3b and el F3l) and 6 were downregulated(VIRMA,TRMT61A,METTL1,CMTR1,YTHDF1 and ALYREF) in ox-LDL group compared to control *** western Blot experiments also confirmed pcr array *** ConclusionThis study identified several DEGs from oxidation-stimulated RPE cells,which may indicate the influence of oxidative damage on related miRNA methylation associated genes and explored potential regulatory gene targets for RPE degeneration study.

关键词： pcr array RNA methylasion Oxidative stress RPE cells

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In vitro treatment of human granulosa cells with irisin and leptin: Quantitative RT-pcr array data (female infertility panel)

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DATA IN BRIEF 2022年 40卷 107781页

作者： Stojchevski, Radoslav Singer, Tomer Ziskovich, Karina Poretsky, Leonid Avtanski, Dimiter Northwell Hlth Friedman Diabet Inst New York NY USA Shady Grove Fertil Clin New York NY USA Northwell Hlth Feinstein Inst Med Res Manhasset NY USA Donald & Barbara Zucker Sch Med Hofstra Northwell Hempstead NY USA

Reproduction is closely related to energy metabolism: physical activity and adiposity (either insufficient weight or obesity) can affect female fertility. Irisin is a myo- and adipokine produced by skeletal muscles during exercise or shivering as well as in smaller amounts by subcutaneous visceral adipocytes [1]. Leptin is a neuroendocrine adipokine regulating satiety and energy expenditure. Circulating levels of both, irisin and leptin, correlate with adiposity status and physical activity [2-6]. This article presents data from quantitative pcr array of the in vitro effects of irisin and leptin on cultured human ovarian granulosa cells. Granulosa cells were purified from follicular fluid samples obtained from women undergoing in vitro fertilization (IVF) procedure and were subjected to treatment with irisin (500 ng/mL) or leptin (100 ng/mL) for 24 h. The array included 84 genes involved in female fertility. (c) 2021 The Authors. Published by Elsevier Inc. This is an open access article under the CC BY license (http://***/licenses/by/4.0/)

关键词： pcr array Ovary Granulosa cells Irisin Leptin Infertility

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pcr array analysis identified hyperproliferation but not autophagy or apoptosis in fibrous epulis

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JOURNAL OF CLINICAL LABORATORY ANALYSIS 2021年第6期35卷 e23784-e23784页

作者： Jiang, Yangyang Fang, Bing Xu, Bin Shanghai Jiao Tong Univ Shanghai Peoples Hosp 9 Dept Orthodont Sch Med Shanghai Peoples R China Univ Chinese Acad Sci Hwa Mei Hosp Dept Stomatol Ningbo Peoples R China

Background The pathogenesis of fibrous epulis is still quite unclear. Our recent genome-wide RNA sequencing analysis revealed that in fibrous epulis, RAS-PI3K-AKT-NF-kappa B pathway regulates the expression of Bcl-2 family and IAP family genes, leading to increased proliferation and the inhibition of apoptosis. The PI3K/AKT signaling pathway can promote autophagy in human gingival fibroblasts;therefore, the purpose of the present study was to identify whether autophagy is involved in the pathogenesis of fibrous epulis. Methods Differentially expressed genes (DEGs) between fibrous epulis lesions and normal gingival tissues were identified using the pcr array. The expression levels of eighteen autophagy-related (ATG) family genes, twelve B-cell lymphoma 2 (Bcl-2) family genes, and eleven cysteine-dependent aspartate-directed protease (caspase) family genes were validated using quantitative real-time pcr (qRT-pcr). Autophagy induction was determined by measuring microtubule-associated protein light chain 3 (LC3) conversion (LC3-I to LC3-II) by immunoblot analysis. Results The pcr array identified six upregulated genes, whereas no genes were expressed at significantly lower levels. The upregulated genes were BCL2, BCL2L1, CXCR4, HSP90AA1, HSPA8, and IGF1, which all belong to the "regulation of autophagy" group but not the "autophagy machinery components" group. qRT-pcr verified that the expression levels of BCL2, BCL2L1 (also known as BCL-XL), and BCL2L2 (also known as BCL-W) were significantly increased in fibrous epulis. No LC3-I to LC3-II conversion was observed. Conclusions The present study reveals that in fibrous epulis, Bcl-2 and Bcl-xL coordinately mediate gingival cell escape from apoptosis, leading to uncontrolled proliferation. Moreover, ATG family genes are not activated, and autophagy is not involved in this process.

关键词： apoptosis ATG family autophagy Bcl‐ 2 family caspase family fibrous epulis pcr array

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miRkit: R framework analyzing miRNA pcr array data

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BMC RESEARCH NOTES 2021年第1期14卷 376-376页

作者： Tsagiopoulou, Maria Togkousidis, Anastasis Pechlivanis, Nikolaos Maniou, Maria Christina Batsali, Aristea Matheakakis, Angelos Pontikoglou, Charalampos Psomopoulos, Fotis Ctr Res & Technol Hellas Inst Appl Biosci Thessaloniki 57001 Greece Univ Crete Sch Med Haemopoiesis Res Lab Iraklion 71003 Greece Univ Crete Sch Med Dept Hematol Iraklion 71003 Greece Aristotle Univ Thessaloniki Sch Biol Dept Genet Dev & Mol Biol Thessaloniki 54124 Greece

Objective: The characterization of microRNAs (miRNA) in recent years is an important advance in the field of gene regulation. To this end, several approaches for miRNA expression analysis and various bioinformatics tools have been developed over the last few years. It is a common practice to analyze miRNA pcr array data using the commercially available software, mostly due to its convenience and ease-of-use. Results: In this work we present miRkit, an open source framework written in R, that allows for the comprehensive analysis of RT-pcr data, from the processing of raw data to a functional analysis of the produced results. The main goal of the proposed tool is to provide an assessment of the samples' quality, perform data normalization by endogenous and exogenous miRNAs, and facilitate differential and functional enrichment analysis. The tool offers fast execution times with low memory usage, and is freely available under a MIT license from . Overall, miRkit offers the full analysis from the raw RT-pcr data to functional analysis of targeted genes, and specifically designed to support the popular miScript miRNA pcr array (Qiagen) technology.

关键词： miRNA qpcr RT-pcr pcr array GO KEGG

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Protective Effects Of Astragalus Polysaccharides On Oxidative Stress In High Glucose-Induced Or SOD2-Silenced H9C2 Cells Based On pcr array Analysis

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DIABETES METABOLIC SYNDROME AND OBESITY-TARGETS AND THERAPY 2019年 12卷 2209-2220页

作者： Sun, Qilin Wu, Xiaoyan Wang, Hao Chen, Wenjie Zhao, Xuelan Yang, Yehong Chen, Wei Fudan Univ Huashan Hosp Dept Geriatr 12 Wu Lu Mu Qi Rd Shanghai 200040 Peoples R China Fudan Univ Expt Teaching Ctr Basic Med Shanghai 200032 Peoples R China Fudan Univ Huashan Hosp Dept Endocrinol 12 Wu Lu Mu Qi Rd Shanghai 200040 Peoples R China

Background: Oxidative stress in cardiac myocytes is an important pathogenesis of diabetic cardiomyopathy (DCM). Previously, we reported that astragalus polysaccharide (APS) has protective effects against the oxidative stress of DCM. This study aimed to determine the effect of APS on the oxidative stress induced by hyperglycemia in H9C2 cells. Methods: Rat H9C2 cells were cultured in vitro and randomly divided into the control group, HG group, APS-HG group, siRNASOD2 group, and APS-siRNASOD2 group. The cellular ultrastructure was measured by transmission electron microscopy. Cell apoptosis was examined by TUNEL staining. Levels of reactive oxygen species (ROS) were detected by a quantitative fluorescence assay (DHE). 8-OH-dG and nitrotyrosine, the indicators of oxidative stress injury, were detected by immunohistochemistry. A pcr array was used to evaluate the expression levels of 84 oxidative stress genes in cultured cells, and the pcr array results were partially verified by Western blot. Results: APS treatment protected the H9C2 cell ultrastructure, reduced the level of cell apoptosis, inhibited cellular ROS production, and reduced the levels of oxidative stress injury indicators 8-OH-dG and nitrotyrosine in high glucose-induced or SOD2-silenced H9C2 cells. It also altered oxidative stress-related genes at the mRNA and protein levels. Conclusion: APS may improve antioxidant capacity and inhibit oxidative stress injury in high glucose induced H9C2 cells.

关键词： diabetic cardiomyopathy cardiomyocyte oxidative stress ROS pcr array astragalus polysaccharide

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基于pcr array技术探究AMPK信号通路对蛋鸡原代肝细胞脂肪变性的调控作用

基于PCR array技术探究AMPK信号通路对蛋鸡原代肝细胞脂肪变性的...

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作者：黄橙江西农业大学

学位级别：硕士

为了研究AMPK信号通路对蛋鸡原代肝细胞脂肪变性的调控作用,本研究选取34-40周龄的海兰褐蛋鸡,通过原位二步灌流法建立蛋鸡肝细胞体外培养模型,利用1m M的油酸/棕榈酸（2:1）高脂培养液处理肝细胞构建脂肪变性模型。试验分为两组,分别... 详细信息

为了研究AMPK信号通路对蛋鸡原代肝细胞脂肪变性的调控作用,本研究选取34-40周龄的海兰褐蛋鸡,通过原位二步灌流法建立蛋鸡肝细胞体外培养模型,利用1m M的油酸/棕榈酸（2:1）高脂培养液处理肝细胞构建脂肪变性模型。试验分为两组,分别为CK组（0m M油酸/棕榈酸）和FFA组（1m M油酸/棕榈酸）,造模24h。随后检测蛋鸡原代肝细胞ICelligence系统下的细胞增殖活性;利用油红O染色观察脂质蓄积情况、糖原染色观察糖原含量变化;通过生化检测试剂盒测定细胞中脂质相关指标（TC、TG）、上清液葡萄糖含量（GLU）、氧化还原相关指标（SOD、T-AOC、MDA）;通过吖啶橙/溴化乙锭染色,观察细胞凋亡情况;通过流式细胞仪测定细胞活性氧水平、细胞线粒体膜电位变化;基于pcr array技术测定AMPK信号通路中84个基因的m RNA表达量;此外,针对关键基因和蛋白（P-AMPK、ACC、P-ACC、AKT、Caspase-3、INSR）进行验证实验。结果如下:1.与CK组比较,FFA组发现大量脂质蓄积、糖原含量明显减少;ICelligence系统测定结果显示FFA组细胞增殖能力较CK组有所降低,但两组细胞活性没有显著差异（P＞0.05）。2.与CK组比较,FFA组细胞中TG、TC、MDA含量显著或极显著上升（P＜0.05或P＜0.01）,SOD和T-AOC的含量极显著下降（P＜0.01）,细胞上清液中GLU含量极显著下降（P＜0.01）。3.与CK组比较,FFA组细胞凋亡率、细胞活性氧极显著上升;线粒体膜电位水平极显著下降（P＜0.01）。4.与CK组比较,FFA组AMPK信号通路中的FASN、ACACB、ADRA2A、ADRA2C、HMGCS1、PFKFB3、PFKFB4、m TOR、TXNIP、FOXO3、TSC1、TSC2和TP53的m RNA的表达量显著或极显著上调（P＜0.05或P＜0.01）,CRTC1、CPT2、CPT1A、INSR、AKT1、PPARGC1B和CAMKK2的m RNA的表达量显著或极显著下调（P＜0.05或P＜0.01）。5.与CK组比较,FFA组细胞的P-AMPK、P-ACC蛋白表达极显著下（P＜0.01）;ACC、Caspase 3蛋白表达显著上升（P＜0.05）;AKT、INSR蛋白表达呈下降趋势（P＞0.05）。结论:蛋鸡原代肝细胞在脂肪变性的影响下,AMPK信号通路中FASN、ACACB、ADRA2A等基因量显著上调,CRTC1、CPT2、CPT1A等基因表达量显著下调,造成脂质、碳水化合物代谢紊乱,形成氧化损伤和细胞周期的改变。

关键词：蛋鸡原代肝细胞脂肪变性 AMPK信号通路 pcr array

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基于pcr array技术探讨化瘀祛痰方调控自噬干预肝脏脂质沉积的机制

基于PCR array技术探讨化瘀祛痰方调控自噬干预肝脏脂质沉积的机制

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作者：孙艳梅辽宁中医药大学

学位级别：硕士

目的:建立高脂血症大鼠模型,以自噬为切入点,探讨化瘀祛痰方对高脂血症大鼠肝脏脂质损伤的干预作用及分子机制。材料与方法:将30只SD雄性大鼠,随机分为空白对照组、化瘀祛痰组、高脂血症组,每组10只。空白对照组给普通饲料,高脂血症组... 详细信息

目的:建立高脂血症大鼠模型,以自噬为切入点,探讨化瘀祛痰方对高脂血症大鼠肝脏脂质损伤的干预作用及分子机制。材料与方法:将30只SD雄性大鼠,随机分为空白对照组、化瘀祛痰组、高脂血症组,每组10只。空白对照组给普通饲料,高脂血症组、化瘀祛痰组给高脂饲料,自由饮水,造模60天。化瘀祛痰组给予化瘀祛痰方煎剂10 ml/(kg·d),1次/日,灌胃30天。空白对照组、高脂血症组每天同一时间给予等体积的磷酸盐缓冲生理盐水(PBS)灌胃。喂养90天后,生化分析仪检测大鼠血清胆固醇(TC)、甘油三酯(TG)、低密度脂蛋白胆固醇(LDL-C)、高密度脂蛋白胆固醇(HDL-C)、HE染色观察肝脏组织形态学变化、油红O染色观察肝脏脂质沉积情况。分离肝脏组织,pcr array技术检测大鼠肝脏m TOR信号通路相关基因表达,实时荧光定量RT-pcr进行验证,Western blot法检测大鼠肝脏组织AMPK调控自噬相关蛋白表达。结果:1.化瘀祛痰方对高脂血症大鼠血脂水平的影响实验结果显示:与空白对照组相比,高脂血症组血清TC、LDL-C水平显著性升高,HDL-C水平显著性降低(P<0.01),TG水平出现升高,但无统计学意义;与高脂血症组相比,化瘀祛痰组大鼠血清中TC、LDL-C水平显著性降低(P<0.01),HDL-C水平显著性升高(P<0.05),TG水平有所降低,但无统计学意义。2.化瘀祛痰方对高脂血症大鼠肝脏组织形态学变化与脂质损伤的影响HE染色显示:空白对照组肝细胞系正常,肝细胞形态正常,细胞核呈圆形,大,中央,细胞质中无脂质积累,小叶内无炎症细胞浸润;高脂血症组肝脏脂肪变性明显,肝细胞肿胀圆形,细胞质疏松,内含大的脂肪滴,有些细胞可以看到细胞核被挤入细胞膜,在细胞质中可以看到圆形的脂肪空泡和不同大小的炎症细胞;化瘀祛痰组肝脂肪变性程度降低,脂质空泡数减少,肝细胞体积减少。油红O染色显示:在高脂血症组中,肝细胞内出现油红着色,脂滴增多,呈现弥漫性;在化瘀祛痰组中,肝细胞脂滴数目显著减少。3.化瘀祛痰方对高脂血症大鼠肝脏m TOR信号通路相关基因表达的影响化瘀祛痰组与高脂血症组以及高脂血症组与空白对照组之间同时发生改变的基因有7个,根据fold change值大于2为上调基因,小于0.5为下调基因,差异性基因分别为Akt1、Bcl2、Igf1、Mapk14、Mapk8、m TOR、Becn1。结果显示:与空白对照组相比,高脂血症组Akt1、Bcl2、Igf1、Mapk14、Mapk8基因表达水平均上升,m TOR、Becn1基因表达水平下降;与高脂血症组相比,化瘀祛痰组Akt1、Bcl2、Igf1、Mapk14、Mapk8基因表达水平均下调,m TOR、Becn1基因表达水平上调。4.实时荧光定量RT-pcr法验证各组大鼠肝脏差异性基因表达对自噬及m TOR相关关键基因进行验证,包括Akt、Bcl2、m TOR、Beclin1(Becn1)。结果显示:与空白对照组相比,高脂血症组Akt和Bcl2 m RNA水平显著升高,m TOR和Beclin1 m RNA水平显著下调(P<0.01,P<0.05),与高脂血症组相比,化瘀祛痰组Akt和Bcl2 m RNA水平显著下调,m TOR、Beclin1 m RNA水平显著上调(P<0.01,P<0.05)。5.化瘀祛痰方对高脂血症大鼠肝脏AMPK信号通路介导自噬关键蛋白表达的影响Western blot法检测各组大鼠肝脏LC3A/B、p-m TOR、m TOR、p-AMPK、AMPK、ULK1蛋白的表达水平,结果显示:与空白对照组相比,高脂血症组LC3A/B、p-AMPK和ULK1蛋白表达水平显著降低(P<0.05,P<0.01),p-m TOR蛋白表达水平显著升高(P<0.01);与高脂血症组相比,化瘀祛痰组LC3A/B、p-AMPK和ULK1蛋白表达水平显著升高(P<0.05),p-m TOR蛋白表达水平显著降低(P<0.01)。结论:1.化瘀祛痰方可纠正高脂血症大鼠血脂异常、改善高脂血症大鼠肝脏脂质损伤;2.化瘀祛痰方可能通过调控自噬相关基因及AMPK信号通路影响自噬改善高脂血症大鼠肝脏脂质损伤。

关键词： pcr array 化瘀祛痰方高脂血症肝脏脂质损伤自噬

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Responses of the zebrafish hypothalamic-pituitary-gonadal-liver axis pcr array to prochloraz are dependent on timing of sampling

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AQUATIC TOXICOLOGY 2016年 175卷 154-159页

作者： Dang, Yao Wang, Jianghua Giesy, John P. Liu, Chunsheng Huazhong Agr Univ Coll Fisheries Wuhan 430070 Peoples R China Collaborat Innovat Ctr Efficient & Hlth Prod Fish Changde 415000 Hunan Peoples R China Univ Hong Kong Sch Biol Sci Hong Kong Hong Kong Peoples R China Univ Saskatchewan Dept Vet Biomed Sci Saskatoon SK S7N 5B3 Canada Univ Saskatchewan Toxicol Ctr Saskatoon SK S7N 5B3 Canada Nanjing Univ Sch Environm State Key Lab Pollut Control & Resource Reuse Nanjing 210008 Jiangsu Peoples R China

A pcr array, based on expression of genes along the hypothalamic-pituitary-gonadal-liver(HPGL) axis of fish, has been suggested as a useful method for screening of endocrine-disrupting chemicals (EDCs). However, effects of circadian rhythm on responses of the HPGL axis to exposure to chemicals were unknown. In this study, profiles of expression of genes along the HPGL axis and concentrations of 17 beta-estradiol (E2) in blood plasma of female zebrafish were compared at two sampling times of day (8:00 AM and 7:00 PM). Prochloraz (PCZ) was selected as a model chemical to evaluate differences in responses of the HPGL axis at these two times of day. Profiles of responses of concentrations of E2 in plasma and expressions of genes along the HPGL axis genes were different between the two times of sampling. Concentrations of E2 were less, and abundances of mRNA for several genes along the HPGL axis were significantly greater or lesser when samples were collected at 7:00 PM than they were when samples were collected at 8:00 AM. Exposure to three concentrations of PCZ (3, 30 or 300 mu g/L) for 48 h resulted in significantly lesser concentrations of plasma E2 and caused compensatory up-regulation of genes included in hypothalamus, pituitary and ovary. Expressions of genes along the HPGL were more responsive to PCZ at 8:00 AM than they were when samples were collected at 7:00 PM. Correlations among parameters in samples collected at the two times indicated the effects might be due to different concentrations of E2 in plasma due to exposure to PCZ. (C) 2016 Elsevier B.V. All rights reserved.

关键词： HPGL axis pcr array Prochloraz Compensatory response Expressions of genes

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Development and Utilization of a Custom pcr array Workflow: Analysis of Gene Expression in Mycoplasma genitalium and Guinea Pig (Cavia porcellus)

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MOLECULAR BIOTECHNOLOGY 2015年第2期57卷 172-183页

作者： Veselenak, Ronald L. Miller, Aaron L. Milligan, Gregg N. Bourne, Nigel Pyles, Richard B. Univ Texas Med Branch Dept Microbiol & Immunol Galveston TX 77555 USA Univ Texas Med Branch Dept Pediat Galveston TX 77555 USA

Transcriptome analysis is a powerful tool for evaluating molecular pathways central to maturation of specific biological processes and disease states. Recently, pcr-based arrays have supplemented microarray and RNA-seq methodologies for studying changes in gene expression levels. pcr arrays are a more cost efficient alternative, however commercially available assemblies are generally limited to only a few more widely researched species (e.g., rat, human, and mouse). Consequently, the investigation of emerging or under-studied species is hindered until such assays are created. To address this need, we present data documenting the success of a developed workflow with enhanced potential to create and validate novel RT-pcr arrays for underrepresented species with whole or partial genome annotation. Utilizing this enhanced workflow, we have achieved a success rate of 80 % for first-round designs for over 400 primer pairs. Of these, similar to 160 distinct targets were sequence confirmed. Proof of concept studies using two unique arrays, one targeting the pathogenic bacterium Mycoplasma genitalium and the other specific for the guinea pig (Cavia porcellus), allowed us to identify significant (P < 0.05) changes in mRNA expression validated by subsequent qpcr. This flexible and adaptable platform provides a valuable and cost-effective alternative for gene expression analysis.

关键词： pcr array Gene expression Transcription Mycoplasma genitalium Cavia porcellus Guinea pig Immune response

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