表达谱芯片服务

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一、Agilent表达谱芯片


基因表达谱芯片是最早实现从高通量的角度检测全基因组差异基因表达的平台。为方便广大科研工作者转录组基因表达筛选分析,中科普瑞引进Agilent表达谱芯片检测平台,为您的转录组mRNA检测和分析提供全方位的服务。在美国FDA组织的MAQC中,作为众多参与该计划的芯片制造商之一,Agilent的表达谱芯片产品无论从检出率,芯片的跨平台比较,数据重复性,平均CV,还是与qPCR的一致性等方面,均表现出卓越的性能。


Agilent表达谱芯片特点

²  独特的喷墨原位合成技术;

²  探针长度60 mer,同时兼顾较高的灵敏性和特异性;

²  由于探针设计较长,芯片检出率高,有利于捕捉对生命活动有更重要意义的低丰度基因;

²  芯片随信息库及时更新,基因信息更新更全,可不断升级到高级芯片版本;

²  灵活的定制方案,客户可任意制作自己的芯片,仅需基因组或EST序列;

²  平均CV<10% (MAQC: Nature Biotechnology Sept, 2006);

²  芯片具有良好的可重复性,相关系数R2>0.95 (MAQC);

²  芯片数据结果与qPCR数据结果具有良好的相关性,相关系数R2>0.9 (MAQC)。


Agilent表达谱芯片类型及参数

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其它物种表达谱芯片或定制芯片

拟南芥、玉米、水稻、烟草、牛、鸡、狗、马、猪、羊、兔、猴、蛙、三文鱼、斑马鱼、线虫、蚊子、果蝇、酵母、大肠杆菌、稻瘟菌(更多物种或需要定制请咨询销售人员)


样品要求(非FFPE样本)

        1. 样品纯度:OD 260/280值应在1.9~2.2 之间;DNA 应该去除干净;

        2. 样本完整性:Agilent 2100 RIN≥ 7,且28S/18S≥ 0.7;

        3. 样品浓度:低浓度不低于100ng/µl;

        4. 样品总量:每个样品总量不少于2µg;

        5. 样品溶剂:要溶解在RNase-free H20或RNase-free TE (pH 8.0)中;

        6. 样品运输:RNA用冻存管保存,并用干冰或液氮运输


Agilent表达谱芯片数据分析 


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基础分析

1. 原始数据处理分析

1)数据归一化

2)箱线图

3)样本聚类图

4)样本相关性分析

5)主成份分析 (PCA)

2. 差异基因筛选

1)表达差异基因筛选

2)散点图

3)火山图

4)差异基因层级聚类热图

3.   差异mRNA功能分析(GO/KEGG) 



Agilent表达谱芯片数据分析展示

1. 原始数据处理分析

2. 差异基因筛选

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3. 差异mRNA功能分析(GO/KEGG

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4. 信号通路调控网络构建(Pathway-Network

信号通路调控网络构建(Pathway-Network)是根据所有差异基因同时参与的Pathway之间的相互调控关系构建信号通路调控网络,从系统的角度研究各个信号通路间的信号传导和调控过程,在多个显著性Pathway中发现受实验影响的核心Pathway,以及实验影响的信号通路之间的调控机理.

 

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Pathway-Network


5. 基因相互作用网络图

基因网络是一组基因的集合体,这些基因通过相互协作来控制生物体重要的生命过程。我们通过筛选的差异基因进行基于实验验证,其他亲缘物种数据库检索、文献挖掘等多种信息进行基因互作网络的构建。


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基因相互作用网络图


6. 转录因子分析及网络构建

转录因子与基因表达调控区域的特异性结合是基因表达的重要调控方式。针对特定转录因子的实验,可对差异基因进行转录因子结合位点的motif分析,从而推测差异基因中有哪些基因可能直接受该转录因子调节。最后结果会用统计学方法进行检验,找到调控目标生物性状,统计学上有显著差别的转录因子。找到差异的转录因子及其调控的靶基因,我们可以构建TF-network,从中得出关键的转录因子及被关键转录因子转录调控的基因,系统的研究转录因子与基因的调控关系。


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转录因子网络构建


7. 共表达网络构建(Coexpression Network)

共表达网络图(Coexpression Network)是根据基因表达信号值的动态变化,计算基因间的共表达关系,得到基因间的表达调控关系及调控方向,从而构建基因的表达调控网络。利用共表达网络图,研究者可通过分析基因调控能力,获得样本随实验变化的核心调控基因。

要求:每组数据3个或3个以上生物学重复


   

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8.时间序列的共表达网络

根据基因表达信号值随着时间序列的变化,计算基因间的共表达关系,得到基因间的表达调控关系及调控方向,从而构建基因的表达调控网络。利用此网络图,研究者可通过分析基因调控能力,获得样本在时间过程中起调控作用的基因。


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时间序列的共表达网络


9.分子建模预测(MAKER 预测)

采用模式识别与数据挖掘技术有效进行预测模型的构建,将部分芯片数据拿来做预测模型,然后部分芯片数据作为测试数据集(独立样本)来验证模型的准确性。目的在于利用实验数据来筛选出一批靶标基因,并以此构建模型,以进行早期诊断、疾病预测和预后分析。


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MAKER 预测


二、中科普瑞基因芯片服务平台


高标准 — 拥有15年以上科技服务实验和分析技术经验的团队成员以GLP-like质量管理体系为您的基因芯片服务体系全线保驾护航。

高效率 — 样品质检合格后15个工作日出具结果报告,专属生物信息和技术支持服务人员为您提供在线结果咨询和解释服务。

高质量 — 符合3大基因芯片厂商质量要求的服务质量体系,项目质量管理专员负责对您的项目全程跟踪和质控。

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三、中科普瑞科技服务团队参与Agilent表达谱芯片发表相关文献

1.  Wang LT, Chiou SS, Chai CY, Hsi E, Yokoyama KK, Wang SN9,Huang SK, Hsu SH. Intestine-specific homeobox gene ISX integrates interleukin-6 signaling, tryptophan catabolism and immune suppression   Cancer Res(2017). IF9.122.

2.       Dai M, Wu L, Wang P, Wen Z, Xu X, Wang DW. CYP2J2 and Its Metabolites EETs Attenuate Insulin Resistance via Regulating Macrophage Polarization in Adipose Tissue. Sci Rep(2017). IF5.228.

3.       Chen P, Zheng X, Zhou Y, Xu Y, Zhu L, Qian Y. Talin-1 interaction network promotes hepatocellular carcinoma progression. Oncotarget(2017). IF5.008.

4.       Dong Y, Song C, Wang Y, Lei Z, Xu F, Guan H, Chen A, Li F.   Inhibition of PRMT5 suppresses osteoclast differentiation and partially protects against ovariectomy-induced bone loss through downregulation of CXCL10 and RSAD2. Cell Signal(2017). IF 4.191.

5.       Tan X, Chen S, Wu J, Lin J, Pan C, Ying X, Pan Z, Qiu L, Liu R, Geng R, Huang W.  PI3K/AKT-mediated upregulation of WDR5 promotes colorectal cancer metastasis by directly targeting ZNF407. Cell Death Dis(2017). IF5.378.

6.       Wang W, Gao F, Zhao Z, Wang H, Zhang L, Zhang D, Zhang Y, Lan Q, Wang J, Zhao J Integrated Analysis of LncRNA mRNA Co-Expression Profiles in Patients with Moyamoya Disease.Sci Rep(2017). IF 5.228.

7.       Yang B, Liu Y, Zhao J, Hei K, Zhuang H, Li Q, Wei W, Chen R, Zhang N, Li Y. Ectopic overexpression of filamin C scaffolds MEK1/2 and ERK1/2 to promote the progression of human hepatocellular carcinoma. Cancer Lett(2017). IF5.992.

8.       Zheng H, Jiang WH, Tian T, Tan HS, Chen Y, Qiao GL, Han J, Huang SY, Yang Y, Li S, Wang ZG, Gao R, Ren H, HaoXing, Ni JS, Wang LH, Ma LJ, Zhou WP. CBX6 overexpression contributes to tumor progression and is predictive of a poor prognosis in hepatocellular carcinoma. Oncotarget(2017). IF5.008.

9.       Ma HD, Ma WT, Liu QZ, Zhao ZB, Liu MZ, Tsuneyama K, Gao JM, Ridgway WM, Ansari AA, Gershwin ME, Fei YY, Lian ZX. Chemokine receptor CXCR3 deficiency exacerbates murine autoimmune cholangitis by promoting pathogenic CD8+ T cell activation. J Autoimmun(2017). IF7.76.

10.     Huang B, Wang W, Li Q, Wang Z, Yan B, Zhang Z, Wang L, Huang M, Jia C, Lu J, Liu S, Chen H, Li M, Cai D, Jiang Y, Jin D, Bai X. Osteoblasts secrete Cxcl9 to regulate angiogenesis in bone. Nat Commun(2017). IF11.329.

11.     Zheng H, Yang Y, Han J, Jiang WH, Chen C, Wang MC, Gao R, Li S, Tian T, Wang J, Ma LJ, Ren H, Zhou WP. TMED3 promotes hepatocellular carcinoma progression via IL-11/STAT3 signaling. Sci Rep(2016). IF 5.228.

12.     Yang C, Khanniche A, DiSpirito JR, Ji P, Wang S, Wang Y, Shen H. Transcriptome Signatures Reveal Rapid Induction of Immune-Responsive Genes in Human Memory CD8+ T Cells. Sci Rep(2016). IF5.228.

13.     Zhao F, Ohgaki H, Xu L, Giangaspero F, Li C, Li P, Yang Z, Wang B, Wang X, Wang Z, Ai L, Zhang J, Luo L, Liu P. Molecular subgroups of adult medulloblastoma: a long-term single-institution study. Neuro Oncol(2016). IF7.371.

14.     Zhang Y, Tang J, Yang N, Liu Q, Zhang Q, Zhang Y, Li N, Zhao Y, Li S, Liu S, Zhou H, Li X, Tian M, Deng J, Xie P, Sun Y, Lu H, Zhang MQ, Jin N, Jiang C. FAT10 Is Critical in Influenza A Virus Replication by Inhibiting Type I IFN. J Immunol(2016). IF4.985.

15.     Li XY, Su YH, Sun B, Ji WD, Peng ZX, Xu Y, Wu MC, Su CQ  An Artificially-Designed Interfering lncRNA Expressed by Oncolytic Adenovirus Competitively Consumes OncomiRs to Exert Antitumor Efficacy in Hepatocellular Carcinoma. Mol Cancer Ther(2016). IF5.579.

16.     Li Z, Li B, Liu J, Guo Z, Liu Y, Li Y, Shen WH, Huang Y, Huang H, Zhang Y, Dong A.The transcription factors AS1 and AS2 interact with LHP1 to repress KNOX genes in Arabidopsis. J Integr Plant Biol(2016). IF3.67.

17.     Li J, Zhao P, Yang L, Li Y, Tian Y, Li S.  System biology analysis of long-term effect and mechanism of Bufei Yishen on COPD revealed by system pharmacology and 3-omics profiling. Sci Rep(2016). IF5.228.

18.     Yang C, Khanniche A, DiSpirito JR, Ji P, Wang S, Wang Y, Shen H. Transcriptome Signatures Reveal Rapid Induction of Immune-Responsive Genes in Human Memory CD8(+) T Cells. Sci Rep(2016). IF5.228  .

19.     Li J, Zhao P, Yang L, Li Y, Tian Y, Li S. System biology analysis of longterm effect and mechanism of Bufei Yishen on COPD revealed by system pharmacology and 3-omics profiling. Sci Rep(2016). IF5.578.

20.     Li C, Nong Q, Solanki MK, Liang Q, Xie J, Liu X, Li Y, Wang W, Yang L, Li Y.  Differential expression profiles and pathways of genes in sugarcane leaf at elongation stage in response to drought stress.Sci Rep(2016). IF5.578.

21.     Zhao X, Chen C, Shen W, Huang G, Le S, Lu S, Li M, Zhao Y, Wang J, Rao X, Li G, Shen M, Guo K, Yang Y, Tan Y, Hu F.  Global Transcriptomic Analysis of Interactions between Pseudomonas aeruginosa and Bacteriophage PaP3. Sci Rep(2016). IF5.578.

22.     Ruan J, Zhang Y, Yuan J, Xin L, Xia J, Liu N, Mu Y, Chen Y, Yang S, Li K. A.long-term high-fat, high-sucrose diet in Bama minipigs promotes lipid deposition and amyotrophy by up-regulating the myostatin pathway. Mol Cell Endocrinol(2016). IF4.405.

23.     Huang B,Liu N, Rong XY , Ruan  JS,Huang Y. Effects of simulated microgravity and spaceflight on morphological differentiation and secondary metabolism of Streptomyces coelicolor A3(2). Appl Microbiol Biotechnol(2015). IF3.811.

24.     Bai J, Liu Z, Xu Z, Ke F, Zhang L, Zhu H, Lou F, Wang H, Fei Y, Shi YL, Wang H. Epigenetic Downregulation of SFRP4 Contributes to Epidermal Hyperplasia in Psoriasis. J Immunol(2015). IF5.362.

25.     Zhang C, Cao L, Rong L, An Z, Zhou W, Ma J, Shen WH, Zhu Y, Dong A. The chromatin-remodeling factor AtINO80 plays crucial roles in genome stability maintenance and in plant development. Plant J(2015). IF6.815.

26.     Xiong D, Ye Y, Fu Y, Wang J, Kuang B, Wang H, Wang X, Zu L, Xiao G, Hao M, Wang J. Bmi-1 expression modulates non-small cell lung cancer progression. Cancer Biol Ther(2015). IF3.63.

27.     Lin X, Huang C, Shi J, Wang R, Sun X, Liu X, Zhao L, Jin M. Investigation of Pathogenesis of H1N1 Influenza Virus and Swine Streptococcus suis Serotype 2 Co-Infection in Pigs by Microarray Analysis. PLoS One(2015). IF3.534.

28.     Leung HW, Wang Z, Yue GG, Zhao SM, Lee JK, Fung KP, Leung PC, Lau CB, Tan NH.Cyclopeptide RA-V inhibits cell adhesion and invasion in both estrogen receptor positive and negative breast cancer cells via PI3K/AKT and NF-kappaB signaling pathways.Biochim Biophys Acta(2015). IF5.297.

29.     Shen JW, Jia WW, Yu YY, Chen J, Cao XK, Du YH, Zhang XB, Zhu SC, Chen W, Xi JJ, Wei TY, Wang GY, Yuan DL, Duan T, Jiang CZ,Kang JH. Pwp1 Is Required for the Differentiation Potential of Mouse Embryonic Stem Cells Through Regulating Stat3. Signaling  Stem cells(2015). IF6.523.

30.     Huang YX Linsen SEV Partial depletion of yolk during zebrafish embryogenesis changes the dynamics of methionine cycle and metabolic genes.BMC Genomics(2015). IF3.99.

31.     Wu Z, Cheng K, Shi L, Li Z, Negi H, Gao G, Kamle S, Li D.  Sal-like protein 2 upregulates p16 expression through a proximal promoter element.Cancer Sci(2015). IF3.523.

32.     Liu H, Du L, Wang R, Wei C, Liu B, Zhu L, Liu P, Liu Q, Li J, Lu SL, Xiao J. High frequency of loss of PTEN expression in human solid salivary adenoid cystic carcinoma and its implication for targeted therapy. Oncotarget(2015). IF 6.359.

33.     Wang D, Chen XB, Zhang ZL, Liu DM, Song GY, Kong XC, Geng SF, Yang JY, Wang BN, Wu L, Li AL,Mao L. A MADS-box gene NtSVP regulates pedicel elongation by directly suppressing a KNAT1-like KNOX gene NtBPL in tobacco (Nicotiana tabacum L.). J EXP BOT(2015). IF5.526.

34.     Sun Y, Zhou L, Fang L, Su Y, Zhu W. Responses in colonic microbial community and gene expression of pigs to a long-term high resistant starch diet   Front. Microbiol.(2015). IF3.989.

35.     Cheng P, Wang YF, Li G, Yang SS, Liu C, Hu H, Jin G, Hu XG. Interplay between menin and Dnmt1 reversibly regulates pancreatic cancer cell growth downstream of the hedgehog signaling pathway. CANCER LETT(2015). IF5.621.

36.     Wu Y, Chen K, Liu X, Huang L, Zhao D, Li L, Gao M, Pei D, Wang C, Liu X. Srebp-1 Interacts with c-Myc to Enhance Somatic Cell Reprogramming. Stem Cells(2015). IF6.523 .

37.     Bai C, Li X, Gao Y, Wang K, Fan Y, Ma SZ, Guan W.  Role of microRNA-21 in the formation of insulin-producing cells from pancreatic progenitor cells. BBA-GENE REGUL MECH    (2015). IF6.332.

38.     Zheng Q, Hou J, Zhou Y, Yang Y, Cao X.  Type I IFN-Inducible Downregulation of MicroRNA-27a Feedback Inhibits Antiviral Innate Response by Upregulating Siglec1/TRIM27. J Immunol(2015). IF4.922.

39.     Li D, Zhao X, Xiao Y, Mei H, Pu J, Xiang X, Jiao W, Song H, Qu H, Huang K, Zheng L, Tong Q.  Intelectin 1 suppresses tumor progression and is associated with improved survival in gastric cancer.M Oncotarget(2015). IF6.359.




 




                



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