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Pratyaydipta Rudra, Wen J Shi, Pamela Russell, Brian Vestal, Boris Tabakoff, Paula Hoffman, Katerina Kechris, Laura Saba
BACKGROUND: MicroRNAs (miRNAs) are small non-coding RNAs that bind messenger RNAs and promote their degradation or repress their translation. There is increasing evidence of miRNAs playing an important role in alcohol related disorders. However, the role of miRNAs as mediators of the genetic effect on alcohol phenotypes is not fully understood. We conducted a high-throughput sequencing study to measure miRNA expression levels in alcohol naïve animals in the LXS panel of recombinant inbred (RI) mouse strains...
August 29, 2018: BMC Genomics
Ting Hu, Hong-Mei Zhu, Zhu Zhang, Jia-Min Wang, Hai-Xia Zhang, Ze Du, Ling-Pingi Li, He Wang, Shan-Ling Liu
OBJECTIVE: To evaluate the clinical significance of chromosomal microarry analysis (CMA) for detection of chromosomal abnormalities in spontaneously aborted fetuses. METHODS: Chorionic villi samples from 431 spontaneously aborted fetuses were detected on the chromosomal abnormalities by CMA in our department form September 2014 to April 2016. RESULTS: The overall success rate of CMA was 100%,and 283 cases were detected with abnormalities (65...
September 2017: Sichuan da Xue Xue Bao. Yi Xue Ban, Journal of Sichuan University. Medical Science Edition
Jingyang Yu, Qianqian Li, Yang Jiao, Qiuli Li
Studies have shown that some plant-specific NAC (NAM, ATAF1/2, CUC2) transcription factors may increase plants resistance to stress. We screened the genes differentially expressed in transgenic SlNAC1 Arabidopsis compared to the wild type by cDNA microarry, to provide scientific basis for studying the genes related to abiotic stress responses in transgenic Arabidopsis. There were 3 046 genes differentially expressed more than twice in the total 43 604 genes of transgenic SlNAC1 Arabidopsis. Gene ontology analysis was used on genes differentially expressed more than five-fold...
January 25, 2017: Sheng Wu Gong Cheng Xue Bao, Chinese Journal of Biotechnology
Yuan-Yu Wei, Zhao-Bo Li, Fan Zhang, Ning-Ning Wang, Shuai Liu, Bao-Hong Yue
OBJECTIVE: Based on previous microarry and bioinformatic analysis results, to investigate the effect of nucleostemin(NS) expression down-regulation on autophagy activity in p53 null HL-60 leukemia cells, so as to provide evidence for studying mechanisms of p53-independent signal pathway of NS in details. METHODS: The autophagy activity of HL-60 cells after down-regulation of NS expression was detected with acidine orange staining, Western blot and transmission electron mcrioscope technique...
June 2017: Zhongguo Shi Yan Xue Ye Xue za Zhi
Ziyu Wu, Sugui Wang, Peng Xue, Shoulin Wang, Gongcheng Wang, Wei Zhang
Several lines of direct evidence show that inhibitory member of the apoptosis-stimulating protein of p53 (iASPP) has an important function in cancer progression. However, its expression pattern and relationship with clinical pathologic characteristics in bladder cancer (BC) have not been completely elucidated. In this study, firstly, samples from 3 patients with invasive BC were detected by liquid chromatography tandem mass spectrometry to confirm overexpression of iASPP in BC, then samples from patients with noninvasive and invasive BC were detected by real-time polymerase chain reaction, Western blot, and tissue microarry immunohistochemistry...
May 2017: Medicine (Baltimore)
Macarena Varas, Camilo Valdivieso, Cecilia Mauriaca, Javiera Ortíz-Severín, Alberto Paradela, Ignacio Poblete-Castro, Ricardo Cabrera, Francisco P Chávez
Here, we provide the dataset associated with our research article on the polyphosphate metabolism entitled, "Multi-level evaluation of Escherichia coli polyphosphate related mutants using global transcriptomic, proteomic and phenomic analyses". By integrating different omics levels (transcriptome, proteome and phenome), we were able to study Escherichia coli polyphosphate mutant strains (Δppk1, Δppx, and Δppk1-ppx). We have compiled here all datasets from DNA microarrys, q-proteomic (Isotope-Coded Protein Labeling, ICPL) and phenomic (Phenotype microarray) raw data we have obtained in all polyP metabolism mutants...
June 2017: Data in Brief
Jun Xiao, Qi-Xian Wang, You-Qing Zhu
MicroRNAs (miRNAs) play important roles in carcinogenesis, but the global miRNA expression profile in gastric stromal tumor tissues remains unclear. This study was to examine the miRNA expression profile in gastric stromal tumor tissues and explore the function of dysregulated miRNAs by performing gene ontology (GO) and pathway enrichment analysis. Total RNA was extracted and purified from 3 pairs of frozen gastric stromal tumor tissues and the adjacent non-tumor tissues by using mirVana™ miRNA isolation kit...
December 2015: Journal of Huazhong University of Science and Technology. Medical Sciences
Long Ma, Kun Wu, Kun Liu, Shuo Gu, Yi Wang, Zongyuan Xu, Xiangyou Yu, Junsong Meng
OBJECTIVE: Ischemia-reperfusion (I/R) is a main cause of acute kidney injury (AKI). The renal expression profiles of microRNA (miRNA) and time course of their changes after renal I/R were explored to screen acute AKI prognostic-related microRNAs and biomarkers. METHODS: The expression profile of miRNA was analyzed for detecting miRNAs in kidney after renal I/R injury. Real-time polymerase chain reaction (PCR) was performed to validate the results of microarray. And the relationship was examined between kidney injury and time course of changes in selected miRNAs...
May 19, 2015: Zhonghua Yi Xue za Zhi [Chinese medical journal]
Jiyong Yin, Jing Sun, Jian Huang, Junsheng Huo
OBJECTIVE: To study the reality detect function of protein microarray which diagnosis the iron deficiency (ID). METHODS: Evaluated anti-interference ability with interference experiment, analyzed the detection stability with many times repeated experiment, detected the same experiment result repeatedly to analyze the detection indate. RESULTS: There was not interference to serum ferritin and soluble transferrin respector from distraction. The protein microarry can be using in 38 d after print probes...
May 2014: Wei Sheng Yan Jiu, Journal of Hygiene Research
Jisheng Li, Yimei Cai, Lupeng Ye, Shaohua Wang, Jiaqian Che, Zhengying You, Jun Yu, Boxiong Zhong
BACKGROUND: The growth and development of the posterior silk gland and the biosynthesis of the silk core protein at the fifth larval instar stage of Bombyx mori are of paramount importance for silk production. RESULTS: Here, aided by next-generation sequencing and microarry assay, we profile 1,229 microRNAs (miRNAs), including 728 novel miRNAs and 110 miRNA/miRNA* duplexes, of the posterior silk gland at the fifth larval instar. Target gene prediction yields 14,222 unique target genes from 1,195 miRNAs...
2014: BMC Genomics
Liping Sun, Jingqiong Hu, Wei Xiong, Xiaomei Chen, Huiyu Li, Shenghua Jie
BACKGROUND: Microvesicles (MVs) packaged with microribonucleic acids (miRNAs) have been shown to be released mainly from tumor cells. However, little information is known for miRNAs from MVs in hepatocellular carcinoma (HCC). Hence, we explored the MVs' miRNAs expression profiles in HCC. METHODS: MVs were collected from peripheral blood of HCC, chronic hepatitis B (CHB) and normal controls. miRNA from MVs were labeled and analyzed by Agilent miRNA microarry. Bioinformatics tools were used to analyze function of the differentially expressed MVs' miRNAs...
December 2013: Acta Gastro-enterologica Belgica
Isao Sakaida
Infused (transplanted) green fluorescent protein (GFP)-positive bone marrow cells (BMCs) migrated into the peri-portal regions of the cirrhotic mouse liver induced continuous CCl4 injection without irradiation (without bone marrow ablation). The infused GFP-positive BMCs differentiated into hepatoblasts detected with Liv2-antibody and then differentiated into albumin-producing hepatocytes. The differentiation "niche" induced by persistent liver damage due to continuous CCl4 injection seems to be an essential factor...
December 2011: Rinsho Byori. the Japanese Journal of Clinical Pathology
Jesús Tamarit-López, Sergi Morais, Rosa Puchades, Angel Maquieira
A novel DNA microarrying platform based on oxygen plasma activation of polycarbonate surface of compact disks (DVD) is presented. Carboxylic acid groups are generated in few seconds on polycarbonate in an efficient, fast, and clean way. Following this surface activation strategy, amino-modified oligonucleotide probes were covalently attached, reaching an immobilization density of 2 pmol cm(-2). Atomic force microscopy imaging revealed the nondestructive character of this treatment when applied for short times, allowing for disk scanning in standard DVD drives...
December 21, 2011: Bioconjugate Chemistry
Christian Eichelberg, Sarah Minner, Hendrik Isbarn, Eike Burandt, Luigi Terracciano, Holger Moch, Alexandra Kell, Roman Heuer, Felix K Chun, Guido Sauter, Margit Fisch, Pierre Tennstedt
PURPOSE: Alpha-methyl CoA racemase (AMACR) is used as an immunohistochemical marker for renal cell carcinoma (RCC) subtyping to distinguish papillary (pap) RCC. Expression of AMACR in other renal tumor subtypes is inhomogeneous, and the clinical and prognostic value of AMACR is unknown. The aim of this study was to asses AMACR protein expression in different RCC subtypes and to investigate its prognostic significance. METHODS: Protein expression of AMACR was analyzed in 1,088 renal tumor samples, among them 809 clear cell RCC and 151 papRCC, by immunohistochemistry using tissue microarry (TMA) technique...
August 2013: World Journal of Urology
Hui-min Han, Lin Guo, Li-jua Jiang, Xiao-yu Jiang, Ya-li Lv, Jin-kui Pang, Zhong-min Bai, Wei-juan Che, Rong-hui Xu, Ping Yu, Qiang Li
OBJECTIVE: To investigate the underlying mechanism for the therapeutic effect of a traditional Chinese medicinal recipe, Antidotal and Myogenic Ointment (AMO), on the foot ulcer in diabetic rat using cDNA microarray technology. METHODS: 45 rats were made diabetic by i. p. injection of streptozocin. The treated animals were then fed for 6 months,and subjected to the dissection of distal popliteal artery after ligation of the vessels. Another month later, grade II burn injury was produced on the bottom of their foot as a model of diabetic foot ulcer...
October 2011: Zhongguo Wei Zhong Bing Ji Jiu Yi Xue, Chinese Critical Care Medicine, Zhongguo Weizhongbing Jijiuyixue
Qin Ma, Lie Yang, Cun Wang, Yong-Yang Yu, Bin Zhou, Zhong-Guang Zhou
OBJECTIVE: To investigate the miRNA expression difference between colon cancer and normal colonic mucosa. METHODS: Twelve (12) pairs of colorectal cancer tissue and normal colonic mucosa were collected, total RNA was extracted and purified. After fluorescent tags being added, hybridization was carried out on miRNA microarray chip (Affymetrix company). SAM analysis was performed to find out the significant expression difference, then the difference was verified by RT-PCR, finally target gene analysis software was utilized to predict the miRNA function...
May 2011: Sichuan da Xue Xue Bao. Yi Xue Ban, Journal of Sichuan University. Medical Science Edition
Mireia Vilardell, Axel Rasche, Anja Thormann, Elisabeth Maschke-Dutz, Luis A Pérez-Jurado, Hans Lehrach, Ralf Herwig
BACKGROUND: Down syndrome (DS; trisomy 21) is the most common genetic cause of mental retardation in the human population and key molecular networks dysregulated in DS are still unknown. Many different experimental techniques have been applied to analyse the effects of dosage imbalance at the molecular and phenotypical level, however, currently no integrative approach exists that attempts to extract the common information. RESULTS: We have performed a statistical meta-analysis from 45 heterogeneous publicly available DS data sets in order to identify consistent dosage effects from these studies...
2011: BMC Genomics
Matthew N McCall, Peter N Murakami, Margus Lukk, Wolfgang Huber, Rafael A Irizarry
BACKGROUND: Microarray technology has become a widely used tool in the biological sciences. Over the past decade, the number of users has grown exponentially, and with the number of applications and secondary data analyses rapidly increasing, we expect this rate to continue. Various initiatives such as the External RNA Control Consortium (ERCC) and the MicroArray Quality Control (MAQC) project have explored ways to provide standards for the technology. For microarrays to become generally accepted as a reliable technology, statistical methods for assessing quality will be an indispensable component; however, there remains a lack of consensus in both defining and measuring microarray quality...
2011: BMC Bioinformatics
Su-Shing Chen, Yu-Ping Wang
In developing an integrated framework for translational bioinformatics, we consider bioimaging in the NIH Roadmap that exploits high-resolution genomic imaging for clinical applications to the diagnosis and treatment of genetic disorders/diseases. On one hand, we develop new image processing techniques, while on the other, we use the fusion of several well known ontological standards - Gene Ontology (GO), Clinical Bioinformatics Ontology (CBO), Foundational Model of Anatomy (FMA) and Microarry Gene Expression Data Ontology (MGED) in this framework...
2009: Summit on Translational Bioinformatics
Xinyun Wang, Ling Yuan, Haiyan Zheng, Juan Liu, Xi Huang, Li Wu, Haihong Yuan, Jianlan Zhao
BACKGROUND: Fragile histidine triad (FHIT) is a candidate tumor suppressor gene. Aberrance of FHIT has been observed in multiple carcinomas induced by environmental carcinogens, especially in lung cancer. In this study, the expression of FHIT protein in cell array was detected to further development of cell array and for a rapid, simple, and economical method. METHODS: The lung cancer samples were collected from the Tianjin Medical University General Hospital, the First Central Hospital and the Tianjin Chest Hospital from May to August in 2005...
February 20, 2009: Zhongguo Fei Ai za Zhi, Chinese Journal of Lung Cancer
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