LmSmdB: An Integrated database for metabolic and gene regulatory network in Leishmania major and Schistosoma mansoni
Publication date: Available online 19 December 2015 Source:Genomics Data Author(s): Priyanka Patel, Vineetha Mandlik, Shailza Singh A database that integrates all the information required for biological processing is essential to be stored in one platform. We have attempted to create one such integrated database that can be a one stop shop for the essential features required to fetch valuable result. LmSmdB (L. major and S. mansoni database) is an integrated database that accounts for the biological networks and regulatory pathways computationally determined by integrating the knowledge of the genome sequences of...
Source: Genomics Data - December 20, 2015 Category: Genetics & Stem Cells Source Type: research
Genome wide expression after different doses of irradiation of a three-dimensional (3D) model of oral mucosal
Publication date: Available online 19 December 2015 Source:Genomics Data Author(s): Maria P. Lambros, Michael K. DeSalvo, Hari Chandana Mulamalla, Jonathan Moreno, Lavanya Kondapalli We evaluated a three-dimensional (3D) human oral cell culture that consisted of two types of cells, oral keratinocytes and fibroblasts as a model of oral mucositis which is a debilitating adverse effect of chemotherapy and radiation treatment. The 3D cell culture model was irradiated with 12 or 2Gy, and total RNA was collected 6h after irradiation to compare global gene expression profiles via microarray analysis. Here we provide...
Source: Genomics Data - December 20, 2015 Category: Genetics & Stem Cells Source Type: research
Transcriptome response to copper heavy metal stress in hard-shelled mussel (Mytilus coruscus)
Publication date: Available online 20 December 2015 Source:Genomics Data Author(s): Meiying Xu, Lihua Jiang, Kang-Ning Shen, Changwen Wu, Guangyuan He, Chung-Der Hsiao The hard-shelled mussel (Mytilus coruscus) has considerably one of the most economically important marine shellfish worldwide and considered as a good invertebrate model for ecotoxicity study for a long time. In the present study, we used Illumina sequencing technology (HiSeq2000) to sequence, assemble and annotate the transcriptome of the hard-shelled mussel which challenged with copper pollution. A total of 21,723,913 paired-end clean reads...
Source: Genomics Data - December 20, 2015 Category: Genetics & Stem Cells Source Type: research
Draft genome sequence of kocuria sp. SM24M-10 isolated from coral mucus
Publication date: Available online 19 December 2015 Source:Genomics Data Author(s): Bruna Rafaella Z. Palermo, Daniel B.A. Castro, Letícia Bianca Pereira, Ana Carolina G. Cauz, Beatriz L. Magalhães, Camila Carlos, Fernanda L.P. da Costa, Guilherme P. Scagion, Juliana S. Higa, Ludimila D. Almeida, Meiriele da S. das Neves, Melina Aparecida Cordeiro, Paula F.V. do Prado, Thiago M. da Silva, Thiago Willian A. Balsalobre, Luciana C. Paulino, Renato Vicentini, Lúcio F.C. Ferraz, Laura M.M. Ottoboni Here, we describe the genomic features of the Actinobacteria Kocuria sp. SM24M-10 isol...
Source: Genomics Data - December 19, 2015 Category: Genetics & Stem Cells Source Type: research
Gene expression profiling of human calcific aortic valve disease
Publication date: Available online 19 December 2015 Source:Genomics Data Author(s): Jaana Rysä Calcific aortic valve disease is a slowly progressive disorder that ranges from mild valve thickening (ie. aortic sclerosis) to severe calcification of valves (ie. aortic stenosis). Gene expression profiling analysis of non-calcified controls, sclerotic, and calcified aortic valves was performed to better understand the progression of calcific aortic valve disease. The complementary information related to processing and statistical analysis of the DNA microarray data is provided in this article. Interpretation of this data...
Source: Genomics Data - December 19, 2015 Category: Genetics & Stem Cells Source Type: research
Complete genome sequence of acinetobacter baumannii XH386 (ST208), a multi-drug resistant bacteria isolated from pediatric hospital in China
Publication date: Available online 19 December 2015 Source:Genomics Data Author(s): Youhong Fang, Jingjing Quan, Xiaoting Hua, Ye Feng, Xi Li, Jianfeng Wang, Zhi Ruan, Shiqiang Shang, Yunsong Yu [Briefly describe the contents of the Data in Brief article. Tell the reader the repository and reference number for the data in the abstract to.] Acinetobacter baumannii is an important bacterium that emerged as a significant nosocomial pathogen worldwide. The rise of A. baumannii was due to its multi-drug resistance (MDR), while it was difficult to treat multi-drug resistant A. baumannii with antibiotics, e...
Source: Genomics Data - December 19, 2015 Category: Genetics & Stem Cells Source Type: research
Gene expression profiling of Ctr9-regulated transcriptome in ERα-positive breast cancer
Publication date: Available online 17 December 2015 Source:Genomics Data Author(s): Hao Zeng, Wei Xu [Briefly describe the contents of the Data in Brief article. Tell the reader the repository and reference number for the data in the abstract to.] Ctr9, the key scaffold subunit in human RNA polymerase II associated factor complex (PAFc), has diverse functions in cells and has been implicated in human diseases. Recently, our study found that loss of Ctr9 led to apparent morphological change, decrease of proliferation, and reduced colony formation in ERα+ breast cancer cells. Moreover, Ctr9 and ERα show position co...
Source: Genomics Data - December 18, 2015 Category: Genetics & Stem Cells Source Type: research
Metagenomic exploration of the bacterial community structure at Paradip Port, Odisha, India
Publication date: Available online 17 December 2015 Source:Genomics Data Author(s): Arnab Pramanik, Pijush Basak, Satabdi Banerjee, Sanghamitra Sengupta, Dhrubajyoti Chattopadhyay, Maitree Bhattacharyya This is a pioneering report on the metagenomic exploration of the bacterial diversity from a busy sea port in Paradip, Odisha, India. In our study, high-throughput sequencing of community 16S rRNA gene amplicon was performed using 454 GS Junior platform. Metagenome contain 34,121 sequences with 16,677,333bp and 56.3% G+C content. Metagenome sequences data are now available at NCBI under the Sequence Read Arc...
Source: Genomics Data - December 18, 2015 Category: Genetics & Stem Cells Source Type: research
Transcriptome profiling of Lactococcus lactis subsp. cremoris CECT 8666 in response to agmatine
In this study we report the transcriptional profiling of L. lactis subsp. cremoris CECT 8666 grown in M17 medium with galactose (GalM17) as carbon source and supplemented with agmatine, compared to that of the strain grown in the same culture medium without agmatine. The transcriptional profiling data of agmatine-regulated genes were deposited in the Gene Expression Omnibus (GEO) database under Accession no. GSE74808. (Source: Genomics Data)
Source: Genomics Data - December 18, 2015 Category: Genetics & Stem Cells Source Type: research
Whole genome analysis of Klebsiella pneumoniae T2-1-1 from human oral cavity
Publication date: Available online 17 December 2015 Source:Genomics Data Author(s): Kok-Gan Chan, Wai-Fong Yin, Xin-Yue Chan Klebsiella pneumoniae T2-1-1 was isolated from the human tongue debris and subjected to whole genome sequencing on HiSeq platform and annotated on RAST. The nucleotide sequence of this genome was deposited to into DDBJ/EMBL/GenBank under the accession JAQL00000000. (Source: Genomics Data)
Source: Genomics Data - December 18, 2015 Category: Genetics & Stem Cells Source Type: research
Transcriptomics in type 2 diabetes: Bridging the gap between genotype and phenotype
Publication date: Available online 17 December 2015 Source:Genomics Data Author(s): Christopher P. Jenkinson, Harald H.H. Göring, Rector Arya, John Blangero, Ravindranath Duggirala, Ralph A. DeFronzo Type 2 diabetes (T2D) is a common, multifactorial disease that is influenced by genetic and environmental factors and their interactions. However, common variants identified by genome wide association studies (GWAS) explain only about 10% of the total trait variance for T2D and less than 5% of the variance for obesity, indicating that a large proportion of heritability is still unexplained. The transcriptomic ...
Source: Genomics Data - December 18, 2015 Category: Genetics & Stem Cells Source Type: research
Analysis of copy number variations in Mexican Holstein cattle using axiom genome-wide BOS 1 array
Publication date: Available online 17 December 2015 Source:Genomics Data Author(s): Ricardo Salomon-Torres, Rafael Villa-Angulo, Carlos Villa-Angulo Recently, for copy number variation (CNV) analysis, bovine researchers have focused mainly on the use of genome-wide SNP genotyping arrays. One of the highest density commercially available SNPchips for cattle is the Affymetrix Axiom Genome-Wide Bos 1, which assays 648,315 informative SNPs across the whole bovine genome. Here, we describe the microarray data, quality controls and validation implemented in a study published in Genetics and Molecular Research Journal i...
Source: Genomics Data - December 18, 2015 Category: Genetics & Stem Cells Source Type: research
Structural insights of microbial community of Deulajhari (India) hot spring using 16s-rRNA based metagenomic sequencing
Publication date: Available online 18 December 2015 Source:Genomics Data Author(s): Archana Singh, Enketeswara Subudhi Insights about the distribution of the microbial community prove to be the major goal of understanding microbial ecology which remains to be fully deciphered. Hot springs being hub for the thermophilic microbiota attract the attention of the microbiologists. Deulajhari hot spring cluster is located in the Angul district of Odisha. Covered within a wooded area, Deulajhari hot spring is also fed by the plant litter resulting in a relatively high amount of total organic content (TOC). For the first ti...
Source: Genomics Data - December 18, 2015 Category: Genetics & Stem Cells Source Type: research
Microarray expression analysis of genes involved in innate immune memory in peritoneal macrophages
In this study of data deposited into Gene Expression Omnibus (GEO) under GSE71111, we analyzed the expression profile of peritoneal macrophages isolated from mice pre-administrated with toll-like receptor (TLR) ligands, mimicking pathogen infection. In these macrophages, increased expression of a group of innate immunity-related genes was sustained over a long period of time, and these genes overlapped with ATF7-regulated genes. We conclude that ATF7 plays an important role in innate immune memory in macrophages. (Source: Genomics Data)
Source: Genomics Data - December 13, 2015 Category: Genetics & Stem Cells Source Type: research
Microarray analysis of microRNA expression in bone marrow-derived progenitor cells from mice with type 2 diabetes
Publication date: March 2016 Source:Genomics Data, Volume 7 Author(s): Jie-Mei Wang, Kezhong Zhang Bone-marrow derived vascular precursors are an important endogenous repair reservoir for vascular repair and neovascularization [1]. Therapies of stem/progenitor cells targeting on angiogenesis are considered hopeful solutions for tissue repair and regeneration. However, the dysfunction of patient-derived progenitor cells has been implicated in diabetes [2], which limited the efficacy of autologous cell therapies in the clinic [3,4]. MicroRNAs are important gene regulators whose functions remain largely unknown. In th...
Source: Genomics Data - December 12, 2015 Category: Genetics & Stem Cells Source Type: research
