Genomics Data最新文献_第7页

Metagenome analysis of the root endophytic microbial community of Indian rice (O. sativa L.) 印度水稻根系内生微生物群落的宏基因组分析

Genomics Data Pub Date : 2017-06-01 Epub Date: 2017-02-28 DOI: 10.1016/j.gdata.2017.02.010

Subhadipa Sengupta , Sayak Ganguli , Pankaj K Singh

引用次数: 30

Bacterial fauna associating with chironomid larvae from lakes of Bengaluru city, India - A 16s rRNA gene based identification 印度Bengaluru市湖泊中与chironomid幼虫相关的细菌区系——基于16s rRNA基因的鉴定

Genomics Data Pub Date : 2017-06-01 Epub Date: 2017-03-03 DOI: 10.1016/j.gdata.2017.03.001

Ramprasad Kuncham , Thiyagarajan Sivaprakasam , Puneeth Kumar R , Sreenath P , Ravi Nayak , Tha. Thayumanavan , Gopireddy V. Subba Reddy

{"title":"Bacterial fauna associating with chironomid larvae from lakes of Bengaluru city, India - A 16s rRNA gene based identification","authors":"Ramprasad Kuncham , Thiyagarajan Sivaprakasam , Puneeth Kumar R , Sreenath P , Ravi Nayak , Tha. Thayumanavan , Gopireddy V. Subba Reddy","doi":"10.1016/j.gdata.2017.03.001","DOIUrl":"10.1016/j.gdata.2017.03.001","url":null,"abstract":"<div>Chironomid larvae that inhabit in aquatic sediments play an important role as vector for bacterial pathogens. Its life cycle consists of four stages i.e. eggs, larvae, pupae and adult. In the present study we identified bacterial species associated with whole larvae of chironomids from 11 lake sediments of Bangalore region using 16s rRNA gene Sanger sequencing. We found that larvae from all lake sediments associated with bacterial species which include key pathogens. Totally we identified 65 bacterial isolates and obtained GenBank accession numbers (KX980423 - KX980487). Phylogenetic tree constructed using MEGA 7 software and tree analysis highlight the predominant bacterial community associated with larvae which include Enterobacteriaceae (43.08%; 28 isolates) and Aeromonas (24.62%; 16 isolates), Shewanella, Delftia, Bacillus (6.15%; 4 isolates each), Pseudomonas (4.62%; 3 isolates) and Exiguobacterium (3.08%; 2 isolates). Current findings state that among bacterial population Aeromonas, Enterobacter and Escherichia with serotypes are commonly associated with larvae in maximum lake points. In other hand Vibrio, Pseudomonas, Klebsiella, Shigella, Bacillus, and other bacterial species were identified moderately in all lakes. Interestingly, we identified first time Shigella Gram negative, rod shaped pathogenic organism of Enterobacteriaceae and Rheinheimera Gram negative, rod shaped organism associating chironomid larvae.</div>","PeriodicalId":56340,"journal":{"name":"Genomics Data","volume":"12 ","pages":"Pages 44-48"},"PeriodicalIF":0.0,"publicationDate":"2017-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.gdata.2017.03.001","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34833192","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 12

RNA-Seq analysis of human cell lines established from normal and neoplastic esophageal squamous epithelium 人正常和肿瘤食管鳞状上皮细胞系的RNA-Seq分析

Genomics Data Pub Date : 2017-06-01 Epub Date: 2017-02-05 DOI: 10.1016/j.gdata.2017.02.002

Ichiro Akagi , Osamu Ishibashi

{"title":"RNA-Seq analysis of human cell lines established from normal and neoplastic esophageal squamous epithelium","authors":"Ichiro Akagi , Osamu Ishibashi","doi":"10.1016/j.gdata.2017.02.002","DOIUrl":"10.1016/j.gdata.2017.02.002","url":null,"abstract":"<div>Esophageal cancer (EC) is the eighth most common cancer globally in 2012 and predominantly occurs in the man (Enzinger and Mayer, 2003; Conteduca et al., 2012). EC is classified mainly into two types, esophageal squamous cell carcinoma (ESCC) and esophageal adenocarcinoma, accounting for 60–70% and 20–30% of all EC cases, respectively. In a previous statistical study it was reported that the numbers of new EC cases and EC-related deaths worldwide in 2008 were estimated to be 482,300 and 406,800, respectively (Jemal et al., 2011). This high mortality rate is largely due to the characteristics of EC such as frequent distant/local metastasis and poor subjective symptoms leading to difficulty with early diagnosis. Patients affected with EC diagnosed at late stages mostly have unsatisfactory prognosis, even though various therapeutic options are available. Therefore, there is an urgent need to develop effective methods that enable the early detection of EC (Orringer, 1993), prompting us to search for novel biomarkers for EC. Here, we provide datasets from RNA-Seq analysis of Het-1A, a normal human esophageal squamous cell line (Stoner et al., 1991), and TE-1, TE-5, and TE-8, which are well-, poorly-, and moderately-differentiated ESCC-derived cell lines, respectively (Nishihira et al., 1993). The raw data of these experiments have been deposited at DNA Data Bank of Japan (DDBJ) under the accession IDs DRR084199, DRR084200, DRR084201, and DRR084202.</div>","PeriodicalId":56340,"journal":{"name":"Genomics Data","volume":"12 ","pages":"Pages 4-6"},"PeriodicalIF":0.0,"publicationDate":"2017-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.gdata.2017.02.002","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48071930","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 4

Draft genome sequence of Bacillus oleronius DSM 9356 isolated from the termite Reticulitermes santonensis 绘制山东白蚁芽孢杆菌DSM 9356的基因组序列

Genomics Data Pub Date : 2017-06-01 Epub Date: 2017-03-24 DOI: 10.1016/j.gdata.2017.03.005

Rodney Owusu-Darko , Mushal Allam , Senzo Mtshali , Arshad Ismail , Elna Maria Buys

引用次数: 6

prepare_taxa_charts.py: A Python program to automate generation of publication ready taxonomic pie chart images from QIIME prepare_taxa_charts.py:一个Python程序，用于从QIIME自动生成准备发布的分类饼图图像

Genomics Data Pub Date : 2017-06-01 Epub Date: 2017-03-29 DOI: 10.1016/j.gdata.2017.03.009

Vijay Lakhujani, Chandan Badapanda

{"title":"prepare_taxa_charts.py: A Python program to automate generation of publication ready taxonomic pie chart images from QIIME","authors":"Vijay Lakhujani, Chandan Badapanda","doi":"10.1016/j.gdata.2017.03.009","DOIUrl":"10.1016/j.gdata.2017.03.009","url":null,"abstract":"<div>QIIME (Quantitative Insights Into Microbial Ecology) is one of the most popular open-source bioinformatics suite for performing metagenome, 16S rRNA amplicon and Internal Transcribed Spacer (ITS) data analysis. Although, it is very comprehensive and powerful tool, it lacks a method to provide publication ready taxonomic pie charts. The script plot_taxa_summary.py bundled with QIIME generate a html file and a folder containing taxonomic pie chart and legend as separate images. The images have randomly generated alphanumeric names. Therefore, it is difficult to associate the pie chart with the legend and the corresponding sample identifier. Even if the option to have the legend within the html file is selected while executing plot_taxa_summary.py, it is very tedious to crop a complete image (having both the pie chart and the legend) due to unequal image sizes. It requires a lot of time to manually prepare the pie charts for multiple samples for publication purpose. Moreover, there are chances of error while identifying the pie chart and legend pair due to random alphanumeric names of the images. To bypass all these bottlenecks and make this process efficient, we have developed a python based program, prepare_taxa_charts.py, to automate the renaming, cropping and merging of taxonomic pie chart and corresponding legend image into a single, good quality publication ready image. This program not only augments the functionality of plot_taxa_summary.py but is also very fast in terms of CPU time and user friendly.</div>","PeriodicalId":56340,"journal":{"name":"Genomics Data","volume":"12 ","pages":"Pages 97-101"},"PeriodicalIF":0.0,"publicationDate":"2017-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.gdata.2017.03.009","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34913532","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1

Draft genome of Bordetella pseudohinzii BH370 isolated from trachea and lung tissues of a laboratory mouse 从实验小鼠的气管和肺组织中分离的拟hinz杆菌BH370的基因组草图

Genomics Data Pub Date : 2017-06-01 Epub Date: 2017-03-21 DOI: 10.1016/j.gdata.2017.03.004

Shih Keng Loong , Kim-Kee Tan , Syuhaida Sulaiman , Pooi Fong Wong , Sazaly AbuBakar

引用次数: 8

Gene expression in rat striatum following carbon monoxide poisoning 一氧化碳中毒后大鼠纹状体的基因表达

Genomics Data Pub Date : 2017-06-01 Epub Date: 2017-03-22 DOI: 10.1016/j.gdata.2017.03.007

Shuichi Hara , Masamune Kobayash , Fumi Kuriiwa , Kunihiko Kurosaki , Hajime Mizukami

{"title":"Gene expression in rat striatum following carbon monoxide poisoning","authors":"Shuichi Hara , Masamune Kobayash , Fumi Kuriiwa , Kunihiko Kurosaki , Hajime Mizukami","doi":"10.1016/j.gdata.2017.03.007","DOIUrl":"10.1016/j.gdata.2017.03.007","url":null,"abstract":"<div>Carbon monoxide (CO) poisoning causes brain damage, which is attenuated by treatment with hydrogen [1], [2], a scavenger selective to hydroxyl radical (<img>OH) [3]. This suggests a role of <img>OH in brain damage due to CO poisoning. Studies have shown strong enhancement of <img>OH production in rat striatum by severe CO poisoning with a blood carboxyhemoglobin (COHb) level >70% due to 3000ppm CO, but not less severe CO poisoning with a blood COHb level at approximately 50% due to 1000ppm CO [4]. Interestingly, 5% O2 causes hypoxia comparable with that by 3000ppm CO and produces much less •OH than 3000ppm CO does [4]. In addition, cAMP production in parallel with <img>OH production [5] might contribute to <img>OH production [6]. It is likely that mechanisms other than hypoxia contribute to brain damage due to CO poisoning [7]. To search for the mechanisms, we examined the effects of 1000ppm CO, 3000ppm CO and 5% O2 on gene expression in rat striatum. All array data have been deposited in the Gene Expression Omnibus (GEO) database under accession number GSE94780.</div>","PeriodicalId":56340,"journal":{"name":"Genomics Data","volume":"12 ","pages":"Pages 74-75"},"PeriodicalIF":0.0,"publicationDate":"2017-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.gdata.2017.03.007","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34892888","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 4

Sequencing and de novo transcriptome assembly of the Chinese giant salamander (Andrias davidianus) 中国大鲵(Andrias davidianus)的测序和转录组组装

Genomics Data Pub Date : 2017-06-01 Epub Date: 2017-03-27 DOI: 10.1016/j.gdata.2017.03.011

Yong Huang, Xiao Chan Gao, Jian Li Xiong, Hong Tao Ren, Xi Hong Sun

{"title":"Sequencing and de novo transcriptome assembly of the Chinese giant salamander (Andrias davidianus)","authors":"Yong Huang, Xiao Chan Gao, Jian Li Xiong, Hong Tao Ren, Xi Hong Sun","doi":"10.1016/j.gdata.2017.03.011","DOIUrl":"https://doi.org/10.1016/j.gdata.2017.03.011","url":null,"abstract":"<div>Next-generation technologies for determination of genomics and transcriptomics composition have a wide range of applications. Andrias davidianus, has become an endangered amphibian species of salamander endemic in China. However, there is a lack of the molecular information. In this study, we obtained the RNA-Seq data from a pool of A. davidianus tissue including spleen, liver, muscle, kidney, skin, testis, gut and heart using Illumina HiSeq 2500 platform. A total of 15,398,997,600bp were obtained, corresponding to 102,659,984 raw reads. A total of 102,659,984 reads were filtered after removing low-quality reads and trimming the adapter sequences. The Trinity program was used to de novo assemble 132,912 unigenes with an average length of 690bp and N50 of 1263bp. Unigenes were annotated through number of databases. These transcriptomic data of A. davidianus should open the door to molecular evolution studies based on the entire transcriptome or targeted genes of interest to sequence. The raw data in this study can be available in NCBI SRA database with accession number of SRP099564.</div>","PeriodicalId":56340,"journal":{"name":"Genomics Data","volume":"12 ","pages":"Pages 109-110"},"PeriodicalIF":0.0,"publicationDate":"2017-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.gdata.2017.03.011","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"92030635","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 8

A metagenomic approach to decipher the indigenous microbial communities of arsenic contaminated groundwater of Assam 一种宏基因组方法来破译阿萨姆邦砷污染地下水的本地微生物群落

Genomics Data Pub Date : 2017-06-01 Epub Date: 2017-03-30 DOI: 10.1016/j.gdata.2017.03.013

Saurav Das , Sudipta Sankar Bora , R.N.S. Yadav , Madhumita Barooah

{"title":"A metagenomic approach to decipher the indigenous microbial communities of arsenic contaminated groundwater of Assam","authors":"Saurav Das , Sudipta Sankar Bora , R.N.S. Yadav , Madhumita Barooah","doi":"10.1016/j.gdata.2017.03.013","DOIUrl":"10.1016/j.gdata.2017.03.013","url":null,"abstract":"<div>Metagenomic approach was used to understand the structural and functional diversity present in arsenic contaminated groundwater of the Ganges Brahmaputra Delta aquifer system. A metagene dataset (coded as TTGW1) of 89,171 sequences (totaling 125,449,864 base pairs) with an average length of 1406bps was annotated. About 74,478 sequences containing 101,948 predicted protein coding regions passed the quality control. Taxonomical classification revealed abundance of bacteria that accounted for 98.3% of the microbial population of the metagenome. Eukaryota had an abundance of 1.1% followed by archea that showed 0.4% abundance. In phylum based classification, Proteobacteria was dominant (62.6%) followed by Bacteroidetes (11.7%), Planctomycetes (7.7%), Verrucomicrobia (5.6%), Actinobacteria (3.7%) and Firmicutes (1.9%). The Clusters of Orthologous Groups (COGs) analysis indicated that the protein regulating the metabolic functions constituted a high percentage (18,199 reads; 39.3%) of the whole metagenome followed by the proteins regulating the cellular processes (22.3%). About 0.07% sequences of the whole metagenome were related to genes coding for arsenic resistant mechanisms. Nearly 50% sequences of these coded for the arsenate reductase enzyme (EC. 1.20.4.1), the dominant enzyme of ars operon. Proteins associated with iron acquisition and metabolism were coded by 2% of the metagenome as revealed through SEED analysis. Our study reveals the microbial diversity and provides an insight into the functional aspect of the genes that might play crucial role in arsenic geocycle in contaminated ground water of Assam.</div>","PeriodicalId":56340,"journal":{"name":"Genomics Data","volume":"12 ","pages":"Pages 89-96"},"PeriodicalIF":0.0,"publicationDate":"2017-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.gdata.2017.03.013","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34913592","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 42

SMRT sequencing data for Garcinia mangostana L. variety Mesta 山竹Garcinia mangostana L.品种Mesta的SMRT测序数据

Genomics Data Pub Date : 2017-06-01 Epub Date: 2017-05-05 DOI: 10.1016/j.gdata.2017.04.003

Mohd Razik Midin , Kok-Keong Loke , Maria Madon , Mohd Shukor Nordin , Hoe-Han Goh , Normah Mohd Noor

引用次数: 4