RNA-Seq reveals changes in the Staphylococcus aureus transcriptome following blue light illumination
Publication date: Available online 26 May 2016 Source:Genomics Data Author(s): Tamarah L. Adair, Bayless E. Drum In an effort to better understand the mechanism by which blue light inhibits the growth of Staphylococcus aureus in culture, a whole transcriptome analysis of S. aureus isolate BUSA2288 was performed using RNA-Seq to analyze the differential gene expression in response to blue light exposure. RNA was extracted from S. aureus cultures pooled from 24 one milliliter well samples that were each illuminated with a dose of 250 J/cm2 of 465 nm blue light and from control cultures grown in the dark. Complementar...
Source: Genomics Data - May 25, 2016 Category: Genetics & Stem Cells Source Type: research
Genome annotation of a Saccharomyces sp. lager brewer's yeast
Publication date: Available online 21 May 2016 Source:Genomics Data Author(s): Patricia Marcela De León-Medina, Ramiro Elizondo-González, Luis Cástulo Damas-Buenrostro, Jan-Maarten Geertman, Marcel Van den Broek, Luis Jesús Galán-Wong, Rocío Ortiz-López, Benito Pereyra-Alférez The genome of lager brewer's yeast is a hybrid, with Saccharomyces eubayanus and Saccharomyces cerevisiae as sub-genomes. Due to their specific use in the beer industry, relatively little information is available. The genome of brewing yeast was sequenced and annotated in this study. We obtained a genome size of 22.7 Mbp t...
Source: Genomics Data - May 20, 2016 Category: Genetics & Stem Cells Source Type: research
Whole Genome Sequence Analysis of an Alachlor and Endosulfan Degrading Pseudomonas strain W15Feb9B isolated from Ochlocknee River, Florida
Publication date: Available online 16 May 2016 Source:Genomics Data Author(s): Ashvini Chauhan, Ashish Pathak, Ayman Y.I. Ewida, Zabrenna Griffiths, Paul Stothard We recently isolated Pseudomonas sp. strain W15Feb9B from Ochlocknee River, Florida and demonstrated potent biodegradative activity against two commonly used pesticides- Alachlor [(2-chloro-2`,6`-diethylphenyl-N (methoxymethyl)acetanilide)] and Endosulfan [(6,7,8,9,10,10-hexachloro-1,5,5a,6,9,9a-hexahydro-6,9methano-2,3,4-benzo(e)di-oxathiepin-3-oxide], respectively. To further identify the repertoire of metabolic functions possessed by strain W15Fe...
Source: Genomics Data - May 16, 2016 Category: Genetics & Stem Cells Source Type: research
Comprehensive and computational analysis of genes in human umbilical vein endothelial cells responsive to X-irradiation
Publication date: Available online 16 May 2016 Source:Genomics Data Author(s): Yukihiro Furusawa, Qing-Li Zhao, Yuichi Hattori, Yoshiaki Tabuchi, Toshiyasu Iwasaki, Takaharu Nomura, Takashi Kondo Radiation exposure such as A-bomb or radiation therapy is considered a major health-risk factor for cardiovascular disease. In order to understand the molecular mechanisms underlying the inflammatory reaction frequently encountered in the vascular system after exposure to ionizing radiation, we carried out a global scale microarray and computational gene expression analyses on human umbilical endothelial cells (H...
Source: Genomics Data - May 16, 2016 Category: Genetics & Stem Cells Source Type: research
αB-crystallin and HspB2 Deficiency is Protective from Diet-Induced Glucose Intolerance
Publication date: Available online 13 May 2016 Source:Genomics Data Author(s): Daniel J. Toft, Miles Fuller, Matthew Schipma, Feng Chen, Vincent L. Cryns, Brian T. Layden Emerging evidence suggests molecular chaperones have a role in the pathogenesis of obesity and diabetes. As αB-crystallin and HspB2 are molecular chaperones and data suggests their expression is elevated in the skeletal muscle of diabetic and obese animals, we sought to determine if αB-crystallin and HspB2 collectively play a functional role in the metabolic phenotype of diet-induced obesity. Using αB-crystallin/HspB2 knockout and litte...
Source: Genomics Data - May 13, 2016 Category: Genetics & Stem Cells Source Type: research
Integrity of genome-wide genotype data from low passage lymphoblastoid cell lines
Publication date: Available online 12 May 2016 Source:Genomics Data Author(s): Nina S. McCarthy, Spencer M. Allan, David Chandler, Assen Jablensky, Bharti Morar We compared genotype data from the HumanExomeCore Array in peripheral blood mononuclear cells and low passage lymphoblastoid cell lines from the same 24 individuals to test for genotypic errors caused by the Epstein-Barr Virus transformation process. Genotype concordance across the 24 comparisons was 99.57% for unfiltered genotype data, and 99.63% following standard genotype quality control filters. Mendelian error rates and levels of heterozygosity w...
Source: Genomics Data - May 11, 2016 Category: Genetics & Stem Cells Source Type: research
Unraveling the rat blood genome-wide transcriptome after oral administration of lavender oil by a two-color dye-swap DNA microarray approach
Publication date: Available online 12 May 2016 Source:Genomics Data Author(s): Motohide Hori, Hiroko Kubo, Junko Shibato, Tomomi Saito, Tetsuo Ogawa, Minoru Wakamori, Yoshinori Masuo, Seiji Shioda, Randeep Rakwal Lavender oil (LO) is a commonly used essential oil in aromatherapy as non-traditional medicine. With an aim to demonstrate LO effects on the body, we have recently established an animal model investigating the influence of orally administered LO in rat tissues, genome-wide. In this brief, we investigate the effect of LO ingestion in the blood of rat. Rats were administered LO at usual therape...
Source: Genomics Data - May 11, 2016 Category: Genetics & Stem Cells Source Type: research
Gene expression analysis of Solanum lycopersicum and Solanum habrochaites under drought conditions
Publication date: Available online 13 April 2016 Source:Genomics Data Author(s): Upama Mishra, Ashutosh Rai, Rajesh Kumar, Major Singh, Hausila Prasad Pandey Drought is one of the limiting environmental factors that affect crop production worldwide. Understanding the molecular mechanism of drought stress is the key to developing drought tolerant crop. In this experiment we performed expression profiling of tomato plants under water deficit conditions using microarray technology. The data set we generated (available in the NCBI/GEO database under GSE22304) has been analyzed to identify genes that are involved ...
Source: Genomics Data - May 5, 2016 Category: Genetics & Stem Cells Source Type: research
Whole transcriptome expression analysis and comparison of two different strains of Plasmodium falciparum using RNA-Seq
Publication date: Available online 23 April 2016 Source:Genomics Data Author(s): Hiasindh Ashmi Antony, Vrushali Pathak, Subhash Chandra Parija, Kanjaksha Ghosh, Amrita Bhattacherjee The emergence and distribution of drug resistance in malaria are serious public health concerns in tropical and subtropical regions of the world. However, the molecular mechanism of drug resistance remains unclear. In the present study, we performed a high-throughput RNA-Seq to identify and characterize the differentially expressed genes between the chloroquine (CQ) sensitive (3D7) and resistant (Dd2) strains of Plasmodium falcip...
Source: Genomics Data - May 5, 2016 Category: Genetics & Stem Cells Source Type: research
The complete mitochondrial genome of the Antarctic stalked jellyfish, Haliclystus antarcticus Pfeffer, 1889 (Staurozoa: Stauromedusae)
Publication date: Available online 25 April 2016 Source:Genomics Data Author(s): Hsing-Hui Li, Ping-Jyun Sung, Hsuan-Ching Ho In present study, the complete mitogenome sequence of the Antarctic stalked jellyfish, Haliclystus antarcticus Pfeffer (Staurozoa: Stauromedusae) has been sequenced by next-generation sequencing method. The assembled mitogenome comprises of 15,766bp including 13 protein coding genes, 7 transfer RNAs, and 2 ribosomal RNA genes. The overall base of Antarctic stalked jellyfish constitutes of 26.5% for A, 19.6% for C, 19.8% for G, 34.1% for T and show 90% identity to Sessile Jelly, Haliclystus...
Source: Genomics Data - May 5, 2016 Category: Genetics & Stem Cells Source Type: research
Combined sequencing of mRNA and DNA from human embryonic stem cells
Publication date: Available online 26 April 2016 Source:Genomics Data Author(s): Florian Mertes, Heiner Kuhl, Wasco Wruck, Hans Lehrach, James Adjaye Combined transcriptome and whole genome sequencing of the same ultra-low input sample down to single cells is a rapidly evolving approach for the analysis of rare cells. Besides stem cells, rare cells originating from tissues like tumor or biopsies, circulating tumor cells and cells from early embryonic development are under investigation. Herein we describe a universal method applicable for the analysis of minute amounts of sample material (150 to 200 cells) de...
Source: Genomics Data - May 5, 2016 Category: Genetics & Stem Cells Source Type: research
Draft genome sequence of the docosahexaenoic acid producing thraustochytrid Aurantiochytrium sp. T66
Publication date: Available online 29 April 2016 Source:Genomics Data Author(s): Bin Liu, Helga Ertesvåg, Inga Marie Aasen, Olav Vadstein, Trygve Brautaset, Tonje Marita Bjerkan Heggeset Thraustochytrids are unicellular, marine protists, and there is a growing industrial interest in these organisms, particularly because some species, including strains belonging to the genus Aurantiochytrium, accumulate high levels of docosahexaenoic acid (DHA). Here, we report the draft genome sequence of Aurantiochytrium sp. T66 (ATCC PRA-276), with a size of 43Mbp, and 11,683 predicted protein-coding sequences. The data ...
Source: Genomics Data - May 5, 2016 Category: Genetics & Stem Cells Source Type: research
De novo transcriptome assembly of two Vigna angularis varieties collected from Korea
Publication date: Available online 5 May 2016 Source:Genomics Data Author(s): Yeonhwa Jo, Sen Lian, Jin Kyong Cho, Hoseong Choi, Sang-Min Kim, Sun-Lim Kim, Bong Choon Lee, Won Kyong Cho The adzuki bean (Vigna angularis), a member of the family Fabaceae, is widely grown in Asia, from East Asia to the Himalayas. The adzuki bean is known as an ingredient that adds sweetness to diverse desserts made in Eastern Asian countries. Libraries prepared from two V. angularis varieties referred to as Taejin Black and Taejin Red were paired-end sequenced using the Illumina HiSeq 2000 system. The raw data in this stud...
Source: Genomics Data - May 5, 2016 Category: Genetics & Stem Cells Source Type: research
De novo transcriptome assembly of Sorghum bicolor variety Taejin
In this study, we conducted de novo transcriptome assembly for sorghum variety Taejin by next-generation sequencing, obtaining 8.748GB of raw data. The raw data in this study can be available in NCBI SRA database with accession number of SRX1715644. Using the Trinity program, we identified 222,161 transcripts from sorghum variety Taejin. We further predicted coding regions within the assembled transcripts by the TransDecoder program, resulting in a total of 148,531 proteins. We carried out BLASTP against the Swiss-Prot protein sequence database to annotate the functions of the identified proteins. To our knowledge, this is...
Source: Genomics Data - May 5, 2016 Category: Genetics & Stem Cells Source Type: research
De novo transcriptome assembly of Setatria italica variety Taejin
In this study, we carried out de novo transcriptome assembly for the foxtail millet variety Taejin collected from Korea using next-generation sequencing. We obtained a total of 8.676GB raw data by paired-end sequencing. The raw data in this study can be available in NCBI SRA database with accession number of SRR3406552. The Trinity program was used to de novo assemble 145,332 transcripts. Using the TransDecoder program, we predicted 82,925 putative proteins. BLASTP was performed against the Swiss-Prot protein sequence database to annotate the functions of identified proteins, resulting in 20,555 potentially novel proteins....
Source: Genomics Data - May 5, 2016 Category: Genetics & Stem Cells Source Type: research
