Microarray analysis of microRNA expression in mouse fetus at 13.5 and 14.5days post-coitum in ear and back skin tissues
This study uncovered a spatiotemporal pattern of miRNA expression in the external ear, which results from continuous transcriptional changes during normal development of body structures. All microarray data are available at the Gene Expression Omnibus (GEO) at NCBI under accession number GSE64945. (Source: Genomics Data)
Source: Genomics Data - July 18, 2016 Category: Genetics & Stem Cells Source Type: research
Transcriptome profiling of TDC cluster deletion mutant of Enterococcus faecalis V583
Publication date: September 2016 Source:Genomics Data, Volume 9 Author(s): Marta Perez, Victor Ladero, Beatriz del Rio, Begoña Redruello, Anne de Jong, Oscar P. Kuipers, Jan Kok, M. Cruz Martin, Maria Fernandez, Miguel A. Alvarez The species Enterococcus faecalis is able to catabolise the amino acid tyrosine into the biogenic amine tyramine by the tyrosine decarboxilase (TDC) pathway Ladero et al. (2012) [1]. The TDC cluster comprises four genes: tyrS, an aminoacyl-tRNA synthetase-like gene; tdcA, which encodes the tyrosine decarboxylase; tyrP, a tyrosine/tyramine exchanger gene and nhaC-2, which e...
Source: Genomics Data - July 18, 2016 Category: Genetics & Stem Cells Source Type: research
Metagenomic analysis of microbial community of an Amazonian geothermal spring in Peru
Publication date: September 2016 Source:Genomics Data, Volume 9 Author(s): Sujay Paul, Yolanda Cortez, Nadia Vera, Gretty K. Villena, Marcel Gutiérrez-Correa Aguas Calientes (AC) is an isolated geothermal spring located deep into the Amazon rainforest (7°21′12″ S, 75°00′54″ W) of Peru. This geothermal spring is slightly acidic (pH5.0–7.0) in nature, with temperatures varying from 45 to 90°C and continually fed by plant litter, resulting in a relatively high degree of total organic content (TOC). Pooled water sample was analyzed at 16S rRNA V3–V4 hypervariable region by amplicon metagenome sequ...
Source: Genomics Data - July 18, 2016 Category: Genetics & Stem Cells Source Type: research
Transcriptomic analyses of Hand2 transgenic embryos
Publication date: September 2016 Source:Genomics Data, Volume 9 Author(s): Noriko Funato, Hiroki Kokubo, Yumiko Saga In this article, we further provide the data generated for the previously published research article “Specification of jaw identity by the Hand2 transcription factor.” To better understand the downstream genes of the basic helix-loop-helix transcription factor Hand2, we generated double-transgenic mice (Hand2 NC ) by intercrossing CAG-floxed CAT-Hand2 mice with Wnt1-Cre mice for conditional activation of Hand2 expression in the neural crest. Altered expression of Hand2 induces transformation o...
Source: Genomics Data - July 18, 2016 Category: Genetics & Stem Cells Source Type: research
The draft genome sequence and annotation of the desert woodrat Neotoma lepida
We present the de novo draft genome sequence for a vertebrate mammalian herbivore, the desert woodrat (Neotoma lepida). This species is of ecological and evolutionary interest with respect to ingestion, microbial detoxification and hepatic metabolism of toxic plant secondary compounds from the highly toxic creosote bush (Larrea tridentata) and the juniper shrub (Juniperus monosperma). The draft genome sequence and annotation have been deposited at GenBank under the accession LZPO01000000. (Source: Genomics Data)
Source: Genomics Data - July 18, 2016 Category: Genetics & Stem Cells Source Type: research
MicroRNA gene expression signatures in long-surviving malignant pleural mesothelioma patients
Publication date: September 2016 Source:Genomics Data, Volume 9 Author(s): Ruby C.Y. Lin, Michaela B. Kirschner, Yuen Yee Cheng, Nico van Zandwijk, Glen Reid Malignant pleural mesothelioma (MPM) is a tumor originating in the mesothelium, the membrane lining the thoracic cavities, and is induced by exposure to asbestos. Australia suffers one of the world's highest rates of MPM and the incidence is yet to peak. The prognosis for patients with MPM is poor and median survival following diagnosis is 4–18months. Currently, no or few effective therapies exist for MPM. Trials of targeted agents such as antiangiogen...
Source: Genomics Data - July 18, 2016 Category: Genetics & Stem Cells Source Type: research
Comparative transcriptome analysis of ginger variety Suprabha from two different agro-climatic zones of Odisha
Publication date: September 2016 Source:Genomics Data, Volume 9 Author(s): Mahendra Gaur, Aradhana Das, Rajesh Kumar Sahoo, Sujata Mohanty, Raj Kumar Joshi, Enketeswara Subudhi Ginger (Zingiber officinale Rosc.), a well-known member of family Zingiberaceae, is bestowed with number of medicinal properties which is because of the secondary metabolites, essential oil and oleoresin, it contains in its rhizome. The drug yielding potential is known to depend on agro-climatic conditions prevailing at the place cultivation. Present study deals with comparative transcriptome analysis of two sample of elite ginger va...
Source: Genomics Data - July 18, 2016 Category: Genetics & Stem Cells Source Type: research
Transcriptional profiling of foam cells in response to hypercholesterolemia
Publication date: September 2016 Source:Genomics Data, Volume 9 Author(s): Young-Hwa Goo, Vijay K. Yechoor, Antoni Paul Hypercholesterolemia is a main risk factor for atherosclerosis development. Arterial macrophages, or foam cells, take-up and process lipoprotein particles deposited in arteries, and store much of the cholesterol carried by these particles in their cytoplasm. However, the effects of exposure to different cholesterol levels on foam cells remain poorly understood. Given the remarkable plasticity of macrophages in response to environmental variables, studies on macrophage biology should ideally be p...
Source: Genomics Data - July 18, 2016 Category: Genetics & Stem Cells Source Type: research
De novo transcriptome assembly of ‘Angeleno’ and ‘Lamoon’ Japanese plum cultivars (Prunus salicina)
Publication date: September 2016 Source:Genomics Data, Volume 9 Author(s): Máximo González, Jonathan Maldonado, Erika Salazar, Herman Silva, Basilio Carrasco Japanese plum (Prunus salicina L.) is a fruit tree of the Rosaceae family, which is an economically important stone fruit around the world. Currently, Japanese plum breeding programs combine traditional breeding and plant physiology strategies with genetic and genomic analysis. In order to understand the flavonoid pathway regulation and to develop molecular markers associated to the fuit skin color (EST-SSRs), we performed a next generation sequencing ...
Source: Genomics Data - July 18, 2016 Category: Genetics & Stem Cells Source Type: research
Functional profiling of cyanobacterial genomes and its role in ecological adaptations
In this study, functional composition of the 84 different cyanobacterial genomes and their adaptations to different environments was examined by identifying the genomic composition for specific cellular processes, which reflect their genomic functional profile and ecological adaptation. It was identified that among cyanobacterial genomes, metabolic genes have major share over other categories and differentiation of genomic functional profile was observed for the species inhabiting different habitats. The cyanobacteria of freshwater and other habitats accumulate large number of poorly characterized genes. Strain specific fu...
Source: Genomics Data - July 18, 2016 Category: Genetics & Stem Cells Source Type: research
Genome-wide identification and characterization of R2R3MYB family in Rosaceae
We described 186, 98 and 86 non-redundant gene models for apple, peach and strawberry, respectively. In this research, we analyzed the intron–exon structure and genomic distribution of R2R3MYB families mentioned above. The phylogenetic comparisons revealed putative functions of some R2R3MYB transcription factors. This analysis found 44 functional subgroups, seven of which were unique for Rosaceae. In addition, our results showed a highly collinearity among some genes revealing the existence of conserved gene models between the three species studied. Although some gene models in these species have been validated under sev...
Source: Genomics Data - July 18, 2016 Category: Genetics & Stem Cells Source Type: research
Identification of differentially expressed genes in sexed pig embryos during post-hatching development in primiparous sows exposed to differing intermittent suckling and breeding strategies
Publication date: Available online 4 June 2016 Source:Genomics Data Author(s): Stephen Tsoi, Milena Blanes, Tai Yuan Chen, Pieter Langendijk, Rebecca Athorn, George Foxcroft, Michael Dyck The aim of commercial pig breeding programs is maximize the number of pigs produced per sow per year. Given that sows exhibit an estrus during lactation is a potential means of increasing productivity of a pig breeding herd without reducing in lactation length, conventionally, weaning of piglets at a relatively young age is often related to post-weaning piglet performance which compromises piglet welfare. Therefore, inte...
Source: Genomics Data - June 3, 2016 Category: Genetics & Stem Cells Source Type: research
Isolation and complete genome sequencing of Mimivirus bombay, a Giant Virus in sewage of Mumbai, India.
We report the isolation and complete genome sequencing of a new Mimiviridae family member, infecting Acanthamoeba castellanii, from sewage in Mumbai, India. The isolated virus has a particle size of about 435 nm and a 1182200-bp genome. A phylogeny based on the DNA polymerase sequence placed the isolate as a new member of the Mimiviridae family lineage A and was named as Mimivirus bombay. Extensive presence of Mimiviridae family members in different environmental niches, with remarkably similar genome size and genetic makeup, point towards an evolutionary advantage that needs to be further investigated. The complete genome...
Source: Genomics Data - May 30, 2016 Category: Genetics & Stem Cells Source Type: research
A comparative analysis of lncRNAs in prostate cancer exosomes and their parental cell lines
Publication date: Available online 26 May 2016 Source:Genomics Data Author(s): Alireza Ahadi, Samantha Khoury, Maria Losseva, Nham Tran Prostate cancer is the second leading cancer in men world-wide. Due to its heterogeneous nature, a considerable amount of research effort has been dedicated in identifying effective clinical biomarkers with a focus on proteins, messenger RNA and microRNAs Khoury and Tran (2015) [1]. However, there is limited data on the role and expression of long noncoding RNAs (lncRNAs) in prostate cancer exosomes [2]. This array dataset which is linked to our publication describes the profil...
Source: Genomics Data - May 25, 2016 Category: Genetics & Stem Cells Source Type: research
Identification of polymorphic and off-target probe binding sites on the Illumina Infinium MethylationEPIC BeadChip
Publication date: Available online 26 May 2016 Source:Genomics Data Author(s): Daniel L. McCartney, Rosie M. Walker, Stewart W. Morris, Andrew M. McIntosh, David J. Porteous, Kathryn L. Evans Genome-wide analysis of DNA methylation has now become a relatively inexpensive technique thanks to array-based methylation profiling technologies. The recently developed Illumina Infinium MethylationEPIC BeadChip interrogates methylation at over 850,000 sites across the human genome, covering 99% of RefSeq genes. This array supersedes the widely used Infinium HumanMethylation450 BeadChip, which has permitted insights ...
Source: Genomics Data - May 25, 2016 Category: Genetics & Stem Cells Source Type: research
