Complete genome sequence of the biofilm-forming Curtobacterium sp. strain BH-2-1-1, isolated from lettuce (Lactuca sativa) originating from a conventional field in Norway
Publication date: Available online 5 November 2016 Source:Genomics Data Author(s): Merete Wiken Dees, May Bente Brurberg, Erik Lysøe Here, we present the 3,795,952bp complete genome sequence of the biofilm-forming Curtobacterium sp. strain BH-2-1-1, isolated from conventionally grown lettuce (Lactuca sativa) from a field in Vestfold, Norway. The nucleotide sequence of this genome was deposited into NCBI GenBank under the accession CP017580. (Source: Genomics Data)
Source: Genomics Data - November 5, 2016 Category: Genetics & Stem Cells Source Type: research
Colorectal cancer and the KIR genes in the human genome: A meta-analysis
Publication date: December 2016 Source:Genomics Data, Volume 10 Author(s): Koroush Ghanadi, Bahareh Shayanrad, Seyyed Amir Yasin Ahmadi, Farhad Shahsavar, Hossein Eliasy Colorectal cancer is one of the most common types of inflammation-based cancers and is occurred due to growth and spread of cancer cells in colon and/or rectum. Previously genetic association of cell cycle genes, both proto-oncogenes and the tumor suppressors has been proved. But there were few studies about association of immune related genes such as killer-cell immunoglobulin-like receptors (KIRs). Thus we intend to perform a meta-analysis to find...
Source: Genomics Data - November 5, 2016 Category: Genetics & Stem Cells Source Type: research
Functional alterations due to amino acid changes and evolutionary comparative analysis of ARPKD and ADPKD genes
Publication date: Available online 3 November 2016 Source:Genomics Data Author(s): Burhan M. Edrees, Mohammad Athar, Zainularifeen Abduljaleel, Faisal A Al-Allaf, Mohiuddin M. Taher, Wajahatullah Khan, Abdellatif Bouazzaoui, Naffaa Al-Harbi, Ramzia Safar, Howaida Al-Edressi, Khawala Alansary, Abulkareem Anazi, Naji Altayeb, Muawia A. Ahmed A targeted customized sequencing of genes implicated in autosomal recessive polycystic kidney disease (ARPKD) phenotype was performed to identify candidate variants using the Ion torrent PGM next-generation sequencing. The results identified four potential pathogenic vari...
Source: Genomics Data - November 3, 2016 Category: Genetics & Stem Cells Source Type: research
Colorectal cancer and KIR genes in the human genome: A meta-analysis
Publication date: Available online 1 November 2016 Source:Genomics Data Author(s): Koroush Ghanadi, Bahareh Shayanrad, Seyyed Amir Yasin Ahmadi, Farhad Shahsavar, Hossein Eliasy Colorectal cancer is one of the most common types of inflammation-based cancers and is occurred due to growth and spread of cancer cells in colon and/or rectum. Previously genetic association of cell cycle genes, both proto-oncogenes and the tumor suppressors has been proved. But there were few studies about association of immune related genes such as killer-cell immunoglobulin-like receptors (KIRs). Thus we intend to perform a meta-analysis...
Source: Genomics Data - November 1, 2016 Category: Genetics & Stem Cells Source Type: research
Gene expression in the mouse brain following early pregnancy exposure to ethanol
Publication date: December 2016 Source:Genomics Data, Volume 10 Author(s): Christine R. Zhang, Suyinn Chong Exposure to alcohol during early embryonic or fetal development has been linked with a variety of adverse outcomes, the most common of which are structural and functional abnormalities of the central nervous system [1]. Behavioural and cognitive deficits reported in individuals exposed to alcohol in utero include intellectual impairment, learning and memory difficulties, diminished executive functioning, attention problems, poor motor function and hyperactivity [2]. The economic and social costs of these outcomes...
Source: Genomics Data - October 26, 2016 Category: Genetics & Stem Cells Source Type: research
Analysis of distribution of DNA methylation in kidney-renal-clear-cell-carcinoma specific genes using entropy
Publication date: December 2016 Source:Genomics Data, Volume 10 Author(s): Nithya Ramakrishnan, R. Bose DNA Methylation is an epigenetic phenomenon in which methyl groups are added to the cytosines, thereby altering the physio-chemical properties of the DNA region and influencing gene expression. Aberrant DNA methylation in a set of genes or across the genome results in many epigenetic diseases including cancer. In this paper, we use entropy to analyze the extent and distribution of DNA methylation in Tumor Suppressor Genes (TSG's) and Oncogenes related to a specific type of cancer (viz.) KIRC (Kidney-renal-clear-cell-...
Source: Genomics Data - October 26, 2016 Category: Genetics & Stem Cells Source Type: research
Transcriptional profiles of WNV neurovirulence in a genetically diverse Collaborative Cross population
Publication date: Available online 14 October 2016 Source:Genomics Data Author(s): Richard Green, Courtney Wilkins, Sunil Thomas, Aimee Sekine, Renee C. Ireton, Martin T. Ferris, Duncan M. Hendrick, Kathleen Voss, Fernando Pardo-Manuel de Villena, Ralph S. Baric, Mark T. Heise, Michael Gale West Nile Virus (WNV) is a mosquito-transmitted virus from the Flaviviridae family that causes fever in 1 in 5 infected people. WNV can also become neuro-invasive and cross the blood-brain barrier leading to severe neurological symptoms in a subset of WNV infected individuals Loraine et al. (2015) . WNV neuro-invasion is b...
Source: Genomics Data - October 13, 2016 Category: Genetics & Stem Cells Source Type: research
Identifying protective host gene expression signatures within the spleen during West Nile virus infection in the collaborative cross model
Publication date: Available online 14 October 2016 Source:Genomics Data Author(s): Richard Green, Courtney Wilkins, Sunil Thomas, Aimee Sekine, Renee C. Ireton, Martin T. Ferris, Duncan M. Hendrick, Kathleen Voss, Fernando Pardo-Manuel de Villena, Ralph Baric, Mark Heise, Michael Gale Flaviviruses are hematophagous arthropod-viruses that pose global challenges to human health. Like Zika virus, West Nile Virus (WNV) is a flavivirus for which no approved vaccine exists Loraine et al. (2015) . The role host genetics play in early detection and response to WNV still remains largely unexplained. In order to captur...
Source: Genomics Data - October 13, 2016 Category: Genetics & Stem Cells Source Type: research
Transcript profiling in the liver of early-lactating dairy cows fed conjugated linoleic acid
Publication date: Available online 11 October 2016 Source:Genomics Data Author(s): Robert Ringseis, Wilhelm Windisch, Klaus Eder In the present study, transcript profiling was carried out in liver biopsies from high-yielding dairy cows at wk. 5 of lactation in order to identify genes and pathways regulated by feeding rumen-protected conjugated linoleic acid (CLA) during the transition period. Analysis of a bovine whole genome microarray revealed a total number of 130 annotated differentially expressed genes (DEGs) in the liver between cows of the CLA group and the control group (filter: P <0.05 and fold change ...
Source: Genomics Data - October 11, 2016 Category: Genetics & Stem Cells Source Type: research
Draft genome sequence of Mycobacterium tuberculosis strain B9741 of Beijing B0/W lineage from HIV positive patient from Siberia
We report a draft genome sequence of Mycobacterium tuberculosis strain B9741 belonging to Beijing B0/W lineage isolated from a HIV patient from Siberia, Russia. This clinical isolate showed MDR phenotype and resistance to isoniazid, rifampin, streptomycin and pyrazinamide. We analyzed SNPs associated with virulence and resistance. The draft genome sequence and annotation have been deposited at GenBank under the accession NZ_LVJJ00000000. (Source: Genomics Data)
Source: Genomics Data - October 11, 2016 Category: Genetics & Stem Cells Source Type: research
Draft genome sequence of Staphylococcus hominis strain Hudgins isolated from human skin implicates metabolic versatility and several virulence determinants
Publication date: Available online 7 October 2016 Source:Genomics Data Author(s): Shelby Calkins, M.B. Couger, Colin Jackson, Jordan Zandler, Garett C. Hudgins, Radwa A. Hanafy, Connie Budd, Donald P. French, Wouter D. Hoff, Noha Youssef Staphylococcus hominis is a predominant member of the human skin microbiome. We here report on the genomic analysis of Staphylococcus hominis strain Hudgins that was isolated from the wrist area of human skin. The partial genome assembly of S. hominis Hudgins consists of 2,211,863bp of DNA with 2174 protein-coding genes and 90 RNA genes. Based on the genomic analysis of KEGG pa...
Source: Genomics Data - October 9, 2016 Category: Genetics & Stem Cells Source Type: research
Whole-genome sequence of Bacillus solimangrovi GH 2-4T, isolated from mangrove soil
Publication date: December 2016 Source:Genomics Data, Volume 10 Author(s): Sooyeon Lim, Dong-Ho Chang, Byoung-Chan Kim Bacillus solimangrovi GH 2-4T was isolated from mangrove soil and subjected to whole genome sequencing on HiSeq platform and annotated on RAST. The nucleotide sequence of this genome was deposited into DDBJ/EMBL/GenBank under the accession MJEH00000000. (Source: Genomics Data)
Source: Genomics Data - October 9, 2016 Category: Genetics & Stem Cells Source Type: research
High concordance between Illumina HiSeq2500 and NextSeq500 for reduced representation bisulfite sequencing (RRBS)
Publication date: Available online 6 October 2016 Source:Genomics Data Author(s): Danqing Yin, Matthew E. Ritchie, Jafar S. Jabbari, Tamara Beck, Marnie E. Blewitt, Andrew Keniry Reduced representation bisulfite sequencing (RRBS) provides an efficient method for measuring DNA methylation at single base resolution in regions of high CpG density. This technique has been extensively tested on the HiSeq2500, which uses a 4-colour detection method, however it is unclear if the method will also work on the NextSeq500 platform, which employs a 2-colour detection system. We created an RRBS library and sequenced it on both ...
Source: Genomics Data - October 5, 2016 Category: Genetics & Stem Cells Source Type: research
Genome sequences of six Phytophthora species threatening forest ecosystems
Publication date: Available online 3 October 2016 Source:Genomics Data Author(s): Nicolas Feau, Greg Taylor, Angela L. Dale, Braham Dhillon, Guillaume J. Bilodeau, Inanç Birol, Steven J.M. Jones, Richard C. Hamelin The Phytophthora genus comprises of some of the most destructive plant pathogens and attack a wide range of hosts including economically valuable tree species, both angiosperm and gymnosperm. Many known species of Phytophthora are invasive and have been introduced through nursery and agricultural trade. As part of a larger project aimed at utilizing genomic data for forest disease diagnostics, pathoge...
Source: Genomics Data - October 2, 2016 Category: Genetics & Stem Cells Source Type: research
Bovine annulus fibrosus cell lines isolated from intervertebral discs
Publication date: Available online 3 October 2016 Source:Genomics Data Author(s): Petra Kraus, Thomas Lufkin The adult bovine (Bos taurus) intervertebral disc is primarily comprised of two major tissue types: The outer annulus fibrosus (AF) and the central nucleus pulposus (NP). We isolated several primary cell lineages of passage (P) 0 cells from the AF tissue omitting typically used enzymatic tissue digestion protocols. The cells grow past p10 without signs of senescence in DMEM+10% FCS on 0.1% gelatin coated/uncoated surfaces of standard cell culture plates and survive freeze-thawing. Preliminary analysis of the AF ...
Source: Genomics Data - October 2, 2016 Category: Genetics & Stem Cells Source Type: research
