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Genomics Data

Zara Ghodsi, Xu Huang, Hossein Hassani
In developmental studies, inferring regulatory interactions of segmentation genetic network play a vital role in unveiling the mechanism of pattern formation. As such, there exists an opportune demand for theoretical developments and new mathematical models which can result in a more accurate illustration of this genetic network. Accordingly, this paper seeks to extract the meaningful regulatory role of the maternal effect genes using a variety of causality detection techniques and to explore whether these methods can suggest a new analytical view to the gene regulatory networks...
March 2017: Genomics Data
Tommaso Giordani, Alberto Vangelisti, Giuseppe Conte, Andrea Serra, Lucia Natali, Annamaria Ranieri, Marcello Mele, Andrea Cavallini
The identification of genes regulating milk secretion by mammary glands is a key-step for exploiting changes in milk composition induced by different diet regimens. Linseed supplementation is a reliable feeding strategy to enhance polyunsaturated fatty acid content in milk fat from sheep, increasing milk quality and nutraceutical value. To investigate the molecular bases of diet induced differences in milk composition, we collected milk from dairy ewes at 90 day of lactation and after 3 weeks of diet supplementation with extruded linseed...
March 2017: Genomics Data
Sophie Tandonnet, Tatiana Teixeira Torres
One limitation of the widely used RNA-seq method is that long transcripts are represented by more reads than shorter transcripts, resulting in a biased estimation of expression levels. The 3' RNA-seq method, which yields only one sequence per transcript, bypasses this limitation. Here, RNA was extracted from two samples, in which we expected to find differentially expressed genes. Each was processed by both traditional and 3' RNA-seq protocols. Both methods yielded similar differentially expressed genes and estimated expression levels in a comparable way, confirming they both represent valid tools for RNA-seq analysis...
March 2017: Genomics Data
Merete Wiken Dees, May Bente Brurberg, Erik Lysøe
The genus Microbacterium contains bacteria that are ubiquitously distributed in various environments and includes plant-associated bacteria that are able to colonize tissue of agricultural crop plants. Here, we report the 3,508,491 bp complete genome sequence of Microbacterium sp. strain BH-3-3-3, 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 CP017674.
March 2017: Genomics Data
Farhad Shahsavar, Ali-Mohammad Varzi, Seyyed Amir Yasin Ahmadi
Anthropological studies based on the highly polymorphic gene, human leukocyte antigen (HLA), provide useful information for bone marrow donor registry, forensic medicine, disease association studies, as well as infertility treatment, designing peptide vaccines against tumors, and infectious or autoimmune diseases. The aim of this study was to determine HLA-A and HLA-B allele frequencies in 100 unrelated Lak/lᴂk/individuals from Lorestan province of Iran. Finally, we compared the results with that previously described in Iranian population...
March 2017: Genomics Data
Aleksey S Rozanov, Alla V Bryanskaya, Anastasia V Kotenko, Sergey E Peltek
The Thermoactinomyces sp. strain Gus2-1 was isolated from hot-spring sediments sample from the hot-spring Gusikha in Bargusin Valley (Baikal Rift Zone, Russia). The sequenced and annotated genome is 2,623,309 bp and encodes 2513 genes. The draft genome sequence of the Thermoactinomyces sp. strain Gus2-1 has been deposited at DDBJ/EMBL/GenBank under the accession JPZM01000000 and the sequences could be found at the site
March 2017: Genomics Data
Leandro Nascimento Lemos, Rosineide Cardoso de Souza, Fabiana de Souza Cannavan, André Patricio, Victor Satler Pylro, Rogério Eiji Hanada, Tsai Siu Mui
The Anthropogenic Amazon Dark Earth soil is considered one of the world's most fertile soils. These soils differs from conventional Amazon soils because its higher organic content concentration. Here we describe the metagenome sequencing of microbial communities of two sites of Anthropogenic Amazon Dark Earth soils from Amazon Rainforest, Brazil. The raw sequence data are stored under Short Read Accession number: PRJNA344917.
December 2016: Genomics Data
Barbara Picone, Clint Rhode, Rouvay Roodt-Wilding
Next generation sequencing platforms have recently been used to rapidly characterize transcriptome sequences from a number of non-model organisms. The present study compares two of the most frequently used platforms, the Roche 454-pyrosequencing and the Illumina sequencing-by-synthesis (SBS), on the same RNA sample obtained from an intertidal gastropod mollusc species, Haliotis midae. All the sequencing reads were deposited in the Short Read Archive (SRA) database are retrievable under the accession number [SRR071314 (Illumina Genome Analyzer II)] and [SRR1737738, SRR1737737, SRR1737735, SRR1737734 (454 GS FLX)] in the SRA database of NCBI...
December 2016: Genomics Data
Heather E Driscoll, James J Vincent, Erika L English, Elizabeth D Dolci
Here we report on a metagenomics investigation of the microbial diversity in a serpentine-hosted aquatic habitat created by chrysotile asbestos mining activity at the Vermont Asbestos Group (VAG) Mine in northern Vermont, USA. The now-abandoned VAG Mine on Belvidere Mountain in the towns of Eden and Lowell includes three open-pit quarries, a flooded pit, mill buildings, roads, and > 26 million metric tons of eroding mine waste that contribute alkaline mine drainage to the surrounding watershed. Metagenomes and water chemistry originated from aquatic samples taken at three depths (0...
December 2016: Genomics Data
Minako Yoshihara, Tetsuya Sato, Daisuke Saito, Osamu Ohara, Takashi Kuramoto, Mikita Suyama
We report sequence data obtained by our recently devised target capture method TargetEC applied to 20 inbred rat strains. This method encompasses not only all annotated exons but also highly conserved non-coding sequences shared among vertebrates. The total length of the target regions covers 146.8 Mb. On an average, we obtained 31.7 × depth of target coverage and identified 154,330 SNVs and 24,368 INDELs for each strain. This corresponds to 470,037 unique SNVs and 68,652 unique INDELs among the 20 strains...
December 2016: Genomics Data
Zhang Qing-Tian, Fan Shu-Tian, Yang Yi-Ming, Xu Pei-Lei, Ai Jun
The fruit of Schisandra chinensis Turcz. (Baill.), namely "Wuweizi" in China, is a well-known herbal medicine and health food. At present, research focused on the extraction of effective chemical component and function identification. Little known about the secondary metabolism gene pathway of chemical composition. Its fruit color usually red, however, the white fruit color variation has been found. It made us interested in exploring which gene change lead to this result. In order to understand the genetic background of S...
December 2016: Genomics Data
Riccardo Baroncelli, Felice Scala, Mariarosaira Vergara, Michael R Thon, Michelina Ruocco
Diaporthe helianthi is a fungus pathogenic to sunflower. Virulent strains of this fungus cause stem canker with important yield losses and reduction of oil content. Here we present the first draft whole-genome sequence of the highly virulent isolate D. helianthi strain 7/96, thus providing a useful platform for future research on stem canker of sunflower and fungal genomics. The genome sequence of the D. helianthi isolate 7/96 was deposited at DDBJ/ENA/GenBank under the accession number MAVT00000000 (BioProject PRJNA327798)...
December 2016: Genomics Data
Manuj K Das, Sumi Chetry, Mohan C Kalita, Prafulla Dutta
BACKGROUND: North-east region of India has consistent role in the spread of multi drug resistant Plasmodium (P.) falciparum to other parts of Southeast Asia. After rapid clinical treatment failure of Artemisinin based combination therapy-Sulphadoxine/Pyrimethamine (ACT-SP) chemoprophylaxis, Artemether-Lumefantrine (ACT-AL) combination therapy was introduced in the year 2012 in this region for the treatment of uncomplicated P. falciparum malaria. In a DNA sequencing based polymorphism analysis, seven codons of P...
December 2016: Genomics Data
Andrey V Mardanov, Lubov B Glukhova, Eugeny V Gruzdev, Alexey V Beletsky, Olga V Karnachuk, Nikolai V Ravin
Complete mitochondrial genome of the acid-tolerant fungus Penicillium ShG4C, isolated from oxidized sediments of an abandoned polymetallic mine site, has been sequenced using high-throughput sequencing approach. The mitochondrial genome represents a circular DNA molecule with size of 26,725 bp. It encodes a usual set of mitochondrial genes, including 15 protein coding genes, large and small ribosomal RNAs and 27 tRNA genes. All genes are located on H-strand DNA and transcribed in one direction. Taxonomic analysis based on concatenated sequences of mitochondrial proteins confirmed taxonomic position of this fungus within the genus Penicillium...
December 2016: Genomics Data
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 [1]. WNV neuro-invasion is believed to be influenced by a number of factors including host genetics. In order to explore these effects and recapitulate the complex immune genetic differences among individuals, we studied gene expression following WNV infection in the Collaborative Cross (CC) model...
December 2016: Genomics Data
Merete Wiken Dees, May Bente Brurberg, Erik Lysøe
Here, we present the 3,795,952 bp 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.
December 2016: Genomics Data
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 variants in PKHD1 gene [c.4870C > T, p.(Arg1624Trp), c.5725C > T, p.(Arg1909Trp), c.1736C > T, p.(Thr579Met) and c.10628T > G, p.(Leu3543Trp)] among 12 out of 18 samples. However, one variant c.4870C > T, p.(Arg1624Trp) was common among eight patients...
December 2016: Genomics Data
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 the association of different genes of KIR and susceptibility to be affected by colorectal cancer...
December 2016: Genomics Data
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 [1]. The role host genetics play in early detection and response to WNV still remains largely unexplained. In order to capture the impact of genetic variation on innate immune responses, we studied gene expression following WNV infection using the collaborative cross (CC). The CC is a mouse genetics resource composed of hundreds of independently bred, octo-parental recombinant inbred mouse lines [2]...
December 2016: Genomics Data
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-carcinoma)...
December 2016: Genomics Data
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