Transcript profiling in the milk of dairy ewes fed extruded linseed
Publication date: Available online 19 November 2016 Source:Genomics Data Author(s): 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 i...
Source: Genomics Data - November 19, 2016 Category: Genetics & Stem Cells Source Type: research
Draft genome sequence of Thermoactinomyces sp. Gus2-1 isolated from the hot-spring Gusikha in Bargusin Valley (Baikal Rift Zone, Russia)
Publication date: March 2017 Source:Genomics Data, Volume 11 Author(s): 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 2,623,309bp 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 https://www.ncbi.nlm.nih.gov/nuccore/JPZM01000000. ...
Source: Genomics Data - November 19, 2016 Category: Genetics & Stem Cells Source Type: research
Traditional versus 3 ′ RNA-seq in a non-model species
Publication date: Available online 18 November 2016 Source:Genomics Data Author(s): 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 exp...
Source: Genomics Data - November 18, 2016 Category: Genetics & Stem Cells Source Type: research
Draft genome sequence of Thermoactinomyces sp. Gus2 –1 isolated from the hot-spring Gusikha in Bargusin Valley (Baikal rift zone, Russia)
Publication date: Available online 14 November 2016 Source:Genomics Data Author(s): 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 2,623,309bp 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 https://www.ncbi.nlm.nih.gov/nuccor...
Source: Genomics Data - November 14, 2016 Category: Genetics & Stem Cells Source Type: research
Metagenome sequencing of the microbial community of two Brazilian anthropogenic Amazon dark earth sites, Brazil
Publication date: Available online 14 November 2016 Source:Genomics Data Author(s): 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 u...
Source: Genomics Data - November 14, 2016 Category: Genetics & Stem Cells Source Type: research
Application of target capture sequencing of exons and conserved non-coding sequences to 20 inbred rat strains
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 146.8Mb. 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. The sequence data can be accessed at DDBJ/EMBL/GenBank under accession number PRJDB4648, and the identified variants h...
Source: Genomics Data - November 14, 2016 Category: Genetics & Stem Cells Source Type: research
Evaluation of de novo assembly technique in the South African abalone Haliotis midae transcriptome: A comparison from Illumina and 454 systems
Publication date: Available online 13 November 2016 Source:Genomics Data Author(s): 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 ...
Source: Genomics Data - November 13, 2016 Category: Genetics & Stem Cells Source Type: research
Single nucleotide-level mapping of DNA double-strand breaks in human HEK293T cells
Publication date: Available online 11 November 2016 Source:Genomics Data Author(s): Bernard J. Pope, Khalid Mahmood, Chol-hee Jung, Peter Georgeson, Daniel J. Park Constitutional biological processes involve the generation of DNA double-strand breaks (DSBs). The production of such breaks and their subsequent resolution are also highly relevant to neurodegenerative diseases and cancer, in which extensive DNA fragmentation has been described Stephens et al. (2011), Blondet et al. (2001) . Tchurikov et al. Tchurikov et al. (2011, 2013) have reported previously that frequent sites of DSBs occur in chromosomal domains in...
Source: Genomics Data - November 11, 2016 Category: Genetics & Stem Cells Source Type: research
Draft whole-genome sequence of the Diaporthe helianthi 7/96 strain, causal agent of sunflower stem canker
Publication date: Available online 11 November 2016 Source:Genomics Data Author(s): Riccardo Baroncelli, Felice Scala, Maria Rosaria 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...
Source: Genomics Data - November 11, 2016 Category: Genetics & Stem Cells Source Type: research
A genomic study on distribution of human leukocyte antigen (HLA)-A and HLA-B alleles in Lak population of Iran
Publication date: Available online 10 November 2016 Source:Genomics Data Author(s): 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 compa...
Source: Genomics Data - November 10, 2016 Category: Genetics & Stem Cells Source Type: research
The complete mitochondrial genome of the acid-tolerant fungus Penicillium ShG4C
Publication date: Available online 10 November 2016 Source:Genomics Data Author(s): 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 26,725bp. It encodes a usual set of mitochondrial genes, including 15 protein coding genes, large and small ribosomal RNAs and 27 tRNA genes...
Source: Genomics Data - November 10, 2016 Category: Genetics & Stem Cells Source Type: research
Genome sequencing and annotation of Aeromonas veronii strain Ae52, a multidrug-resistant isolate from septicaemic gold fish (Carassiu sauratus) in Sri Lanka
Publication date: Available online 10 November 2016 Source:Genomics Data Author(s): S.S.S. De S. Jagoda, Karim Honein, Appudurai Arulkanthan, Hideki Ushio, Shuichi Asakawa Here we report the draft genome sequence and annotation of A. veronii strain Ae52 isolated from the kidney of a morbund, septicaemic gold fish (Carassius auratus) in Sri Lanka. This clinical isolate showed resistance to multiple antimicrobials; amoxycillin, neomycin, trimethoprim- sulphonamide, chloramphenicol, tetracycline, enrofloxacin, erythromycin and nitrofurantoin. The size of the draft genome is 4.56 Mbp with 58.66% of G+C content consistin...
Source: Genomics Data - November 10, 2016 Category: Genetics & Stem Cells Source Type: research
De novo transcriptome assembly of Schisandra chinensis Turcz. (Baill.)
This study provides transcriptome of S. chinensis, which might be useful for comparative transcriptome analyses and understand gene expression of secondary metabolites. Specifications [standardized info for the reader]. Image 1 Organism/cell line/tissue Schisandra chinensis/white fruit and skin and red fruit and skin Sex N/A Sequencer or array type Illumina HiSeq2500 Data format Raw data: Fastaq file Experimental factors De novo transcriptome assembly of Schisandra chinensis Turcz. (Baill.) Experimental features RNAs were isolated from the red fruit and with white fruit and skin, respectively. Consent N/A Sample ...
Source: Genomics Data - November 10, 2016 Category: Genetics & Stem Cells Source Type: research
Evidence of triple mutant Pfdhps ISGNGA haplotype in Plasmodium falciparum isolates from North-east India: An analysis of sulfadoxine resistant haplotype selection
Conclusion This study suggests that sulfadoxine resistant isolates are still migrating from its epicenter to the other parts of Southeast Asia and hence control and elimination of the drug resistant isolates have become impedimental. Moreover, P. falciparum populations in different areas may undergo selection of particular sulfadoxine resistant haplotypes either in the presence of drug or after its removal to maintain their plasticity. (Source: Genomics Data)
Source: Genomics Data - November 6, 2016 Category: Genetics & Stem Cells Source Type: research
Metagenomic investigation of the microbial diversity in a chrysotile asbestos mine pit pond, Lowell, Vermont, USA
Publication date: Available online 5 November 2016 Source:Genomics Data Author(s): 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 min...
Source: Genomics Data - November 5, 2016 Category: Genetics & Stem Cells Source Type: research
