Multiple sclerosis is accompanied by lack of KIR2DS1 gene: A meta-analysis
Publication date: Available online 28 September 2016 Source:Genomics Data Author(s): Farhad Shahsavar, Shaghayegh Mapar, Seyyed Amir Yasin Ahmadi Multiple sclerosis (MS) is a disease in which we can recognize destruction of the myelin that is around nerve cells of brain and spinal cord called as oligodendrocytes. Both genetic and environmental factors play roles in MS. One of these genes is the killer-cell immunoglobulin-like receptor (KIR) which expressed on surface of natural killer cells (NKs). These genes have loci (not locus) in human genome, so they inherit as haplotypes. The results of previous studies show tha...
Source: Genomics Data - September 30, 2016 Category: Genetics & Stem Cells Source Type: research
Brain transcriptomes of honey bees (Apis mellifera) experimentally infected by two pathogens: Black queen cell virus and Nosema ceranae
Publication date: Available online 28 September 2016 Source:Genomics Data Author(s): Vincent Doublet, Robert J. Paxton, Cynthia M. McDonnell, Emeric Dubois, Sabine Nidelet, Robin F.A. Moritz, Cédric Alaux, Yves Le Conte Regulation of gene expression in the brain plays an important role in behavioral plasticity and decision making in response to external stimuli. However, both can be severely affected by environmental factors, such as parasites and pathogens. In honey bees, the emergence and re-emergence of pathogens and potential for pathogen co-infection and interaction have been suggested as major components t...
Source: Genomics Data - September 30, 2016 Category: Genetics & Stem Cells Source Type: research
Leading edge analysis of transcriptomic changes during pseudorabies virus infection
Publication date: Available online 30 September 2016 Source:Genomics Data Author(s): Damarius S. Fleming, Laura C. Miller Eight RNA samples taken from the tracheobronchial lymph nodes (TBLN) of pigs that were either infected or non-infected with a feral isolate of porcine pseudorabies virus (PRV) were used to investigate changes in gene expression related to the pathogen. The RNA was processed into fastq files for each library prior to being analyzed using Illumina Digital Gene Expression Tag Profiling sequences (DGETP) which were used as the downstream measure of differential expression. Analyzed tags consisted of 21 ...
Source: Genomics Data - September 30, 2016 Category: Genetics & Stem Cells Source Type: research
Functional high-resolution time-course expression analysis of human embryonic stem cells undergoing cardiac induction
Publication date: December 2016 Source:Genomics Data, Volume 10 Author(s): Ilaria Piccini, Marcos Araúzo-Bravo, Guiscard Seebohm, Boris Greber Cardiac induction of human embryonic stem cells (hESCs) is a process bearing increasing medical relevance, yet it is poorly understood from a developmental biology perspective. Anticipated technological progress in deriving stably expandable cardiac precursor cells or in advancing cardiac subtype specification protocols will likely require deeper insights into this fascinating system. Recent improvements in controlling hESC differentiation now enable a near-homogeneous induct...
Source: Genomics Data - September 30, 2016 Category: Genetics & Stem Cells Source Type: research
Whole-genome sequence of Dermabacter vaginalis AD1-86T, isolated from vaginal fluid of Korean woman
Publication date: December 2016 Source:Genomics Data, Volume 10 Author(s): Sooyeon Lim, Dong-Ho Chang, Byoung-Chan Kim Dermabacter vaginalis AD1–86T was isolated from the vaginal fluid of a Korean woman. Whole genome sequencing analysis was conducted using a PacBio RS II platform and annotated on RAST. The nucleotide sequence of this genome was deposited into DDBJ/EMBL/GenBank under the accession NZ_CP012117. (Source: Genomics Data)
Source: Genomics Data - September 30, 2016 Category: Genetics & Stem Cells Source Type: research
Draft genome sequence and detailed analysis of Pantoea eucrina strain Russ and implication for opportunistic pathogenesis
Publication date: Available online 20 September 2016 Source:Genomics Data Author(s): Farzaneh Moghadam, MB Couger, Breeanna Russ, Randi Ramsey, Radwa A. Hanafy, Connie Budd, Donald P. French, Wouter D. Hoff, Noha Youssef The genus Pantoea is a predominant member of host-associated microbiome. We here report on the genomic analysis of Pantoea eucrina strain Russ that was isolated from a trashcan at Oklahoma State University, Stillwater, OK. The draft genome of Pantoea eucrina strain Russ consists of 3,939,877bp of DNA with 3704 protein-coding genes and 134 RNA genes. This is the first report of a genome sequence ...
Source: Genomics Data - September 20, 2016 Category: Genetics & Stem Cells Source Type: research
Draft genome sequence of Microbacterium oleivorans strain Wellendorf implicates heterotrophic versatility and bioremediation potential
Publication date: Available online 17 September 2016 Source:Genomics Data Author(s): Anton P. Avramov, M.B. Couger, Emily L. Hartley, Craig Land, Rachel Wellendorf, Radwa A. Hanafy, Connie Budd, Donald P. French, Wouter D. Hoff, Noha Youssef Microbacterium oleivorans is a predominant member of hydrocarbon-contaminated environments. We here report on the genomic analysis of M. oleivorans strain Wellendorf that was isolated from an indoor door handle. The partial genome of M. oleivorans strain Wellendorf consists of 2,916,870bp of DNA with 2831 protein-coding genes and 49 RNA genes. The organism appears to be a v...
Source: Genomics Data - September 16, 2016 Category: Genetics & Stem Cells Source Type: research
De novo transcriptome assembly of mangosteen (Garcinia mangostana L.) fruit
Publication date: December 2016 Source:Genomics Data, Volume 10 Author(s): Deden Derajat Matra, Toshinori Kozaki, Kazuo Ishii, Roedhy Poerwanto, Eiichi Inoue Garcinia mangostana L. (Mangosteen), of the family Clusiaceae, is one of the economically important tropical fruits in Indonesia. In the present study, we performed de novo transcriptomic analysis of Garcinia mangostana L. through RNA-Seq technology. We obtained the raw data from 12 libraries through Ion Proton System. Clean reads of 191,735,809 were obtained from 307,634,890 raw reads. The raw data obtained in this study can be accessible in DDBJ database with...
Source: Genomics Data - September 13, 2016 Category: Genetics & Stem Cells Source Type: research
Genome wide binding (ChIP-seq) of murine Bapx1 and Sox9 proteins in vivo and in vitro
Publication date: Available online 8 September 2016 Source:Genomics Data Author(s): Sumantra Chatterjee, Petra Kraus, V. Sivakamasundari, Sook Peng Yap, Vibhor Kumar, Shyam Prabhakar, Thomas Lufkin This work pertains to GEO submission GSE36672, in vivo and in vitro genome wide binding (ChIP-Seq) of Bapx1 and Sox9 proteins. We have previously shown that transcriptional profiling combined with genome wide binding data is a powerful means to elucidate the molecular mechanism behind cell type specification and the generation of tissues and subsequent organs Chatterjee et al. (2014) . In our previously published work w...
Source: Genomics Data - September 8, 2016 Category: Genetics & Stem Cells Source Type: research
De novo transcriptome assembly of mangosteen (Garcinia mangostana L.) fruits
Publication date: Available online 9 September 2016 Source:Genomics Data Author(s): Deden Derajat Matra, Toshinori Kozaki, Kazuo Ishii, Roedhy Poerwanto, Eiichi Inoue Garcinia mangostana L. (Mangosteen), of the family Clusiaceae, is one of the economically important tropical fruits in Indonesia. In the present study, we performed de novo transcriptomic analysis of Garcinia mangostana L. through RNASeq technology. We obtained the raw data from 12 libraries through Ion Proton System. Clean reads of 191,735,809 were obtained from 307,634,890 raw reads. The raw data obtained in this study can be accessible in DDBJ datab...
Source: Genomics Data - September 8, 2016 Category: Genetics & Stem Cells Source Type: research
Transcriptome profiling of Curcuma longa L. cv. Suvarna
Publication date: Available online 9 September 2016 Source:Genomics Data Author(s): Ambika Sahoo, Basudeba Kar, Suprava Sahoo, Asit Ray, Sanghamitra Nayak Turmeric is an economically valued crop, because of its utility in the food, pharmaceutical industries and Ayurvedic medicine, attracts the attention in many areas of research work. In the present study, we executed resequencing through transcriptome assembly of the turmeric cultivar Suvarna (CL_Suv_10). Resequencing of Suvarna variety has generated 5 Gbases raw data with 75bp paired-end sequence. The raw data has been submitted to SRA database of NCBI with access...
Source: Genomics Data - September 8, 2016 Category: Genetics & Stem Cells Source Type: research
Behavioral and omics analyses study on potential involvement of dipeptide balenine through supplementation in diet of senescence-accelerated mouse prone 8
This study investigates effects of dipeptide balenine, as a major component of whale meat extract (hereafter, WME), supplementation on senescence-accelerated mouse prone 8 (SAMP8), an Alzheimer's disease (AD) model at level of learning and memory formation and brain expression profiles genome-wide in brain. Mice fed experimental balenine (+WME) supplemented diet for 26weeks were subjected to four behavioral tests – open field, Y-maze, new object recognition, and water-filled multiple T-maze – to examine effects on learning and memory. Brain transcriptome of SAMP8 mice-fed the WME diet over control low-safflower oil (LS...
Source: Genomics Data - September 8, 2016 Category: Genetics & Stem Cells Source Type: research
Draft genome sequence of the extremely halophilic Halorubrum sp. SAH-A6 isolated from rock salts of the Danakil depression, Ethiopia
Publication date: Available online 30 August 2016 Source:Genomics Data Author(s): Ashagrie Gibtan, Mingyeong Woo, Dokyung Oh, Kyounghee Park, Han-Seung Lee, Jae Hak Sohn, Dong-Woo Lee, Jung-Kue Shin, Sang-Jae Lee The draft genome sequence of Halorubrum sp. SAH-A6, isolated from commercial rock salts of the Danakil depression, Ethiopia. The genome comprised 3,325,770bp, with the G+C content of 68.0%. The strain has many genes which are responsible for secondary metabolites biosynthesis, transport and catabolism as compared to other Halorubrum archaea members. Abundant genes responsible for numerous transport syst...
Source: Genomics Data - August 29, 2016 Category: Genetics & Stem Cells Source Type: research
Comparative analysis of transcriptomes in aerial stems and roots of Ephedra sinica based on high-throughput mRNA sequencing
Publication date: December 2016 Source:Genomics Data, Volume 10 Author(s): Taketo Okada, Hironobu Takahashi, Yutaka Suzuki, Sumio Sugano, Masaaki Noji, Hiromichi Kenmoku, Masao Toyota, Shigehiko Kanaya, Nobuo Kawahara, Yoshinori Asakawa, Setsuko Sekita Ephedra plants are taxonomically classified as gymnosperms, and are medicinally important as the botanical origin of crude drugs and as bioresources that contain pharmacologically active chemicals. Here we show a comparative analysis of the transcriptomes of aerial stems and roots of Ephedra sinica based on high-throughput mRNA sequencing by RNA-Seq. De novo ass...
Source: Genomics Data - August 28, 2016 Category: Genetics & Stem Cells Source Type: research
The genome of the insecticidal Chromobacterium subtsugae PRAA4-1 and its comparison with that of Chromobacterium violaceum ATCC 12472
Publication date: December 2016 Source:Genomics Data, Volume 10 Author(s): Michael B. Blackburn, Michael E. Sparks, Dawn E. Gundersen-Rindal The genome of Chromobacterium subtsugae strain PRAA4-1, a betaproteobacterium producing insecticidal compounds, was sequenced and compared with the genome of C. violaceum ATCC 12472. The genome of C. subtsugae displayed a reduction in genes devoted to capsular and extracellular polysaccharide, possessed no genes encoding nitrate reductases, and exhibited many more phage-related sequences than were observed for C. violaceum. The genomes of both species possess a number of gene clu...
Source: Genomics Data - August 28, 2016 Category: Genetics & Stem Cells Source Type: research
