Transcriptional profiling of the effect of lipopolysaccharide (LPS) pretreatment in blood from probiotics-treated dairy cows
In this study the transcriptional profile in whole blood collected from probiotics-treated cows was investigated in response to stimulation with lipopolysaccharides (LPS) in vitro. Microarray experiment was performed between LPS-treated and control samples using the Agilent one-color bovine v2 bovine (v2) 4x44K array slides. Global gene expression analysis identified 13,658 differentially expressed genes (fold change cutoff ≥2, P <0.05), 3816 upregulated genes and 9842 downregulated genes in blood in response to LPS. Treatment with LPS resulted in increased expression of TLR4 (Fold change (FC) =3.16) and transcrip...
Source: Genomics Data - August 25, 2016 Category: Genetics & Stem Cells Source Type: research
Nonsyndromic cleft lip with or without cleft palate and cancer: Evaluation of a possible common genetic background through the analysis of GWAS data
This study is the first to characterize possible pleiotropic risk loci for NSCL/P and cancer in a systematic manner. The data represent a starting point for future research by identifying a genetic link between NSCL/P and cancer. (Source: Genomics Data)
Source: Genomics Data - August 25, 2016 Category: Genetics & Stem Cells Source Type: research
Draft genome sequence of Mameliella alba strain UMTAT08 isolated from clonal culture of toxic dinoflagellate Alexandrium tamiyavanichii
Publication date: Available online 26 August 2016 Source:Genomics Data Author(s): Muhd Danish-Daniel, Gan Han Ming, Mohd Ezhar Mohd Noor, Yik Sung Yeong, Gires Usup Mameliella alba strain UMTAT08 was isolated from clonal culture of paralytic shellfish toxin producing dinoflagellate, Alexandrium tamiyavanichii. Genome of the strain UMTAT08 was sequenced in order to gain insights into the dinoflagellate-bacteria interactions. The draft genome sequence of strain UMTAT08 contains 5.84Mbp with an estimated G+C content of 65%, 5717 open reading frames, 5 rRNAs and 49 tRNAs. It contains genes related to nutrients uptake, q...
Source: Genomics Data - August 25, 2016 Category: Genetics & Stem Cells Source Type: research
Fine resolution mapping of double-strand break sites for human ribosomal DNA units
Publication date: Available online 24 August 2016 Source:Genomics Data Author(s): Bernard J. Pope, Khalid Mahmood, Chol-hee Jung, Daniel J. Park DNA breakage arises during a variety of biological processes, including transcription, replication and genome rearrangements. In the context of disease, extensive fragmentation of DNA has been described in cancer cells and during early stages of neurodegeneration (Stephens et al., 2011; Blondet et al., 2001). Stults et al. (2009) reported that human rDNA gene clusters are hotspots for recombination and that rDNA restructuring is among the most common chromosomal alterations ...
Source: Genomics Data - August 23, 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: Available online 24 August 2016 Source:Genomics Data 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...
Source: Genomics Data - August 23, 2016 Category: Genetics & Stem Cells Source Type: research
Resequencing of Curcuma longa L. cv. Kedaram through transcriptome profiling reveals various novel transcripts
Publication date: September 2016 Source:Genomics Data, Volume 9 Author(s): Ambika Sahoo, Sudipta Jena, Suprava Sahoo, Sanghamitra Nayak, Basudeba Kar Curcuma longa L. (Turmeric), of the family Zingiberaceae, is one of the economically as well as medicinally important plant species. It is a sterile, polyploid and vegetatively propagated spice crop cultivated usually in Southeast Asia. In the current study, we carried out re-sequencing through transcriptome profiling of Curcuma longa cv. Kedaram (Cl_Ked_6). We acquired a total of 1GB raw data by resequencing through paired-end sequencing using Nextseq 500 platform. Th...
Source: Genomics Data - August 22, 2016 Category: Genetics & Stem Cells Source Type: research
Resequencing ofCurcuma longaL. cv. Kedaram through transcriptome profiling reveals various novel transcripts
Publication date: Available online 17 August 2016 Source:Genomics Data Author(s): Ambika Sahoo, Sudipta Jena, Suprava Sahoo, sanghamitra Nayak, Basudeba Kar Curcuma longaL. (Turmeric), of the family Zingiberaceae, is one of the economically as well as medicinally important plant species. It is a sterile, polyploid and vegetatively propagated spice crop cultivated usually in Southeast Asia. In the current study, we carried out re-sequencing through transcriptome profiling ofCurcuma longacv. Kedaram (Cl_Ked_6). We acquired a total of 1GB raw data by resequencing through paired-end sequencing using Nextseq 500 plat for...
Source: Genomics Data - August 17, 2016 Category: Genetics & Stem Cells Source Type: research
Draft genome sequence of pathogenic bacteria Vibrio parahaemolyticus strain Ba94C2, associated with acute hepatopancreatic necrosis disease isolate from South America
Publication date: September 2016 Source:Genomics Data, Volume 9 Author(s): Leda Restrepo, Bonny Bayot, Irma Betancourt, Andres Pinzón Vibrio parahaemolyticus is a pathogenic bacteria which has been associated to the early mortality syndrome (EMS) also known as hepatopancreatic necrosis disease (AHPND) causing high mortality in shrimp farms. Pathogenic strains contain two homologous genes related to insecticidal toxin genes, PirA and PirB, these toxin genes are located on a plasmid contained within the bacteria. Genomic sequences have allowed the finding of two strains with a divergent structure related to the geogra...
Source: Genomics Data - August 17, 2016 Category: Genetics & Stem Cells Source Type: research
Corrigendum to “Transcriptome of the freshwater amphipod Gammarus pulex hepatopancreas” [Genomics Data 8 (2016) 91–92]
Publication date: Available online 12 August 2016 Source:Genomics Data Author(s): E. Gismondi, J.P. Thomé (Source: Genomics Data)
Source: Genomics Data - August 12, 2016 Category: Genetics & Stem Cells Source Type: research
Draft genome sequence of pathogenic bacteria Vibrio parahaemolyticus strain 15094, associated with acute hepatopancreatic necrosis disease isolate from South America
Publication date: Available online 11 August 2016 Source:Genomics Data Author(s): Leda Restrepo, Bonny Bayot, Irma Betancourt, Andres Pinzón Vibrio parahaemolyticus is a pathogenic bacteria which has been associated to the early mortality syndrome (EMS) also known as hepatopancreatic necrosis disease (AHPND) causing high mortality in shrimp farms. Pathogenic strains contain two homologous genes related to insecticidal toxin genes, PirA and PirB, these toxin genes are located on a plasmid contained within the bacteria. Genomic sequences have allowed the finding of two strains with a divergent structure related to the...
Source: Genomics Data - August 11, 2016 Category: Genetics & Stem Cells Source Type: research
Transcriptional profiling of regenerating embryonic mouse hearts
Publication date: Available online 12 August 2016 Source:Genomics Data Author(s): Manuela Magarin, Herbert Schulz, Ludwig Thierfelder, Jörg-Detlef Drenckhahn The postnatal mammalian heart is considered a terminally differentiated organ unable to efficiently regenerate after injury. In contrast, we have recently shown a remarkable regenerative capacity of the prenatal heart using myocardial tissue mosaicism for mitochondrial dysfunction in mice. This model is based on inactivation of the X-linked gene encoding holocytochrome c synthase (Hccs) specifically in the developing heart. Loss of HCCS activity results in resp...
Source: Genomics Data - August 11, 2016 Category: Genetics & Stem Cells Source Type: research
Whole genome sequencing of Mycobacterium tuberculosis SB24 isolated from Sabah, Malaysia
Publication date: Available online 10 August 2016 Source:Genomics Data Author(s): Noraini Philip, Kenneth Francis Rodrigues, Timothy William, Daisy Vanitha John Mycobacterium tuberculosis (M. tuberculosis) is the causative agent of tuberculosis (TB) that causes millions of death every year. We have sequenced the genome of M. tuberculosis isolated from cerebrospinal fluid (CSF) of a patient diagnosed with tuberculous meningitis (TBM). The isolated strain was referred as M. tuberculosis SB24. Genomic DNA of the M. tuberculosis SB24 was extracted and subjected to whole genome sequencing using PacBio platform. The draft ...
Source: Genomics Data - August 10, 2016 Category: Genetics & Stem Cells Source Type: research
Draft genome sequence of Micrococcus luteus strain O'Kane implicates metabolic versatility and the potential to degrade polyhydroxybutyrates
Publication date: Available online 8 August 2016 Source:Genomics Data Author(s): Radwa A. Hanafy, M.B. Couger, Kristina Baker, Chelsea Murphy, Shannon D. O'Kane, Connie Budd, Donald P. French, Wouter D. Hoff, Noha Youssef Micrococcus luteus is a predominant member of skin microbiome. We here report on the genomic analysis of Micrococcus luteus strain O'Kane that was isolated from an elevator. The partial genome assembly of Micrococcus luteus strain O'Kane is 2.5Mb with 2256 protein-coding genes and 62 RNA genes. Genomic analysis revealed metabolic versatility with genes involved in the metabolism and transport o...
Source: Genomics Data - August 8, 2016 Category: Genetics & Stem Cells Source Type: research
Draft genome sequence of Pseudomonas moraviensis strain Devor implicates metabolic versatility and bioremediation potential
Publication date: Available online 4 August 2016 Source:Genomics Data Author(s): Neil T. Miller, Danny Fuller, M.B. Couger, Mark Bagazinski, Philip Boyne, Robert C. Devor, Radwa A. Hanafy, Connie Budd, Donald P. French, Wouter D. Hoff, Noha Youssef Pseudomonas moraviensis is a predominant member of soil environments. We here report on the genomic analysis of Pseudomonas moraviensis strain Devor that was isolated from a gate at Oklahoma State University, Stillwater, OK, USA. The partial genome of Pseudomonas moraviensis strain Devor consists of 6016489bp of DNA with 5290 protein-coding genes and 66 RNA genes. T...
Source: Genomics Data - August 4, 2016 Category: Genetics & Stem Cells Source Type: research
Comparative analysis of transcriptomes in aerial stems and roots of Ephedra sinicabased on high-throughput mRNA sequencing
Publication date: Available online 4 August 2016 Source:Genomics Data 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 no...
Source: Genomics Data - August 4, 2016 Category: Genetics & Stem Cells Source Type: research
