Genome sequencing and annotation of a Campylobacter coli strain isolated from milk with multidrug resistance
Publication date: Available online 5 May 2016 Source:Genomics Data Author(s): Kun C. Liu, Karen C. Jinneman, Jason Neal-McKinney, Wen-Hsin Wu, Daniel H. Rice As the most prevalent bacterial cause of human gastroenteritis, food-borne Campylobacter infections pose a serious threat to public health. Whole Genome Sequencing (WGS) is a tool providing quick and inexpensive approaches for analysis of food-borne pathogen epidemics. Here we report the WGS and annotation of a Campylobacter coli strain, FNW20G12, which was isolated from milk in the United States in 1997 and carries multidrug resistance. The draft genome...
Source: Genomics Data - May 5, 2016 Category: Genetics & Stem Cells Source Type: research
Copy number analysis of the low-copy repeats at the primate NPHP1 locus by array comparative genomic hybridization
Publication date: June 2016 Source:Genomics Data, Volume 8 Author(s): Bo Yuan, Pengfei Liu, Jeffrey Rogers, James R. Lupski Array comparative genomic hybridization (aCGH) has been widely used to detect copy number variants (CNVs) in both research and clinical settings. A customizable aCGH platform may greatly facilitate copy number analyses in genomic regions with higher-order complexity, such as low-copy repeats (LCRs). Here we present the aCGH analyses focusing on the 45kb LCRs [1] at the NPHP1 region with diverse copy numbers in humans. Also, the interspecies aCGH analysis comparing human and nonhuman primat...
Source: Genomics Data - May 5, 2016 Category: Genetics & Stem Cells Source Type: research
Microarray data analyses of yeast RNA Pol I subunit RPA12 deletion strain
Publication date: June 2016 Source:Genomics Data, Volume 8 Author(s): Kamlesh Kumar Yadav, Ram Rajasekharan The ribosomal RNA (rRNA) biosynthesis is the most energy consuming process in all living cells and the majority of total transcription activity is dedicated for synthesizing rRNA. The cells may adjust the synthesis of rRNA with the availability of resources. rRNA is mainly synthesized by RNA polymerase I that is composed of 14 subunits. Deletion of RPA12, 14, 39 and 49 are viable. RPA12 is a very small protein (13.6kDa), and the amount of protein in the cells is very high (12,000 molecules per cell), but the ...
Source: Genomics Data - May 5, 2016 Category: Genetics & Stem Cells Source Type: research
Expression of microRNAs in HPV negative tonsil cancers and their regulation of PDCD4
Publication date: June 2016 Source:Genomics Data, Volume 8 Author(s): Samantha Khoury, Alireza Ahadi, Xiaoying Zhang, Nham Tran Global rates of tonsil cancer have been increasing since the turn of the millennia, however we still have a limited understanding of the genes and pathways which control this disease. This array dataset which is linked to our publication (Zhang et al., 2015) describes the profiling of human miRNAs in tonsil and normal adjacent tissues. With this dataset, we identified a list of microRNA (miRNA) which were highly over represented in tonsil cancers and showed that several miRNAs were abl...
Source: Genomics Data - May 5, 2016 Category: Genetics & Stem Cells Source Type: research
Transcriptome of the freshwater amphipod Gammarus pulex hepatopancreas
Publication date: June 2016 Source:Genomics Data, Volume 8 Author(s): E. Gismondi, J.P. Thomé So far, ecotoxicological studies used biomarkers of exposure or of effects in order to investigate the impacts of contaminated areas on biota (Peakall, 1994 [6]). However, although these results are important in the ecotoxicological risk assessment, biomarkers are very specific and only provide information on the biological processes or physiological pathways targeted by the biomarkers experimenters choose to test (Monsinjon and Knigge, 2007 [5]). In recent years, proteomics have become a major tool in ecotoxicology, as t...
Source: Genomics Data - May 5, 2016 Category: Genetics & Stem Cells Source Type: research
Identification of myogenic regulatory genes in the muscle transcriptome of beltfish (Trichiurus lepturus): A major commercial marine fish species with robust swimming ability
Publication date: June 2016 Source:Genomics Data, Volume 8 Author(s): Hui Zhang, Chung-Ming Chang, Kang-Ning Shen, Weiwei Xian, Chung-Der Hsiao The beltfish (Trichiurus lepturus) is considered as one of the most economically important marine fish in East Asia. It is a top predator with a robust swimming ability that is a good model to study muscle physiology in fish. In the present study, we used Illumina sequencing technology (NextSeq500) to sequence, assemble and annotate the muscle transcriptome of juvenile beltfish. A total of 57,509,280 clean reads (deposited in NCBI SRA database with accession number of...
Source: Genomics Data - May 5, 2016 Category: Genetics & Stem Cells Source Type: research
Striatal transcriptome analysis of a congenic mouse line (chromosome 11: 50–60Mb) exhibiting reduced methamphetamine sensitivity
Publication date: June 2016 Source:Genomics Data, Volume 8 Author(s): Neema Yazdani, Ying Shen, W. Evan Johnson, Camron D. Bryant Addiction to psychostimulants such as Methamphetamine (MA) is a significant public health issue in the United States and currently, there are no FDA approved pharmacological interventions. Previously, using short term-selected mouse lines for high and low MA sensitivity that were derived from an F2 cross between C57BL/6J (B6) and DBA/2J (D2) strains, we identified a quantitative trait locus (QTL) on chromosome (chr) 11 that influenced sensitivity to MA-induced locomotor activity (D2&...
Source: Genomics Data - May 5, 2016 Category: Genetics & Stem Cells Source Type: research
Complete genome sequence of Erysipelothrix rhusiopathiae strain GXBY-1 isolated from acute swine erysipelas outbreaks in south China
Publication date: June 2016 Source:Genomics Data, Volume 8 Author(s): Hai-bo Tang, Jiang Xie, Libo Wang, Fang Liu, Jianmin Wu Erysipelothrix rhusiopathiae (E. rhusiopathiae) is an important pathogenic microorganism affecting swine industry. Here, we report the finished annotated genome sequence of E. rhusiopathiae GXBY-1, isolated from acute swine erysipelas in Binyang County, Guangxi, China. The GXBY-1 strain, which exhibits high pathogenicity for swine, contains 1,876,490bp with G+C content of 36.50%, and contains 1734 protein-coding genes, 57 tRNAs and 27 rRNAs. The nucleotide sequence of this genome was ...
Source: Genomics Data - May 5, 2016 Category: Genetics & Stem Cells Source Type: research
Identification of CELF1 RNA targets by CLIP-seq in human HeLa cells
We present therefore the first map of CELF1 binding sites in human cells. (Source: Genomics Data)
Source: Genomics Data - May 5, 2016 Category: Genetics & Stem Cells Source Type: research
Sequence analysis of pfcrt and pfmdr1 genes and its association with chloroquine resistance in Southeast Indian Plasmodium falciparum isolates
Conclusions The point mutation K76T of pfcrt is high in P. falciparum suggesting a sustained high CQ resistance even after five years of the introduction of ACTs for antimalarial therapy. The present study suggests a strong association of CQ resistance with pfcrt T76, but not with the pfmdr1 Y86 mutation. However, sequence analysis showed that Y184F mutation on pfmdr1 gene was found to be associated with high resistance. Also, a new pfcrt haplotype ‘CVIKT’ associated with CQ resistance was found to be present in Indian strains of P. falciparum. The data obtained from this study helps in continuous monitoring of drug re...
Source: Genomics Data - May 5, 2016 Category: Genetics & Stem Cells Source Type: research
Peeping into genomic architecture by re-sequencing of Ochrobactrum intermedium M86 strain during laboratory adapted conditions
Publication date: June 2016 Source:Genomics Data, Volume 8 Author(s): Kushal N. Gohil, Priya S. Neurgaonkar, Aditi Paranjpe, Syed G. Dastager, Mahesh S. Dharne Advances in de novo sequencing technologies allow us to track deeper insights into microbial genomes for restructuring events during the course of their evolution inside and outside the host. Bacterial species belonging to Ochrobactrum genus are being reported as emerging, and opportunistic pathogens in this technology driven era probably due to insertion and deletion of genes. The Ochrobactrum intermedium M86 was isolated in 2005 from a case of non-ul...
Source: Genomics Data - May 5, 2016 Category: Genetics & Stem Cells Source Type: research
High-quality draft genome sequence of Enterobacter sp. Bisph2, a glyphosate-degrading bacterium isolated from a sandy soil of Biskra, Algeria
Publication date: June 2016 Source:Genomics Data, Volume 8 Author(s): Ouided Benslama, Abderrahmane Boulahrouf Enterobacter sp. strain Bisph2 was isolated from a sandy soil from Biskra, Algeria and exhibits glyphosate-degrading activity. Multilocus sequence analysis of the 16S rRNA, rpoB, hsp60, gyrB and dnaJ genes demonstrated that Bisph2 might be a member of a new species of the genus Enterobacter. Genomic sequencing of Bisph2 was used to better clarify the relationships among Enterobacter species. Annotation and analysis of the genome sequence showed that the 5.535.656bp genome of Enterobacter sp. Bisph2 consis...
Source: Genomics Data - May 5, 2016 Category: Genetics & Stem Cells Source Type: research
Genome-wide functional annotation of Phomopsis longicolla isolate MSPL 10-6
This study represents the first reported genome-wide functional annotation of a seed borne fungal pathogen in the Diaporthe–Phomopsis complex. The P. longicolla genome annotation will enable research into the genetic basis of fungal infection of soybean seed and provide information for the study of soybean–fungal interactions. The genome annotation will also be a valuable resource for the research and agricultural communities. It will aid in the development of new control strategies for this pathogen. The annotations can be downloaded from: http://bioinformatics.towson.edu/phomopsis_longicolla/download.html. NCBI acces...
Source: Genomics Data - April 5, 2016 Category: Genetics & Stem Cells Source Type: research
Genetics of PCOS: A systematic bioinformatics approach to unveil the proteins responsible for PCOS
In this study, we have studied the proteins involved in PCOS and the structural aspects of the proteins that are taken into consideration using computational tools. The proteins involved are modeled using Modeller 9v14 and Ab-initio programs. All the 43 proteins responsible for PCOS were subjected to phylogenetic analysis to identify the relatedness of the proteins. Further, microarray data analysis of PCOS datasets was analyzed that was downloaded from GEO datasets to find the significant protein-coding genes responsible for PCOS, which is an addition to the reported protein-coding genes. Various statistical analyses were...
Source: Genomics Data - March 30, 2016 Category: Genetics & Stem Cells Source Type: research
Whole genome sequence and genome annotation of Colletotrichum acutatum, causal agent of anthracnose in pepper plants in South Korea
Publication date: Available online 28 March 2016 Source:Genomics Data Author(s): Joon-Hee Han, Jae-Kyung Chon, Jong-Hwa Ahn, Ik-Young Choi, Yong-Hwan Lee, Kyoung Su Kim Colletotrichum acutatum is a destructive fungal pathogen which causes anthracnose in a wide range of crops. Here we report the whole genome sequence and annotation of C. acutatum strain KC05, isolated from an infected pepper in Kangwon, South Korea. Genomic DNA from the KC05 strain was used for the whole genome sequencing using a PacBio sequencer and the MiSeq system. The KC05 genome was determined to be 52,190,760bp in size with a G+C cont...
Source: Genomics Data - March 27, 2016 Category: Genetics & Stem Cells Source Type: research
