Draft genome sequence of Mycobacterium tuberculosisstrain B9741 of Beijing B0/W lineage from HIV positive patient from Siberia
We report a draft genome sequence of Mycobacterium tuberculosis strain B9741 belonging to Beijing B0/W lineage isolated from a HIV patient from Siberia, Russia. This clinical isolate showed MDR phenotype and resistance to isoniazid, rifampin, streptomycin and pyrazinamide. We analyzed SNPs associated with virulence and resistance. The draft genome sequence and annotation have been deposited at GenBank under the accession NZ_LVJJ00000000. (Source: Genomics Data)
Source: Genomics Data - August 3, 2016 Category: Genetics & Stem Cells Source Type: research
Microarray analyses for identifying genes conferring resistance to pepper leaf curl virus in chilli pepper (Capsicum spp.)
In this study, we generated transcriptome profiles of PepLCV resistant genotype (BS-35) and susceptible genotype (IVPBC-535) after artificial viral inoculation using microarray technology and detail experimental procedures and analyses are described. A total of 319 genes differentially expressed between resistant and susceptible genotypes were identified, out of that 234 unique genes were found to be up-regulated >2-fold in resistant line BS-35 when compared to susceptible, IVPBC-535. The data set we generated has been analyzed to identify genes that are involved in the regulation of resistance against PepLCV. The r...
Source: Genomics Data - August 3, 2016 Category: Genetics & Stem Cells Source Type: research
Metagenomic analysis of fungal taxa inhabiting Mecca region, Saudi Arabia
Publication date: September 2016 Source:Genomics Data, Volume 9 Author(s): Tarek A.A. Moussa, Hassan S. Al-Zahrani, Omar A. Almaghrabi, Nevien M. Sabry, Michael P. Fuller The data presented contains the sequences of fungal Internal Transcribed Spacer (ITS) and 18S rRNA gene from a metagenome of the Mecca region, Saudi Arabia. Sequences were amplified using fungal specific primers, which amplified the amplicon aligned between the 18S and 28S rRNA genes. A total of 460 fungal species belonging to 133 genera, 58 families, 33 orders, 13 classes and 4 phyla were identified in four contrasting locations. The raw se...
Source: Genomics Data - July 29, 2016 Category: Genetics & Stem Cells Source Type: research
Metagenomics analysis of fungal taxa inhabiting Mecca region, Saudi Arabia
Publication date: Available online 21 July 2016 Source:Genomics Data Author(s): Tarek A.A. Moussa, Hassan S. AlZahrani, Omar A. Almaghrabi, Nevien M. Sabry, Michael P. Fuller The data presented contains the sequences of fungal Internal Transcribed Spacer (ITS) and 18S rRNA gene from a metagenome of Mecca region, Saudi Arabia. Sequences were amplified using fungal specific primers, which amplified the amplicon lined between the 18S and 28S rRNA genes. A total of 460 fungal species belonging to 133 genera, 58 families, 33 orders, 13 classes and 4 phyla was identified in the four sites. The raw sequencing data u...
Source: Genomics Data - July 21, 2016 Category: Genetics & Stem Cells Source Type: research
A cross strain Plasmodium falciparum microarray optimized for the transcriptome analysis of Plasmodium falciparum patient derived isolates
Publication date: Available online 20 July 2016 Source:Genomics Data Author(s): Amit Kumar Subudhi, P.A. Boopathi, Sheetal Middha, Jyoti Acharya, Sudha Narayana Rao, Raja C. Mugasimangalam, Paramendra Sirohi, Sanjay K. Kochar, Dhanpat K. Kochar, Ashis Das Malarial parasite P. falciparum, an apicomplexan protozoan has a 23.3MB nuclear genome and encodes ~5600 transcripts.The genetic diversity of the parasite within and across geographical zones is a challenge to gene expression studies which are essential for understanding of disease process, outcome and developing markers for diagnostics and prognos...
Source: Genomics Data - July 20, 2016 Category: Genetics & Stem Cells Source Type: research
Context based computational analysis and characterization of ARS consensus sequences (ACS) of Saccharomyces cerevisiae genome
In this study, DNA properties such as base composition, correlation, sequence dependent thermodynamic and DNA structural profiles, and their positions have been considered for characterizing ORC-ACS and nrACS. Analysis reveals that ORC-ACS depict marked differences in nucleotide composition and context features in its vicinity compared to nrACS. Interestingly, an A-rich motif was also discovered in ORC-ACS sequences within its nucleosome-free region. Profound changes in the conformational features, such as DNA helical twist, inclination angle and stacking energy between ORC-ACS and nrACS were observed. Distribution of ACS ...
Source: Genomics Data - July 19, 2016 Category: Genetics & Stem Cells Source Type: research
The draft genome sequence of Mangrovibacter sp. strain MP23, an endophyte isolated from the roots of Phragmites karka
Publication date: Available online 19 July 2016 Source:Genomics Data Author(s): Pratiksha Behera, Parag Vaishampayan, Nitin K. Singh, Samir R. Mishra, Vishakha Raina, Mrutyunjay Suar, Ajit K. Pattnaik, Gurdeep Rastogi Till date, only one draft genome has been reported within the genus Mangrovibacter. Here, we report the second draft genome shotgun sequence of a Mangrovibacter sp. strain MP23 that was isolated from the roots of Phargmites karka ( Phragmites karka ), an invasive weed growing in the Chilika Lagoon, Odisha, India. Strain MP23 is a facultative anaerobic, nitrogen-fixing endophytic bacteria t...
Source: Genomics Data - July 19, 2016 Category: Genetics & Stem Cells Source Type: research
Draft genome sequence of Staphylococcus aureus KT/312045, an ST1-MSSA PVL positive isolated from pus sample in East Coast Malaysia
Publication date: Available online 7 July 2016 Source:Genomics Data Author(s): Zarizal Suhaili, Soo-Sum Lean, Noor Muzamil Mohamad, Abdul R. Abdul Rachman, Mohd Nasir Mohd Desa, Chew Chieng Yeo Most of the efforts in elucidating the molecular relatedness and epidemiology of Staphylococcus aureus in Malaysia have been largely focused on methicillin-resistant S. aureus (MRSA). Therefore, here we report the draft genome sequence of the methicillin-susceptible Staphylococcus aureus (MSSA) with sequence type 1 (ST1), spa type t127 with Panton-Valentine Leukocidin (pvl) pathogenic determinant isolated from pus sa...
Source: Genomics Data - July 18, 2016 Category: Genetics & Stem Cells Source Type: research
De novo sequencing of Eucommia ulmoides flower bud transcriptomes for identification of genes related to floral development
This study provides a valuable resource for further conservation genetics and functional genomics research on E. ulmoides. (Source: Genomics Data)
Source: Genomics Data - July 18, 2016 Category: Genetics & Stem Cells Source Type: research
Characterization of the replication timing program of 6 human model cell lines
We present the genomic data of replication timing in 6 human model cell lines: U2OS (GSM2111308), RKO (GSM2111309), HEK 293T (GSM2111310), HeLa (GSM2111311), MRC5-SV (GSM2111312) and K562 (GSM2111313). A short comparative analysis was performed that allowed us to define regions common to the 6 cell lines. These replication timing data can be taken into account when performing studies that use these model cell lines. (Source: Genomics Data)
Source: Genomics Data - July 18, 2016 Category: Genetics & Stem Cells Source Type: research
Transcriptional profiling of immortalized and K-ras-transformed mouse fibroblasts upon PKA stimulation by forskolin in low glucose availability
Publication date: September 2016 Source:Genomics Data, Volume 9 Author(s): Ferdinando Chiaradonna, Yuri Pirola, Francesca Ricciardiello, Roberta Palorini Forskolin (FSK) induces activation of protein kinase A (PKA). This activation protects specifically some cancer cells from death induced by glucose starvation. Cell effects upon FSK treatment prompted us to investigate in detail the physiological role of PKA in the activation of pro-survival mechanisms in glucose starvation. In this regard we performed a microarray analysis of normal NIH3T3 and transformed NIH3T3-K-ras mouse fibroblasts cultured at 1mM glucose...
Source: Genomics Data - July 18, 2016 Category: Genetics & Stem Cells Source Type: research
Transcriptomic and functional resources for the small hive beetle Aethina tumida, a worldwide parasite of honey bees
Publication date: September 2016 Source:Genomics Data, Volume 9 Author(s): Matthew R. Tarver, Qiang Huang, Lilia de Guzman, Tom Rinderer, Beth Holloway, Justin Reese, Daniel Weaver, Jay D. Evans The small hive beetle (SHB), Aethina tumida, is a major pest of managed honey bee (Apis mellifera) colonies in the United States and Australia, and an emergent threat in Europe. While strong honey bee colonies generally keep SHB populations in check, weak or stressed colonies can succumb to infestations. This parasite has spread from a sub-Saharan Africa to three continents, leading to immense management and reg...
Source: Genomics Data - July 18, 2016 Category: Genetics & Stem Cells Source Type: research
Whole-genome sequence of Sunxiuqinia dokdonensis DH1T, isolated from deep sub-seafloor sediment in Dokdo Island
Publication date: September 2016 Source:Genomics Data, Volume 9 Author(s): Sooyeon Lim, Dong-Ho Chang, Byoung-Chan Kim Sunxiuqinia dokdonensis DH1T was isolated from deep sub-seafloor sediment at a depth of 900m below the seafloor off Seo-do (the west part of Dokdo Island) in the East Sea of the Republic of Korea and subjected to whole genome sequencing on HiSeq platform and annotated on RAST. The nucleotide sequence of this genome was deposited into DDBJ/EMBL/GenBank under the accession LGIA00000000. (Source: Genomics Data)
Source: Genomics Data - July 18, 2016 Category: Genetics & Stem Cells Source Type: research
De Novo transcriptome assembly of Zingiber officinale cv. Suruchi of Odisha
Publication date: September 2016 Source:Genomics Data, Volume 9 Author(s): Mahendra Gaur, Aradhana Das, Rajesh Kumar Sahoo, Basudeba Kar, Sanghamitra Nayak, Enketeswara Subudhi Zingiber officinale Rosc., known as ginger, is an Asian crop, popularly used in every household kitchen and commercially used in bakery, beverage, food and pharmaceutical industries. The present study deals with de novo transcriptome assembly of an elite ginger cultivar Suruchi by next generation sequencing methodology. From the analysis 10.9GB raw data was obtained which can be available in NCBI accession number SAMN03761185. We id...
Source: Genomics Data - July 18, 2016 Category: Genetics & Stem Cells Source Type: research
Complete genome sequencing and comparative genomic analysis of functionally diverse Lysinibacillus sphaericus III(3)7
Publication date: September 2016 Source:Genomics Data, Volume 9 Author(s): Andrés Rey, Laura Silva-Quintero, Jenny Dussán Lysinibacillus sphaericus III(3)7 is a native Colombian strain, the first one isolated from soil samples. This strain has shown high levels of pathogenic activity against Culex quinquefaciatus larvae in laboratory assays compared to other members of the same species. Using Pacific Biosciences sequencing technology we sequenced, annotated (de novo) and described the genome of strain III(3)7, achieving a complete genome sequence status. We then performed a comparative analysis between the new...
Source: Genomics Data - July 18, 2016 Category: Genetics & Stem Cells Source Type: research
