Co-expression network analysis identified six hub genes in association with progression and prognosis in human clear cell renal cell carcinoma (ccRCC)
Publication date: Available online 4 November 2017 Source:Genomics Data Author(s): Lushun Yuan, Liang Chen, Kaiyu Qian, Guofeng Qian, Chin-Lee Wu, Xinghuan Wang, Yu Xiao Human clear cell renal cell carcinoma (ccRCC) is one of the most common types of malignant adult kidney tumors. We constructed a weighted gene co-expression network to identify gene modules associated with clinical features of ccRCC (n =97). Six hub genes (CCNB2, CDC20, CEP55, KIF20A, TOP2A, and UBE2C) were identified in both co-expression and protein-protein interaction (PPI) networks, which were highly correlated with pathologic stage. The signi...
Source: Genomics Data - November 4, 2017 Category: Genetics & Stem Cells Source Type: research

Transcriptome analysis of the Chinese giant salamander (Andrias davidianus) using RNA-sequencing
This study provided a valuable resource for understanding transcriptomic information of A. davidianus and laid a foundation for further research on functional gene cloning, genomics, genetic diversity analysis and molecular marker exploitation in A. davidianus. (Source: Genomics Data)
Source: Genomics Data - October 29, 2017 Category: Genetics & Stem Cells Source Type: research

Small RNAome sequencing delineates the small RNA landscape of pluripotent adult stem cells in the planarian Schmidtea mediterranea
Publication date: Available online 25 October 2017 Source:Genomics Data Author(s): Yue Li, An Zeng, Xiao-Shuan Han, Ge Li, Yong-Qin Li, Bairong Shen, Qing Jing Small noncoding RNAs play a pivotal role in the regulation of gene expression, and are key regulators of animal development. Freshwater planarian exhibits an extraordinary ability to regenerate any missing body parts, representing an emerging model for studying mechanism underlying stem cell regulation and tissue regeneration. Here, we utilized next-generation sequencing (NGS) to identify small RNAs that are expressed in planarian adult stem cells, and are ...
Source: Genomics Data - October 25, 2017 Category: Genetics & Stem Cells Source Type: research

Comparative analysis of genome sequences of the conifer tree pathogen, Heterobasidion annosum s.s.
Publication date: December 2017 Source:Genomics Data, Volume 14 Author(s): Jaeyoung Choi, Gir-Won Lee, Ki-Tae Kim, Jongbum Jeon, Nicolas Détry, Hsiao-Che Kuo, Hui Sun, Fred O. Asiegbu, Yong-Hwan Lee The causal agent of root and butt rot of conifer trees, Heterobasidion annosum, is widespread in boreal forests and economically responsible for annual loss of approximately 50 million euros to forest industries in Finland alone and much more at European level. In order to further understand the pathobiology of this fungus at the genome level, a Finnish isolate of H. annosum sensu stricto (isolate 03012) was sequenc...
Source: Genomics Data - October 25, 2017 Category: Genetics & Stem Cells Source Type: research

Annotation of nerve cord transcriptome in earthworm Eisenia fetida
Publication date: Available online 12 October 2017 Source:Genomics Data Author(s): Vasanthakumar Ponesakki, Sayan Paul, Dinesh Kumar Sudalai Mani, Veeraragavan Rajendiran, Kanniah Paulkumar, Sivasubramaniam Sudhakar In annelid worms, the nerve cord serves as a crucial organ to control the sensory and behavioral physiology. The inadequate genome resource of earthworms has prioritized the comprehensive analysis of their transcriptome dataset to monitor the genes express in the nerve cord and predict their role in the neurotransmission and sensory perception of the species. The present study focuses on identifying the...
Source: Genomics Data - October 12, 2017 Category: Genetics & Stem Cells Source Type: research

Whole genome shotgun sequencing of Indian strains of Streptococcus agalactiae
Publication date: Available online 2 October 2017 Source:Genomics Data Author(s): Balaji Veeraraghavan, Naveen Kumar Devanga Ragupathi, Sridhar Santhanam, Valsan Philip Verghese, Francis Yesurajan Inbanathan, Charles Livingston Group B streptococcus is known as a leading cause of neonatal infections in developing countries. The present study describes the whole genome shotgun sequences of four Group B Streptococcus (GBS) isolates. Molecular data on clonality is lacking for GBS in India. The present genome report will add important information on the scarce genome data of GBS and will help in deriving comparative ge...
Source: Genomics Data - October 2, 2017 Category: Genetics & Stem Cells Source Type: research

Computational deciphering of biotic stress associated genes in tomato (Solanum lycopersicum)
We report here 57 novel genes associated with biotic stress of tomato along with 50 genes having physical location over different chromosomes. We also report 52 cis-regulating elements and 69 putative miRNAs which are involved in regulation of these biotic stresses associated genes. These putative candidate genes associated with biotic stress can be used in molecular breeding in the endeavor of tomato productivity along with its sustainable germplasm management. (Source: Genomics Data)
Source: Genomics Data - September 28, 2017 Category: Genetics & Stem Cells Source Type: research

Complete mitochondrial genome sequence of fruit-piercing moth Eudocima phalonia (Linnaeus, 1763) (Lepidoptera: Noctuoidea)
Publication date: Available online 28 September 2017 Source:Genomics Data Author(s): Kuppusamy Sivasankaran, Pratheesh Mathew, Sekar Anand, Stanislaus Antony Ceasar, Soosaimanikam Mariapackiam, Savarimuthu Ignacimuthu The complete mitochondrial genome of the fruit piercing moth Eudocima phalonia (Linnaeus, 1763) (Lepidoptera: Noctuoidea) was sequenced and characterized (Genbank Accession No: KY196412). The complete mitogenome is a circular molecule of 15,575bp length, consisting of 13 protein-coding genes (PCGs), two ribosomal RNA genes (rrnS and rrnL), 22 transfer RNA (tRNA) genes and an A+T-rich region (D-loop). ...
Source: Genomics Data - September 28, 2017 Category: Genetics & Stem Cells Source Type: research

A new version of the grapevine reference genome assembly (12X.v2) and of its annotation (VCost.v3)
Publication date: Available online 18 September 2017 Source:Genomics Data Author(s): A. Canaguier, J. Grimplet, G. Di Gaspero, S. Scalabrin, E. Duchêne, N. Choisne, N. Mohellibi, C. Guichard, S. Rombauts, I. Le Clainche, A. Bérard, A. Chauveau, R. Bounon, C. Rustenholz, M. Morgante, M.-C. Le Paslier, D. Brunel, A.-F. Adam-Blondon (Source: Genomics Data)
Source: Genomics Data - September 19, 2017 Category: Genetics & Stem Cells Source Type: research

Rhizospheric metagenome of the terrestrial mangrove fern Acrostichum from Indian Sunderbans
This study reports the analyses of the rhizospheric microbiome of the terrestrial mangrove fern Acrostichum aureum Linn. from the Indian Sunderbans. Samples were collected using standard protocols and 16S rRNA gene V3–V4 region amplicon sequencing was performed to identify the microbial communities prevalent in the rhizosphere. A total of 1,931,252 quality checked reads were assembled into 204,818 contigs and were analysed using QIIME to reveal the abundance of Proteobacteria, Acidobacteria and Planctomycetes. The data is available at the NCBI - Sequence Read Archive with accession number: SRX2660456. This is the first r...
Source: Genomics Data - September 5, 2017 Category: Genetics & Stem Cells Source Type: research

Stroke-associated pattern of gene expression previously identified by machine-learning is diagnostically robust in an independent patient population
The objective of this study was to assess the diagnostic capacity and temporal stability of this stroke-associated transcriptional signature in an independent patient population. Publicly available whole blood microarray data generated from 23 ischemic stroke patients at 3, 5, and 24h post-symptom onset, as well from 23 cardiovascular disease controls, were obtained via the National Center for Biotechnology Information Gene Expression Omnibus. Expression levels of the ten candidate genes (ANTXR2, STK3, PDK4, CD163, MAL, GRAP, ID3, CTSZ, KIF1B, and PLXDC2) were extracted, compared between groups, and evaluated for their dis...
Source: Genomics Data - September 2, 2017 Category: Genetics & Stem Cells Source Type: research

Draft genome sequence of an endophytic bacterium, Paenibacillus tyrfis strain SUK123, isolated from Santiria apiculata stem
Publication date: December 2017 Source:Genomics Data, Volume 14 Author(s): Emmanuel Haruna, Noraziah M. Zin, Jonathan M. Adams Here we report the draft genome sequence of an endophytic Paenibacillus tyrfis strain isolated from the Universiti Kebangsaan Malaysia reserve forest, Malaysia. The genome size was approximately 8.04Mb, and the assembly consisted of 107 scaffolds with 168 contigs, and had a G+C content of 53%. Phylogenetic analysis of strain SUK123 using the 16S rRNA gene revealed that it belonged to the family Paenibacillaceae with the highest similarity to Paenibacillus elgii SDT (99%). Whole genome comparis...
Source: Genomics Data - August 19, 2017 Category: Genetics & Stem Cells Source Type: research

Draft genome sequence of an endophytic Paenibacillus tyrfis strain SUK123 isolated from Santiria apiculata stem
Publication date: Available online 17 August 2017 Source:Genomics Data Author(s): Emmanuel Haruna, Noraziah M. Zin, Jonathan M. Adams Here we report the draft genome sequence of an endophytic Paenibacillus tyrfis strain isolated from the Universiti Kebangsaan Malaysia reserve forest, Malaysia. The genome size was approximately 8.04Mb, and the assembly consisted of 107 scaffolds with 168 contigs, and had a G+C content of 53%. Phylogenetic analysis of strain SUK123 using the 16S rRNA gene revealed that it belonged to the family Paenibacillaceae with the highest similarity to Paenibacillus elgii SDT (99%). Whole genome c...
Source: Genomics Data - August 17, 2017 Category: Genetics & Stem Cells Source Type: research

Genome of Pseudomonas nitroreducens DF05 from dioxin contaminated sediment downstream of the San Jacinto River waste pits reveals a broad array of aromatic degradation gene determinants
Publication date: Available online 17 August 2017 Source:Genomics Data Author(s): Rupa Iyer, Brian Iken, Ashish Damania P. nitroreducens DF05 is a Gram negative, motile, aerobic, rod-shaped and psychrotrophic bacterium that was isolated from contaminated San Jacinto River sediment near River Terrace Park in Channelview, Texas. The draft genome of strain DF05 consists of a total of 192 contigs assembled at the scaffold level totaling 6,487,527bp and encoding for 5862 functional proteins, 1116 of which are annotated as hypothetical proteins. The bacterial chromosome has a GC content of 65.15% and contains 22 rRNA and 70...
Source: Genomics Data - August 17, 2017 Category: Genetics & Stem Cells Source Type: research

Gene expression profiling of ramie roots during hydroponic induction and adaption to aquatic environment
In this study, ramie tender stems was grown in the soil or in a hydroponic water solution, and cultured in the same environmental conditions. Root samples of terrestrial ramie, and different developmental stages of hydroponic ramie (5days, 30days), were firstly pooled for reference transcriptome sequencing by Illumina Hiseq 2000. Gene expression levels of each samples were quantified using the BGISEQ500 platform to help understand the distribution of aquatic root development related genes at the macro level (GSE98903). Our data resources provided an opportunity to elucidate the adaptation mechanisms of ramie seedlings root...
Source: Genomics Data - August 17, 2017 Category: Genetics & Stem Cells Source Type: research