Genomics Data最新文献_第3页

Genome-wide miRNA, gene and methylation analysis of triple negative breast cancer to identify changes associated with lymph node metastases 三阴性乳腺癌的全基因组miRNA、基因和甲基化分析，以确定与淋巴结转移相关的变化

Genomics Data Pub Date : 2017-12-01 DOI: 10.1016/j.gdata.2017.07.004

Kelly A. Avery-Kiejda , Andrea Mathe , Rodney J. Scott

{"title":"Genome-wide miRNA, gene and methylation analysis of triple negative breast cancer to identify changes associated with lymph node metastases","authors":"Kelly A. Avery-Kiejda , Andrea Mathe , Rodney J. Scott","doi":"10.1016/j.gdata.2017.07.004","DOIUrl":"10.1016/j.gdata.2017.07.004","url":null,"abstract":"<div>Triple negative breast cancer (TNBC) is a particularly important breast cancer subtype with an aggressive clinical phenotype that is associated with a higher likelihood of metastasis. This subtype is characterized by an absence of the estrogen (ER) and progesterone (PR) receptors, as well as the human epidermal growth factor receptor 2 (HER2/HER neu). The absence of the three receptors significantly reduces targeted treatment options for patients with TNBC and as such, there is an urgent need to identify novel treatment targets. Here, we provide detailed information regarding the design of a multi-platform dataset that describes genome-wide assessment of miRNA (assessed by microarray, GSE38167) and gene expression (assessed by microarray, GSE61723), as well as methylation (assessed by Illumina HM450K BeadChip, GSE78751) in TNBCs, matched normal adjacent tissues and matched lymph node metastases. The use of this multi-platform dataset is likely to uncover novel markers and key pathways involved in progression to lymph node metastasis in TNBC.</div>","PeriodicalId":56340,"journal":{"name":"Genomics Data","volume":"14 ","pages":"Pages 1-4"},"PeriodicalIF":0.0,"publicationDate":"2017-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.gdata.2017.07.004","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35192135","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 9

Annotation of nerve cord transcriptome in earthworm Eisenia fetida 蚯蚓的神经索转录组注释

Genomics Data Pub Date : 2017-12-01 DOI: 10.1016/j.gdata.2017.10.002

Vasanthakumar Ponesakki , Sayan Paul , Dinesh Kumar Sudalai Mani, Veeraragavan Rajendiran, Paulkumar Kanniah, Sudhakar Sivasubramaniam

{"title":"Annotation of nerve cord transcriptome in earthworm Eisenia fetida","authors":"Vasanthakumar Ponesakki , Sayan Paul , Dinesh Kumar Sudalai Mani, Veeraragavan Rajendiran, Paulkumar Kanniah, Sudhakar Sivasubramaniam","doi":"10.1016/j.gdata.2017.10.002","DOIUrl":"https://doi.org/10.1016/j.gdata.2017.10.002","url":null,"abstract":"<div>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 potential transcripts and predicting their functional features by annotating the transcriptome dataset of nerve cord tissues prepared by Gong et al., 2010 from the earthworm Eisenia fetida. Totally 9762 transcripts were successfully annotated against the NCBI nr database using the BLASTX algorithm and among them 7680 transcripts were assigned to a total of 44,354 GO terms. The conserve domain analysis indicated the over representation of P-loop NTPase domain and calcium binding EF-hand domain. The COG functional annotation classified 5860 transcript sequences into 25 functional categories. Further, 4502 contig sequences were found to map with 124 KEGG pathways. The annotated contig dataset exhibited 22 crucial neuropeptides having considerable matches to the marine annelid Platynereis dumerilii, suggesting their possible role in neurotransmission and neuromodulation. In addition, 108 human stem cell marker homologs were identified including the crucial epigenetic regulators, transcriptional repressors and cell cycle regulators, which may contribute to the neuronal and segmental regeneration. The complete functional annotation of this nerve cord transcriptome can be further utilized to interpret genetic and molecular mechanisms associated with neuronal development, nervous system regeneration and nerve cord function.</div>","PeriodicalId":56340,"journal":{"name":"Genomics Data","volume":"14 ","pages":"Pages 91-105"},"PeriodicalIF":0.0,"publicationDate":"2017-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.gdata.2017.10.002","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"91634588","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 14

Draft genome sequence of an endophytic bacterium, Paenibacillus tyrfis strain SUK123, isolated from Santiria apiculata stem 从尖叶参茎中分离的一株内生细菌——提尔菲拟芽孢杆菌SUK123的基因组序列草图

Genomics Data Pub Date : 2017-12-01 DOI: 10.1016/j.gdata.2017.08.005

Emmanuel Haruna , Noraziah M. Zin , Jonathan M. Adams

{"title":"Draft genome sequence of an endophytic bacterium, Paenibacillus tyrfis strain SUK123, isolated from Santiria apiculata stem","authors":"Emmanuel Haruna , Noraziah M. Zin , Jonathan M. Adams","doi":"10.1016/j.gdata.2017.08.005","DOIUrl":"https://doi.org/10.1016/j.gdata.2017.08.005","url":null,"abstract":"<div>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 comparison of SUK123 with related species using average nucleotide identity (ANI) analysis revealed a similarity of 98% to Paenibacillus tyrfis Mst1T, 94% to Paenibacillus elgii B69T, 91% to Paenibacillus ehimensis A2T, 68% to Paenibacillus polymyxa SC2T and 69% to Paenibacillus alvei DMS29T. The draft genome was deposited at the European Nucleotide Archive (PRJEB21373).</div>","PeriodicalId":56340,"journal":{"name":"Genomics Data","volume":"14 ","pages":"Pages 44-46"},"PeriodicalIF":0.0,"publicationDate":"2017-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.gdata.2017.08.005","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"91634590","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 4

Draft genome sequence of the halophilic Halobacillus mangrovi KTB 131 isolated from Topan salt of the Jeon-nam in Korea 从韩国全南Topan盐中分离的嗜盐红树盐杆菌KTB 131的基因组序列草图

Genomics Data Pub Date : 2017-12-01 DOI: 10.1016/j.gdata.2017.07.010

Mingyeong Woo , Sun-Hee Park , Kyounghee Park , Min-Kyu Park , Ji-Yeon Kim , Han-Seung Lee , Jae Hak Sohn , Dong-Woo Lee , Gaewon Nam , Kee-Sun Shin , Sang-Jae Lee

引用次数: 3

RNA-seq data from different developmental stages of Rafflesia cantleyi floral buds 莱佛士花蕾不同发育阶段的RNA-seq数据

Genomics Data Pub Date : 2017-12-01 DOI: 10.1016/j.gdata.2017.07.008

Safoora Amini , Halimah Alias , Mohd Afiq Aizat-Juhari , Mohd-Noor Mat-Isa , Jumaat Haji Adam , Hoe-Han Goh , Kiew-Lian Wan

{"title":"RNA-seq data from different developmental stages of Rafflesia cantleyi floral buds","authors":"Safoora Amini , Halimah Alias , Mohd Afiq Aizat-Juhari , Mohd-Noor Mat-Isa , Jumaat Haji Adam , Hoe-Han Goh , Kiew-Lian Wan","doi":"10.1016/j.gdata.2017.07.008","DOIUrl":"10.1016/j.gdata.2017.07.008","url":null,"abstract":"<div>Rafflesia cantleyi, known as one of the world's largest flowers, is a specialised holoparasite due to dramatic morphological modifications. It possesses highly reduced vegetative structure and only appears as a flower for sexual reproduction. Moreover, it has an unusual life cycle in that its floral bud development takes up to nine months. In order to fully understand the highly modified floral organ structure and long life cycle of R. cantleyi, we used Illumina sequencing technology (HiSeq) for sequence generation followed by de novo assembly of sequence reads. We obtained the RNA-seq data from three different stages of floral bud, representing the early, mid and advanced developmental stages. These data are available via BioProject accession number PRJNA378435. More than 10.3Gb raw sequence data were generated, corresponding to 102,203,042 raw reads. Following removal of low-quality reads and trimming of adapter sequences, a total of 91,638,836 reads were obtained. De novo assembly of these sequences using Trinity resulted in 89,690 unique transcripts with an N50 of 1653bp. The obtained transcriptomic data will be useful for further study to understand the molecular interactions that result in R. cantleyi floral development.</div>","PeriodicalId":56340,"journal":{"name":"Genomics Data","volume":"14 ","pages":"Pages 5-6"},"PeriodicalIF":0.0,"publicationDate":"2017-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.gdata.2017.07.008","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35232022","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 5

Whole genome sequencing of Microbacterium sp. AISO3 from polluted San Jacinto River sediment reveals high bacterial mobility, metabolic versatility and heavy metal resistance 来自受污染的圣哈辛托河沉积物的微细菌sp. AISO3的全基因组测序显示出高的细菌流动性、代谢多样性和重金属抗性

Genomics Data Pub Date : 2017-12-01 DOI: 10.1016/j.gdata.2017.07.009

Rupa Iyer , Ashish Damania , Brian Iken

引用次数: 3

Genome sequence of the oleaginous yeast Rhodotorula toruloides strain CGMCC 2.1609 产油酵母红酵母菌株CGMCC 2.1609的基因组序列

Genomics Data Pub Date : 2017-09-01 DOI: 10.1016/j.gdata.2017.05.009

Christine Sambles, Sabine Middelhaufe, Darren Soanes, Dagmara Kolak, Thomas Lux, Karen Moore, Petra Matoušková, David Parker, Rob Lee, John Love, Stephen J. Aves

引用次数: 13

Whole genome sequencing and annotation of halophilic Salinicoccus sp. BAB 3246 isolated from the coastal region of Gujarat 古吉拉特邦沿海地区嗜盐盐球菌(Salinicoccus sp. bab3246)全基因组测序和注释

Genomics Data Pub Date : 2017-09-01 DOI: 10.1016/j.gdata.2017.06.006

Vishal Mevada , Shradhdha Patel , Jignesh Pandya , Himani Joshi , Rajesh Patel

{"title":"Whole genome sequencing and annotation of halophilic Salinicoccus sp. BAB 3246 isolated from the coastal region of Gujarat","authors":"Vishal Mevada , Shradhdha Patel , Jignesh Pandya , Himani Joshi , Rajesh Patel","doi":"10.1016/j.gdata.2017.06.006","DOIUrl":"10.1016/j.gdata.2017.06.006","url":null,"abstract":"<div>Salinicoccus sp. BAB 3246 is a halophilic bacterium isolated from a marine water sample collected from the coastal region of Gujarat, India, from a surface water stream. Based on 16sRNA sequencing, the organism was identified as Salinicoccus sp. BAB 3246 (Genebank ID: KF889285). The present work was performed to determine the whole genome sequence of the organism using Ion Torrent PGM platform followed by assembly using the CLC genomics workbench and genome annotation using RAST, BASys and MaGe. The complete genome sequence was 713,204bp identified by with second largest size for Salinicoccus sp. reported in the NCBI genome database. A total of 652 degradative pathways were identified by KEGG map analysis. Comparative genomic analysis revealed Salinicoccus sp. BAB 3246 as most highly related to Salinicoccus halodurans H3B36. Data mining identified stress response genes and operator pathway for degradation of various environmental pollutants. Annotation data and analysis indicate potential use in pollution control in industrial influent and saline environment.</div>","PeriodicalId":56340,"journal":{"name":"Genomics Data","volume":"13 ","pages":"Pages 30-34"},"PeriodicalIF":0.0,"publicationDate":"2017-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.gdata.2017.06.006","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35163474","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 6

Genome sequence of Bradyrhizobium sp. LMTR 3, a diazotrophic symbiont of Lima bean (Phaseolus lunatus) 利马豆重氮共生菌慢生根瘤菌sp. LMTR 3的基因组序列

Genomics Data Pub Date : 2017-09-01 DOI: 10.1016/j.gdata.2017.06.007

Ernesto Ormeño-Orrillo , Luis Rey , David Durán , Carlos A. Canchaya , Doris Zúñiga-Dávila , Juan Imperial , Esperanza Martínez-Romero , Tomás Ruiz-Argüeso

引用次数: 3

The draft genome sequence of Hymenobacter sp. CRA2 isolated from Nama Karoo shrub land soils from South Africa 南非纳玛卡鲁灌丛土壤中膜杆菌cr2的基因组序列草图

Genomics Data Pub Date : 2017-09-01 DOI: 10.1016/j.gdata.2017.06.001

Mubanga H. Kabwe , Nerissa Govender , Surendra Vikram , Oliver M. Bezuidt , Thulani P. Makhalanyane

引用次数: 0