Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1214758 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR32175970_1.fastq.gz | Fastqsanger.gz | |||
| SRR32175970_2.fastq.gz | Fastqsanger.gz | |||
| SRR32175971_1.fastq.gz | Fastqsanger.gz | |||
| SRR32175971_2.fastq.gz | Fastqsanger.gz | |||
| SRR32175972_1.fastq.gz | Fastqsanger.gz |
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Project description:The microarrays experiments was performed with the purpose of identify transcriptional networks activated by copper. This experiment correspond the work tituled Enterococcus faecalis reconfigure the activation of its transcriptional regulatory networks under different copper exposure levels (work in preparation).Mauricio Latorrea,b, Jessica Galloway-Peñac,d,e, Jung Hyeo Rhoc,d, Marko Budinichf, Barbara E. Murrayc,d,e, Alejandro Maassb,f, Mauricio Gonzáleza,b,f*. a INTA, Laboratorio de Bioinformática y Expresión Génica, INTA, Universidad de Chile, Santiago, Chile. b Center for Genome Regulation (Fondap 15090007), University of Chile, Santiago, Chile. c Division of Infectious Disease, Department of Medicine, University of Texas Medical School, Houston, Texas, United States of America. d Center for the Study of Emerging and Reemerging Pathogens, University of Texas Medical School, Houston, Texas, United States of America. e Department of Microbiology and Molecular Genetics, University of Texas Medical School, Houston, Texas, United States of America f Mathomics, Center for Mathematical Modeling (UMI2807CNRS), Santiago, Chile. * Corresponding author. Address: El Líbano 5524, Santiago 11, Chile. Fax: +56 (2) 2214030.
2013-11-12 | GSE45131 | GEO
Project description:The microarrays experiments was performed with the purpose of identify transcriptional networks activated by copper. This experiment correspond the work tituled Enterococcus faecalis reconfigure the activation of its transcriptional regulatory networks under different copper exposure levels (work in preparation).Mauricio Latorrea,b, Jessica Galloway-PeM-CM-1ac,d,e, Jung Hyeo Rhoc,d, Marko Budinichf, Barbara E. Murrayc,d,e, Alejandro Maassb,f, Mauricio GonzM-CM-!leza,b,f*. a INTA, Laboratorio de BioinformM-CM-!tica y ExpresiM-CM-3n GM-CM-)nica, INTA, Universidad de Chile, Santiago, Chile. b Center for Genome Regulation (Fondap 15090007), University of Chile, Santiago, Chile. c Division of Infectious Disease, Department of Medicine, University of Texas Medical School, Houston, Texas, United States of America. d Center for the Study of Emerging and Reemerging Pathogens, University of Texas Medical School, Houston, Texas, United States of America. e Department of Microbiology and Molecular Genetics, University of Texas Medical School, Houston, Texas, United States of America f Mathomics, Center for Mathematical Modeling (UMI2807CNRS), Santiago, Chile. * Corresponding author. Address: El LM-CM--bano 5524, Santiago 11, Chile. Fax: +56 (2) 2214030. A eight chip study (two technical replicates) using total RNA recovered from four separate cultures of: Enterococcus faecalis OG1RF (N medium growth), Enterococcus faecalis OG1RF copM-NM-^T mutant strain (N medium growth), Enterococcus faecalis OG1RF copM-NM-^T mutant low copper treatment (N medium growth + 0.05 mM CuSO4) and Enterococcus faecalis OG1RF copM-NM-^T mutant low copper treatment (N medium growth + 0.5 mM CuSO4). Each chip measures the expression level of 3,114 genome genes from Enterococcus faecalis strain V583 (A7980-00-01).
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Project description:In this study we characterize the gill transcriptome changes that coincide with the arrival of contaminating oil in field-collected Gulf killifish Fundulus grandis. Gill transcription was contrasted before and after the arrival of oil, and between oil impacted and reference sites. Animals were sampled from field sites at four times. The oil impacted site is Grand Terre Island Louisiana (GT) and the two reference sites are Bay St. Louis Mississippi (BSL) and Bayou La Batre Alabama (BLB). The first timepoint (05/01/2010 to 05/09/2010) was before the arrival of contaminating oil, the second and third timepoints (06/28/2010 to 06/29/2010, and 08/30/2010 to 09/01/2010) were after the arrival of contaminating oil, and the fourth timepoint 08/28/2011) was over a year after the arrival of contaminating oil.
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Project description:Blanc Du bois grapes are gaining popularity in the South eastern US due to its distinctive flavor and disease tolerance characteristics. Berry composition at harvest is a major contributing factor of wine quality. Blanc Du bois grapes are harvested from EL-38 and EL-39 stages depending on the style of wine desired or harvested early to avoid rain nearing harvest. In the current study, gel-free proteome analysis was applied to investigate changes in enzymes, primary and secondary metabolism proteins during ripening and late ripe stage. Grape berries from EL-33, EL-34, EL-36, EL-38 and EL-39 were collected based on brix, acidity and density. Protein extracts from different berry stages were resolved by electrophoresis. Proteins were extracted from the gel as a single band, detained and subjected to proteolysis with sequencing grade trypsin. Trypsin digested peptides from different berry protein extracts were separated on a nano LC and the eluent was sprayed onto to a LTQ Orbitrap Velos mass spectrometer. The raw files were analyzed using Proteome Discoverer with Sequest and Mascot search nodes using Vitis species FASTA database (70,263 entries) and the data were further validated by Scaffold software. A total of 1091, 1131, 1078, 1042 and 1066 proteins were detected in EL-33, EL-34, EL-36, EL-38 and EL-39 of berries respectively. Statistical ANOVA analysis revealed 927 proteins present across the stages that are involved in various biochemical and metabolic pathways. Seventeen proteins including dihydroflavonol reductase, sucrose phosphate synthase, PR proteins increased more than three-fold between ripe and late ripe berry stages. Other proteins that increased during ripe and late ripe stage berries were alcohol dehydrogenase 1, anthocyanidin reductase, phospho-2-dehydro-3-deoxyheptonate aldolase, fatty acid hydroperoxide lyase, cinnamyl alcohol dehydrogenase, -isopiperitenol (-)-carveol and SAM-methyltransferases.
2018-04-09 | PXD004157 | Pride
Project description:Palaeogenomics analysis of Palaeoloxodon naumanni
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Project description:The emerging roles of endolysosomes (EL) in AF have yet to be discovered, especially how the EL contribute to the development of AF within a slow time frame. To identify the EL role in AF, we applied proteomics, transcriptomics, integrated analysis, electron tomography, western blotting and enzyme assays. To understand the cellular and EL driven dominant pathways, in AF, we applied an organelle protein isolation method, that was previously developed by us (Ayagama et al,.2021) on to an AF goat model. Our findings include upregulation of AMPK pathway, EL-specific proteins that were not identified in the TL, such as GAA, DYNLRB1, CLTB, SIRT3, CCT2, and muscle specific HSPB2. The structural anomalies such as autophago-vacuole formation, irregularly stacked mitochondria, and glycogen deposition provide an insight into of the contribution of EL contribution and the related pathways and molecular mechanisms.
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