Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

61 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcriptome analysis of Paracoccus denitrificans during Cu-limitation

ABSTRACT: Transcriptional profiling of Paracoccus denitrificans PD1222 wild type grown to mid-exponential phase in minimal media with either 13 uM (Cu-H) or 0.5 uM (Cu-L) Cu regimes. The goal was to define the effects of Cu-limitation on denitrification genes Two growth conditions, three biological replicates of each condition. Each sample hybridised in a two-channel hybridization against Paracoccus denitrificans genomic DNA as the comparator/reference, which also acted as a control for spot quality. Cu-concentration 13 uM (Cu-H) versus 0.5 uM Cu (Cu-L) in anaerobic growth conditions.

ORGANISM(S): Paracoccus denitrificans PD1222

SUBMITTER: Matthew Sullivan

PROVIDER: E-GEOD-48577 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Transcriptome analysis of Paracoccus denitrificans during Cu-limitation

Project description:Transcriptional profiling of Paracoccus denitrificans PD1222 wild type grown to mid-exponential phase in minimal media with either 13 uM (Cu-H) or 0.5 uM (Cu-L) Cu regimes. The goal was to define the effects of Cu-limitation on denitrification genes

2013-11-18 | GSE48577 | GEO

Integrated analysis of physiology, transcriptomics and metabonomics revealed the mechanisms of high pH mitigating copper toxicity in Citrus sinensis roots

Project description:Limited data are available on the impacts of copper (Cu)-pH-interaction-responsive genes in roots. Citrus sinensis seedlings were treated with 300 (Cu-toxicity) or 0.5 uM (control) CuCl2 x pH 3.0 or 4.8 for 17 weeks. Thereafter, we investigated the impacts of Cu-pH interactions on transcriptomics in roots.

2023-02-17 | GSE225124 | GEO

RNA sequencing analysis of covR-deficient Streptococcus agalactiae during Cu intoxication

Project description:Total RNA was isolated from mid-log phase Streptococcus agalactiae cells deficient in CovR (∆covR strain GU2400), grown in Todd-Hewitt broth (THB) medium, supplemented with 0.5 mM Cu and sequenced using Illumina NextSeq500

2021-06-01 | GSE167900 | GEO

RNA sequencing analysis of SczA-deficient Streptococcus agalactiae during Cu intoxication

Project description:Total RNA was isolated from mid-log phase Streptococcus agalactiae cells deficient in SczA (∆sczA strain GU2791), grown in Todd-Hewitt broth (THB) medium supplemented with 0.5 mM Cu and sequenced using Illumina NextSeq500.

2021-06-01 | GSE167903 | GEO

RNA sequencing analysis of CopY-deficient Streptococcus agalactiae during Cu stress

Project description:Total RNA was isolated from mid-log phase Streptococcus agalactiae cells deficient in CopY (∆copY strain GU2857), grown in Todd-Hewitt broth (THB) medium supplemented with 0.5 mM Cu and sequenced using Illumina NextSeq500.

2021-06-01 | GSE167897 | GEO

RNA sequencing analysis of Streptococcus agalactiae 874391 (wild-type) during Cu intoxication

Project description:Total RNA was isolated from mid-log phase Streptococcus agalactiae 874391 wild-type cells grown in Todd-Hewitt broth (THB) medium supplemented with 0.5 mM Cu and sequenced using Illumina NextSeq500

2021-06-01 | GSE167895 | GEO

ChIP Seq analysis of the Cu metalloregulatory transcription factor Cuf1 in Cryptococcus neoformans in response to Cu availability

Project description:The essential yet toxic nature of Cu ions in living cells requires exquisite control of Cu homeostasis. The fungal pathogen C. neoformans regulates Cu homeostasis for survival during a complex host colonization process. During pulmonary infection host innate immune cells use Cu in an attempt to toxify C. neoformans, which responds by activating expression of Cu detoxifying proteins. However, during brain colonization expression of the fungal Cu import machinery is activated and required for virulence. To achieve the genetic plasticity required for adaptation to a continuum of distinct Cu environments within the host, C. neoformans utilizes the Cu-responsive transcription factor, Cuf1. Cuf1 is unique as it senses and responds to both high and low Cu environments, activating different sets of genes dependent on environmental Cu status. Cells lacking Cuf1 are compromised for colonization of the lungs and brain, highlighting Cuf1 as an important virulence factor. A genome-wide assessment of the Cuf1 binding sites in the genome of C. neoformans driven by Cu status identified novel genes required for adaptation to high and low Cu environments. These genes and their regulation provide new insights with respect to adaptive responses to changes in host Cu availability and could reveal new targets for therapeutic intervention in cryptococcosis.

2018-10-29 | GSE110120 | GEO

Systems analysis of Chlamydomonas Cu nutrition reveals connections between Cu and multiple O2-dependent metabolic steps

Project description:We used digital gene expression (NlaIII sequence tags) and RNA-Seq to compare the transcriptomes of Cu-replete vs. Cu–deficient Chlamydomonas wild-type cells to reveal dozens of mRNAs whose abundance is modified. Half of the corresponding genes are targets of CRR1, a master regulator of nutritional copper sensing, and are associated with candidate CRR1 binding sites. The targets include many plastid-localized proteins, like FDX5 encoding a ferredoxin isoform, and CGL78, encoding a protein conserved in the green lineage, indicative of modified plastid metabolism. Immunoblot analysis and proteome profiles recapitulate the transcriptome profiles. New evidence for Cu sparing is suggested by up-regulation of AOF1 encoding a copper-independent but flavin-dependent amine oxidase and down-regulation of two metal- binding proteins. Genes encoding redox proteins, many of which function in lipid metabolism, are over-represented, which is compatible with the role of Cu in biology. Lipid profiles indicate a CRR1-dependent increase in Cu-deficient cells in the proportion of unsaturated (16:2, 16:3, 16:4, 18:2) fatty acids at the expense of the more saturated (16:0, 16:1, 18:0) precursors, especially on plastid galactolipids, which validates the increased expression of acyl-ACP and plastid-localized w-6 desaturases. CRR1-independent changes in the transcriptome suggest a role for Cu in oxygen sensing in Chlamydomonas. Sampling of Chlamydomonas CC-1021 (2137) and crr1-2, crr1:CRR1 mutant cells (the mutant is knock-down for the transcription factor crr1, which plays a key role in the transcriptional response to copper levels) cultivated in TAP or minimal medium under Cu-sufficient (control) and Cu-defficient conditions. poly-A purification, NlaIII digestion/random fragmentation

2011-10-23 | E-GEOD-25124 | biostudies-arrayexpress

Transcriptomic profiling of Cu-regulated genes in an oceanic diatom

Project description:Copper (Cu) plays an essential role in cellular metabolism and limits phytoplankton growth and production in parts of the open sea. Whole transcriptome analysis provides a powerful tool to explore gene expression profiles and cellular metabolic pathways regulated by Cu. In this study, we identified Cu-regulated genes by profiling the transcriptomes of an oceanic diatom, Thalassiosira oceanica 1005, adapted to survive in a Cu-limited and Cu-replete environment. The results provide insights to the mechanisms of adaptation and acclimation of T. oceanica to low Cu environments.

2020-02-29 | GSE145010 | GEO

Systems analysis of Chlamydomonas Cu nutrition reveals connections between Cu and multiple O2-dependent metabolic steps

2011-10-24 | GSE25124 | GEO