Iron precipitates
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ABSTRACT:
PROVIDER: PRJNA432859 | ENA |
REPOSITORIES: ENA
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Project description:Nitrate-reducing iron(II)-oxidizing bacteria are widespread in the environment contribute to nitrate removal and influence the fate of the greenhouse gases nitrous oxide and carbon dioxide. The autotrophic growth of nitrate-reducing iron(II)-oxidizing bacteria is rarely investigated and poorly understood. The most prominent model system for this type of studies is enrichment culture KS, which originates from a freshwater sediment in Bremen, Germany. To gain insights in the metabolism of nitrate reduction coupled to iron(II) oxidation under in the absence of organic carbon and oxygen limited conditions, we performed metagenomic, metatranscriptomic and metaproteomic analyses of culture KS. Raw sequencing data of 16S rRNA amplicon sequencing, shotgun metagenomics (short reads: Illumina; long reads: Oxford Nanopore Technologies), metagenome assembly, raw sequencing data of shotgun metatranscriptomes (2 conditions, triplicates) can be found at SRA in https://www.ncbi.nlm.nih.gov/bioproject/PRJNA682552. This dataset contains proteomics data for 2 conditions (heterotrophic and autotrophic growth conditions) in triplicates.
2021-05-17 | PXD023186 | Pride
Project description:Iron-reducing bacteria 1 Raw sequence reads
| PRJNA314288 | ENA
Project description:Morus alba L. Raw protein sequence reads and sequence
2024-02-08 | PXD049451 | iProX
Project description:Transcriptional profiles from Acidithiobacillus ferrooxidans type strain ATCC23270 grown in the presence of iron or elemental sulfur as energy source until mid logarithmic phase were compared. Cells were harvested after 48 hs of growth in 9K-FeII pH 1.6 and after 120 hs of growth in 9K-S0 pH 3.5. Pellets were washed to remove precipitates, frozen and stored at -80C until RNA extraction.<br><br>In toto 8 different hybridizations were performed using 4 independent biological samples of A. ferrooxidans (with dye-swap), 4 arrays of array design FCV-CNRS AFE Oligoarray v.1 and 4 arrays of array design FCV-CNRS AFE Oligoarray v.2. This experimental design produced 8 raw data files and 1 transformed and/or normalized data file.
2009-12-31 | E-MEXP-1990 | biostudies-arrayexpress
Project description:Purpose: The goal of this study was to probe for the effects of iron-deficiency anemia on the cardiac transciprtome using RNA-seq Methods: C57B6 mice were weaned onto a control or iron-deficient diet for 6 weeks. Hearts were removed and total mRNA was submitted for RNA-seq. Sequencing data was aligned using STAR and differetial gene expression analysis conducted in R using EdgeR and DESeq2. qRT–PCR validation for genes of interest was performed using TaqMan and SYBR Green assays. Results: We mapped about 24 million sequence reads per sample to the mouse genome (build mm10) and identified 13,590 transcripts in the hearts of control and iron-deficient mice after removing lowly expressed genes and PCR duplicates. Differential gene expression analysis showed approximately 78% downregulated and 22% upregulated genes in iron-deficiency anemia compared to controls. PCA plot showed control and iron-deficient hearts clustering in two distinct and separate clusters. Conclusions: Our study represents the first whole-transcriptomic study on cardiac samples obtained from iron-deficient and anemic mice, with biologic replicates, generated by RNA-seq technology. The RNA-seq data presented here can be used by others to explore which pathways are affected by iron-deficiency anemia
2020-12-03 | GSE162493 | GEO
Project description:We found that co-culturing BNL CL.2 liver cells with RAW 264.7 macrophages increased IRP binding in the first. To further investigate this modulation we investigated the gene expression profile in BNL CL.2 cells cultured alone, with iron, with RAW 264.7 macrophages or in the presence of both iron and macrophages. This novel reconstituted liver cell-macrophage communication pathway with the present gene expression data provides a platform for addressing how macrophages participate in the iron homeostasis of liver cells and, ultimately, in systemic iron homeostasis.
2016-10-22 | GSE32090 | GEO
Project description:Purpose: In previous work, we found that iron supplementation to cells rescues impairment of cell viability and proliferation upon lysosomal dysfunction due to inhibition of the vATPase complex. The goal of this study is to characterize the transcriptomic changes (RNA-seq) upon Bafilomycin mediated lysosomal dysfunction with and without iron (Ferric Ammonium Citrate) supplementation. Methods: mRNA profiles of wild type HEK293T cells treated +/- ferric ammonium citrate (0.1mg/ml) and +/- BafilomycinA1 (10nM) were generated by deep sequencing, in triplicate, using Illumina NextSeq500. Results: We mapped about 30-40 million sequence reads per sample to the human genome (build GRCh38). Conclusions: Our study characterizes the transcriptomic changes upon lysosomal dysfunction upon small molecule (Bafilomycin A1) inhibition of vATPase complex. We conclude that there are several notable trasncriptomic changes upon lysosomal dysfunction some of which are reversed by iron supplementation.
2019-12-06 | GSE141507 | GEO
Project description:We found that co-culturing BNL CL.2 liver cells with RAW 264.7 macrophages increased IRP binding in the first. To further investigate this modulation we investigated the gene expression profile in BNL CL.2 cells cultured alone, with iron, with RAW 264.7 macrophages or in the presence of both iron and macrophages. This novel reconstituted liver cell-macrophage communication pathway with the present gene expression data provides a platform for addressing how macrophages participate in the iron homeostasis of liver cells and, ultimately, in systemic iron homeostasis. We used microarrays to determine the gene expression modulation in BNL CL.2 cells in response to 24h culture with 100 micromolar ferric ammonium citrate (FAC), co-culture with RAW 264.7 macrophages or both
2016-10-22 | E-GEOD-32090 | biostudies-arrayexpress
Project description:Iron accumulation in microglia has been observed in Alzheimer’s disease and other neurodegenerative disorders and is thought to contribute to disease progression through various mechanisms including neuroinflammation. To study the interaction between iron accumulation and inflammation, we treated human induced pluripotent stem cell-derived microglia (iPSC-MG) with an increasing concentration of iron, in combination with inflammatory stimuli such as interferon gamma and amyloid β, and performed RNA sequencing.
| EGAS00001006112 | EGA
Project description:Iron is limiting in the environment, bacteria respond to this deprivation by activating genes required for bacterial iron homeostasis. Transcriptional regulation in response to iron in Gram-negative bacteria is largely mediated by the ferric uptake regulator protein Fur, which in the presence of iron binds to a specific sequence in the promoter regions of genes under its control and acts as a repressor. Here we describe comparative global gene expression analysis using DNA microarray based on the whole genome sequence of the magnetotactic bacterium Magnetospirillum magneticum AMB-1 was conducted between wild type strain and a non-magnetic NMA61 mutant strain, generated by mini-Tn5 transposon mutagenesis which is incapable of assimilating iron to cytoplasm. No induction of the fur genes in NMA61 mutant strain was considered to be due to low intracellular iron concentration. In the iron-replete condition, among 4492 genes, 434 genes were down-regulated and 527 genes were up-regulated in the wild type strain. Among 434 genes down-regulated, 299 genes were not down-regulated in NMA61 mutant strain, indicating these genes are candidates of Fur-regulated. Keywords: Iron, magnetotactic bacteria
2007-07-07 | GSE5832 | GEO