Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR9093100_1.fastq.gz | Fastqsanger.gz | |||
| SRR9093100_2.fastq.gz | Fastqsanger.gz | |||
| SRR9093101_1.fastq.gz | Fastqsanger.gz | |||
| SRR9093101_2.fastq.gz | Fastqsanger.gz | |||
| SRR9093092_1.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:Landfill leachate water is often treated in a biological processing step. In most cases a stable operation of the industrial scale plants is controlled by sum parameters such as process relevant ion concentrations, dry matter concentration and dissolved oxygen concentration. A deeper understanding of the current status of the individual cell or the biocoenosis would help to understand malfunctions or the reason for inefficient plant performance. In a simple batch experimental setup, samples of two different conditions have been generated to unravel bacterial proteome changes in response to medium term lack of oxygen supply and landfill leachate addition. The first condition was an activated sludge sample condition from an industrial scale landfill leachate treatment plant with the process stages of nitrification and denitrification. After 45 days without aeration and with addition of leachate and carbon sources as fed batch, the second sample (condition 2) was taken. A comprehensive LC-MS/MS based protemic screen was performed aiming for the identification and quantification of waste water specific bacteria proteomes. To this end, a novel combination of two protein extraction methods has been established meeting the requirements for LC-MS/MS anaylsis. Around 600 proteins were identified of which 90 % were quantified in at least 3 replicates. Numerous essential proteins to maintain the cell redox homeostasis are overexpressed in the condition 1 which was aerated with oxygen and stressed by the ultrafiltration compared to condition 2, which was not aerated in a lab experiment. In addition, heat and cold shock proteins and two proteins related to the apoptosis of organisms (spermidine/putrescine transport system and apoptosis-inducing factor) were identified.
2022-02-23 | PXD011917 | Pride
Project description:Waste decomposition in landfills is a complex and microbe-mediated process. Understanding the microbial community composition and structure is critical for accelerating decomposition and reducing adverse impact on the environment. Here, we examined the microbial communities along with landfill depth and age (LDA) in a sanitary landfill in Beijing, China using 16s rRNA Illumina sequencing and GeoChip 4.6. We found that Clostridiales and Methanofollis were the predominant bacteria and archaea in the present landfill, respectively. Interestingly, in contrast with the decreasing trend of microbial diversity in soil, both phylogenetic and functional diversities were higher in deeper and older refuse in the landfill. Phylogenetic compositions were obviously different in the refuse with the same LDA and such difference is mainly attributed to the heterogeneity of refuse instead of random process. Nevertheless, functional structures were similar within the same LDA, indicating that microbial community assembly in the landfill may be better reflected by functional genes rather than phylogenetic identity. Mantel test and canonical correspondence analysis suggested that environmental variables had significant impacts on both phylogenetic composition and functional structure. Higher stress genes, genes for degrading toxic substances and endemic genes in deeper and older refuse indicated that they were needed for the microorganisms to survive in the more severe environments. This study suggests that landfills are a repository of stress-resistant and contaminant-degrading microorganisms, which can be used for accelerating landfill stabilization and enhancing in situ degradation. Fifteen refuse samples with five landfill depths and ages (6m/2a, 12m/4a, 18m/6a, 24m/8a and 30m/10a) were collected from a sanitary landfill in Beijing, China. Three replicates in every landfill depth and age
2016-06-15 | E-GEOD-68712 | biostudies-arrayexpress
Project description:Waste decomposition in landfills is a complex and microbe-mediated process. Understanding the microbial community composition and structure is critical for accelerating decomposition and reducing adverse impact on the environment. Here, we examined the microbial communities along with landfill depth and age (LDA) in a sanitary landfill in Beijing, China using 16s rRNA Illumina sequencing and GeoChip 4.6. We found that Clostridiales and Methanofollis were the predominant bacteria and archaea in the present landfill, respectively. Interestingly, in contrast with the decreasing trend of microbial diversity in soil, both phylogenetic and functional diversities were higher in deeper and older refuse in the landfill. Phylogenetic compositions were obviously different in the refuse with the same LDA and such difference is mainly attributed to the heterogeneity of refuse instead of random process. Nevertheless, functional structures were similar within the same LDA, indicating that microbial community assembly in the landfill may be better reflected by functional genes rather than phylogenetic identity. Mantel test and canonical correspondence analysis suggested that environmental variables had significant impacts on both phylogenetic composition and functional structure. Higher stress genes, genes for degrading toxic substances and endemic genes in deeper and older refuse indicated that they were needed for the microorganisms to survive in the more severe environments. This study suggests that landfills are a repository of stress-resistant and contaminant-degrading microorganisms, which can be used for accelerating landfill stabilization and enhancing in situ degradation.
2016-06-15 | GSE68712 | GEO
Project description:To study their metabolic potential in natural ecosystems, we developed a species-independent LAB microarray, containing 2,269 30-mer oligonucleotides, and targeting 406 genes that play a key role in the production of sugar catabolites, bacteriocins, exopolysaccharides, and aromas, in probiotic and biosafety characteristics, and in stress response. Also, genes linked to negative traits such as antibiotic resistance and virulence are represented. This experiment is a validation experiment, where we hybridized labelled DNA from 20 LAB strains, covering 86% of all oligos. Keywords: Platform validation experiment
2009-10-20 | GSE9082 | GEO
Project description:To study their metabolic potential in natural ecosystems, we developed a species-independent LAB microarray, containing 2,269 30-mer oligonucleotides, and targeting 406 genes that play a key role in the production of sugar catabolites, bacteriocins, exopolysaccharides, and aromas, in probiotic and biosafety characteristics, and in stress response. Also, genes linked to negative traits such as antibiotic resistance and virulence are represented. This experiment is a validation experiment, where we hybridized labelled RNA from 20 LAB strains, covering 86% of all oligos. Keywords: Platform validation experiment
2009-10-20 | GSE9140 | GEO
Project description:Assessment of technical error in a dual-channel, two timepoint experiment using White lab Drosophila melanogaster microarrays Keywords: repeat sample
2005-05-12 | GSE2641 | GEO
Project description:Nine Curtobacterium strains (three from three clades) were subjected to a lab desiccation experiment with no access to moisture or nutrients to compare between clades. RNA was extracted at days 0, 1, and 32 and sequenced
2024-04-19 | GSE230266 | GEO
Project description:We identified target genes for NHR-25 by ChIP-seq at L1 stage of C. elegans. Transcription factor genes were tagged with GFP and their expression examined at L1 stage. Since there are no direct target genes known for NHR-25 that can be used for assessment of enrichment efficiency by quantitative PCR (qPCR), we chose to repeat ChIP-seq experiment of another GFP tagged transcription factor, PHA-4 for which the ChIP-seq was performed during a pilot experiment of modENCODE project using the same transgenic strain and antibody (a gift from Tony Hyman lab).
2013-12-03 | GSE44710 | GEO
Project description:This experiment was annotated by TAIR (http://arabidopsis.org). This experiment looks at changes in gene expression in response to constitutive expression of the transcription factor CBF2. Experimenter name = Jonathan Vogel Experimenter phone = 517-355-2299 Experimenter fax = 517-353-5174 Experimenter department = MSU-DOE Plant Research Lab Experimenter institute = Michigan State University Experimenter address = East Lansing Experimenter zip/postal_code = MI 48824 Experimenter country = USA Keywords: genetic_modification_design
2006-08-15 | GSE5536 | GEO