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Mesocosm experiment examining microbial community response to three cyanobacteria algaecide treatments

ABSTRACT: Mesocosm experiment examining microbial community response to three cyanobacteria algaecide treatments

PROVIDER: PRJNA785661 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR17182600_1.fastq.gz	Fastqsanger.gz
	SRR17182600_2.fastq.gz	Fastqsanger.gz
	SRR17182601_1.fastq.gz	Fastqsanger.gz
	SRR17182601_2.fastq.gz	Fastqsanger.gz
	SRR17182602_1.fastq.gz	Fastqsanger.gz

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Project description:Current advances in genomics and computational biology have afforded novel insight as to how the phenotype is generated from the genotype – systems biology. We argue that systems biology, when viewed through an ecological lens, provides an unprecedented opportunity to understand how genes cascade through multiple levels of biological organization to alter ecosystem function. To test this approach, we established six monocultures of Arabidopsis thaliana ‘Columbia’- wild-type plants, six monocultures of a single gene variant (mutant) to the wild-type, and six mixtures with equal density plantings of each genotype in mesocosm chambers (50 x 50 x 45 cm). The mutant harbored a T-DNA insertion in the main nitrate reductase gene (nia2). This is the gateway enzyme for N metabolism, which resulted in activity levels that were 38% of the wild-type. Mesocosms were instrumented to monitor soil and air temperature, water and humidity status, and CO2 differentials. Transcript expression profiles were generated for each of the monoculture populations by collecting and processing 100 leaves per mesocosm at generation 2 and 4. Design: Expression profiles were generated for each monoculture population by pooling 100 leaves per mesocosm into one sample. This resulted in 6 biological replicates for each genotype per generation. Thus, a total of 48 samples were generated (6 wild-type + 6 nia2 mutants x 2 generations x 2 CO2 treatments) and hybridized onto microarrays. We used a direct loop design analyzing generations separately (diagrams of hybridization designs are linked as supplementary PDF files).

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