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Soil pot experiment

ABSTRACT: Soil pot experiment Raw sequence reads

PROVIDER: PRJNA1094631 | ENA |

REPOSITORIES: ENA

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Dataset's files

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			Action	DRS
	SRR29355244_1.fastq.gz	Fastqsanger.gz
	SRR29355244_2.fastq.gz	Fastqsanger.gz
	SRR29355245_1.fastq.gz	Fastqsanger.gz
	SRR29355245_2.fastq.gz	Fastqsanger.gz
	SRR29355246_1.fastq.gz	Fastqsanger.gz

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pot experiment

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iPOTs: Internet of Things-based pot system controlling optional treatment of soil water condition for plant phenotyping under drought stress

Project description:A cultivation facility that can assist users in controlling the soil water condition is needed for accurately phenotyping plants under drought stress in an artificial environment. Here we report the Internet of Things (IoT)-based pot system controlling optional treatment of soil water condition (iPOTs), an automatic irrigation system that mimics the drought condition in a growth chamber. The Wi-Fi-enabled iPOTs system allows water supply from the bottom of the pot, based on the soil water level set by the user, and automatically controls the soil water level at a desired depth. The iPOTs also allows users to monitor environmental parameters, such as soil temperature, air temperature, humidity, and light intensity, in each pot. To verify whether the iPOTs mimics the drought condition, we conducted a drought stress test on rice varieties and near-isogenic lines, with diverse root system architecture, using the iPOTs system installed in a growth chamber. Similar to the results of a previous drought stress field trial, the growth of shallow-rooted rice accessions was severely affected by drought stress compared with that of deep-rooted accessions. The microclimate data obtained using the iPOTs system increased the accuracy of plant growth evaluation. Transcriptome analysis revealed that pot positions in the growth chamber had little impact on plant growth. Together, these results suggest that the iPOTs system represents a reliable platform for phenotyping plants under drought stress.

2021-08-24 | GSE171578 | GEO

Soil Health Experiment 2018, 2019

Project description:Soil Health Experiment 2018, 2019 Raw sequence reads

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Fengqiu N depisition experiment soil sample

Project description:Fengqiu N depisition experiment soil sample Raw sequence reads

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soil in 10-year fallow (burning experiment)

Project description:soil in 10-year fallow (burning experiment) Raw sequence reads

| PRJNA1001269 | ENA

Biomass experiment

Project description:Biomass experiment Raw sequence reads

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pot disturbance

Project description:pot disturbance

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RNA-Seq Analysis to confirm Different Transcriptomic Profiles of Soil-Derived Functional Module Consortia.

Project description:Purpose: Deconstructing the soil microbiome into reduced-complexity functional modules represents a novel method of microbiome analysis. The goals of this study are to confirm differences in transcriptomic patterns among five functional module consortia. Methods: mRNA profiles of 3 replicates each of functional module enrichments of soil inoculum in M9 media with either 1) xylose, 2) n-acetylglucosamine, 3) glucose and gentamycin, 4) xylan, or 5) pectin were generated by sequencing using an Illumina platform (GENEWIZ performed sequencing). Sequence reads that passed quality filters were aligned to a soil metagenome using Burrows Wheeler Aligner. Resulting SAM files were converted to raw reads using HTSeq, and annotated using Uniref90 or EGGNOG databases. Results: To reduce the size of the RNA-Seq counts table and increase its computational tractability, transcripts containing a minimum of 75 total counts, but no more than 3 zero counts, across the 15 samples were removed. The subsequent dataset was normalized using DESeq2, resulting in a dataset consisting of 6947 unique transcripts across the 15 samples, and 185,920,068 reads. We identified gene categories that were enriched in a sample type relative to the overall dataset using Fisher’s exact test. Conclusions: our dataset confirms that the functional module consortia generated from targeted enrichments of a starting soil inoculum had distinct functional trends by enrichment type.

2020-01-14 | GSE143587 | GEO

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