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Soil DNA

ABSTRACT: soil DNA Raw sequence reads

PROVIDER: PRJNA1013134 | ENA |

REPOSITORIES: ENA

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Dataset's files

Source:

			Action	DRS
	SRR25992070_1.fastq.gz	Fastqsanger.gz
	SRR25992070_2.fastq.gz	Fastqsanger.gz
	SRR25992071_1.fastq.gz	Fastqsanger.gz
	SRR25992071_2.fastq.gz	Fastqsanger.gz
	SRR25992072_1.fastq.gz	Fastqsanger.gz

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Soil DNA

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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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Bulk RNA sequencing data of rice roots protoplasted for 2.5 hours and 3 hours, as well as rice roots grown in gel, non-compacted soil and compacted soil conditions

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