Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

SPRUCE soil qSIP

ABSTRACT: SPRUCE soil qSIP Raw sequence reads

PROVIDER: PRJNA649571 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR12347200_1.fastq.gz	Fastqsanger.gz
	SRR12347200_2.fastq.gz	Fastqsanger.gz
	SRR12347300_1.fastq.gz	Fastqsanger.gz
	SRR12347300_2.fastq.gz	Fastqsanger.gz
	SRR12347400_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 868

Similar Datasets

SPRUCE soil field qSIP

Project description:SPRUCE soil field qSIP 16S RrNA gene Raw sequence reads

| PRJNA729971 | ENA

Toolik Lake Alaska soil qSIP

Project description:Toolik Lake Alaska soil qSIP Raw sequence reads

| PRJNA649546 | ENA

TRACE, Puerto Rico, soil qSIP

Project description:TRACE, Puerto Rico, soil qSIP Raw sequence reads

| PRJNA649787 | ENA

Mixed Conifer Forest, Northern Arizona, soil qSIP

Project description:Mixed Conifer Forest, Northern Arizona, soil qSIP Raw sequence reads

| PRJNA649802 | ENA

Norway spruce

Project description:Norway spruce bacteria Raw sequence reads

| PRJNA430787 | ENA

Decomposing leaves in freshwater qSIP

Project description:Decomposing leaves in freshwater qSIP Raw sequence reads

| PRJNA669516 | ENA

Decomposing leaves in freshwater qSIP ITS2

Project description:Decomposing leaves in freshwater qSIP ITS2 Raw sequence reads

| PRJNA669386 | ENA

qSIP samples Shredding Caddisfly gut and food microbiome

Project description:qSIP samples Shredding Caddisfly gut and food microbiome Raw sequence reads

| PRJNA708319 | ENA

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