Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Soil crust metagenome

ABSTRACT: JTNP temporal soil crust metagenome project Raw sequence reads

PROVIDER: PRJNA705683 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR13849500_1.fastq.gz	Fastqsanger.gz
	SRR13849500_2.fastq.gz	Fastqsanger.gz
	SRR13849600_1.fastq.gz	Fastqsanger.gz
	SRR13849600_2.fastq.gz	Fastqsanger.gz
	SRR13849501_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 431

Similar Datasets

soil crust metagenome

Project description:soil crust metagenome Raw sequence reads

| PRJNA625283 | ENA

soil crust metagenome

Project description:soil crust metagenome Raw sequence reads

| PRJNA471954 | ENA

soil crust metagenome

Project description:soil crust metagenome Metagenome

| PRJNA524392 | ENA

soil crust metagenome

Project description:soil crust metagenome Assembly

| PRJNA560457 | 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

Moab biological soil crust

Project description:Moab biological soil crust Metagenome

| PRJNA691698 | ENA

Dynamic transcriptional response of Microcoleus vaginatus to hydration and dehydration in a desert biological soil crust

Project description:Biological soil crusts (BSCs) are cyanobacteria-dominated microbial communities that cover extensive portions of the world’s arid and semi-arid deserts. The infrequent periods of hydration are often too short to allow for dormancy strategies based on sporulation; consequently, survival is based on the unique capabilities of vegetative cells to resuscitate from and re-enter a stress resistant dormant state, one of which is migration within the crust layers in response to hydration. In this study, we sought to characterize the events that govern the emergence of the dominant cyanobacterium from dormancy, its subsequent growth, and the events triggered by re-desiccation and a transition back to dormant state. We performed a 48 hour laboratory wetting experiment of a desert BSC and tracked the response of Microcoleus vaginatus using a whole genome transcriptional time-course including night/day periods. This allowed the identification of genes with a diel expression pattern, genes involved uniquely in the signaling after hydration and those that contribute primarily to desiccation preparation.

2012-10-30 | GSE40188 | GEO

Dynamic transcriptional response of Microcoleus vaginatus to hydration and dehydration in a desert biological soil crust

2012-10-30 | E-GEOD-40188 | biostudies-arrayexpress

soil crust metagenome

Project description:Biological soil crust microbial communities from Mojave Desert, California, United States - LAC_S3 metagenome

| PRJNA620795 | ENA

soil crust metagenome

Project description:Biological soil crust microbial communities from Mojave Desert, California, United States - CLC_S2 metagenome

| PRJNA620791 | ENA