Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Reclaiming soil

ABSTRACT: Reclaiming soil Raw sequence reads

PROVIDER: PRJNA1243361 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR32911300_1.fastq.gz	Fastqsanger.gz
	SRR32911300_2.fastq.gz	Fastqsanger.gz
	SRR32911301_1.fastq.gz	Fastqsanger.gz
	SRR32911301_2.fastq.gz	Fastqsanger.gz
	SRR32911302_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 168

Similar Datasets

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

Morus alba Raw protein sequence reads

Project description:Morus alba L. Raw protein sequence reads and sequence

2024-02-08 | PXD049451 |

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

Project description:We report raw bulk RNA sequencing data rice roots (X.kitaake) protoplasted for 2.5 hours and 3 hours to eliminate the effects of protoplasting duration on our scRNA-seq analysis, as well as rice roots grown in gel, non-compacted soil and compacted soil conditions to verify our findsing with scRNA-seq studies

2024-12-08 | GSE283428 | GEO

Single-cell RNA-seq of Kitaake rice roots grown in gel, and non-compacted soil conditions

Project description:We report both raw and processed scRNA-seq profiling reveals how root tissues adapt to soil conditions and compaction stress

2024-02-01 | GSE251706 | GEO

Comparative transcriptomics of Burkholderia pseudomallei from soil media and infected host

Project description:Burkholderia pseudomallei can adapt to and thrive in a variety of environments, including soil and water, and also can infect different hosts, including humans, leading to the tropical disease melioidosis. Modulation of gene and protein expression is one of this pathogen's adaptive survival mechanisms, which could lead to changes in the bacteria's cell membrane, metabolism, and virulence. To better understand bacterial adaptation and host-pathogen interactions, this study compared the expression profiles of B. pseudomallei from infected mice to B. pseudomallei cultivated in soil extract media. B. pseudomallei in vivo was created by infecting mice through the intraperitoneal route and harvesting the spleens on day 5 post infection. Total RNA was isolated and sequenced from the harvested spleen. Sequence reads were mapped to the B. pseudomallei UKMD286 strain genome sequence.

2022-07-22 | E-MTAB-11200 | biostudies-arrayexpress

Strategies for the interpretation of soil metaproteomic data

Project description:Evaluation of different strategies to interpret metaproteomics data acquired on soil samples from a floodplain along the Seine River (France) incorporating sample-specific metagenomics data, soil genome catalogue database, and generic sequence database.

2022-02-17 | PXD026798 | Pride

Soil

Project description:Soil Raw sequence reads

| PRJNA1270750 | ENA

soil

Project description:soil Raw sequence reads

| PRJNA832480 | ENA

soil

Project description:soil Raw sequence reads

| PRJNA832908 | ENA

soil

Project description:soil Raw sequence reads