Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ABSTRACT: Blueberry/Forest Soil Microbiome-rRNA operon profiles Raw sequence reads

PROVIDER: PRJNA657272 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR12455800_1.fastq.gz	Fastqsanger.gz
	SRR12455801_1.fastq.gz	Fastqsanger.gz
	SRR12455802_1.fastq.gz	Fastqsanger.gz
	SRR12455803_1.fastq.gz	Fastqsanger.gz
	SRR12455804_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 72

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 |

Quantitative profiling of differentially expressed miRNAs in siCTL- and siOASL-transfected HUVECs

Project description:Purpose: The goal of this study is to compare endothelial small RNA transcriptome to identify the target of OASL under basal or stimulated conditions by utilizing miRNA-seq. Methods: Endothelial miRNA profilies of siCTL or siOASL transfected HUVECs were generated by illumina sequencing method, in duplicate. After sequencing, the raw sequence reads are filtered based on quality. The adapter sequences are also trimmed off the raw sequence reads. rRNA removed reads are sequentially aligned to reference genome (GRCh38) and miRNA prediction is performed by miRDeep2. Results: We identified known miRNA in species (miRDeep2) in the HUVECs transfected with siCTL or siOASL. The expression profile of mature miRNA is used to analyze differentially expressed miRNA(DE miRNA). Conclusions: Our study represents the first analysis of endothelial miRNA profiles affected by OASL knockdown with biologic replicates.

2022-09-06 | GSE186354 | GEO

blueberry rhizosphere soil

Project description:blueberry rhizosphere soil Raw sequence reads

| PRJNA1102520 | ENA

blueberry root-associated microbiome

Project description:blueberry root-associated microbiome Raw sequence reads

| PRJNA1156347 | ENA

Microbiota alteration upon blueberry consumption

Project description:We demonstrate that blueberry supplementation led to global changes in the gut microbiome, which could possibly contribute to physiological changes in mice

2021-01-13 | GSE161772 | GEO

Project description:Microplastic-associated biofilms: rRNA operon profiles

| PRJNA780327 | ENA

forest microbiome

Project description:forest microbiome Raw sequence reads

| PRJNA782644 | ENA

Vaccinium

Project description:Blueberry Raw sequence reads

| PRJNA353989 | ENA

uncultured prokaryote

Project description:16S rRNA amplicon from forest subsurface soil Raw sequence reads

| PRJNA379156 | ENA