Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Midge larval habitat soil

ABSTRACT: Midge larval habitat soil Raw sequence reads

PROVIDER: PRJNA862140 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR20652029_1.fastq.gz	Fastqsanger.gz
	SRR20652029_2.fastq.gz	Fastqsanger.gz
	SRR20652030_1.fastq.gz	Fastqsanger.gz
	SRR20652030_2.fastq.gz	Fastqsanger.gz
	SRR20652031_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 88

Similar Datasets

Differential expression for rice-gall midge interaction

Project description:We exposed Kavya rice seedlings to different gall midge biotypes, GMB1 and GMB4M, which exhibit incompatible and compatible interactions, respectively.

2011-11-16 | GSE22538 | GEO

Habitat type and host grazing regimen influence the soil microbial diversity and communities within potential biting midge larval habitats.

Project description: Not available

| S-EPMC9854200 | biostudies-literature

Submerged Analog Habitat Environment

Project description:Submerged Analog Habitat Environment Raw sequence reads

| PRJNA639658 | ENA

Unlocking soil carbon potential in giant panda habitat

Project description:<p>Forest management in giant panda habitats necessitates strategies that simultaneously support biodiversity and ecosystem carbon sequestration. Here, we demonstrate that protecting understory vegetation is indispensable for sustaining the soil carbon sink in restored subalpine coniferous plantations. Through a field experiment comparing natural forest with unthinned and thinned plantations (with or without understory removal), we uncovered a critical microbial mechanism. Understory removal triggered a detrimental cascade by elevating soil pH and shifting the carbon pool from labile to recalcitrant dominance. This environmental shift imposed a strong deterministic filter (Normalized stochasticity ratio, NST = 39.8%) on the microbial community, displacing pH-sensitive, labile carbon-dependent taxa (e.g., Gaiella) while enriching oligotrophs adept at recalcitrant carbon degradation (e.g., Ktedonobacter, Streptomyces). Community restructuring drove a functional metamorphosis: it reduced antibiotic synthesis and, under the dual stress of high pH and carbon quality decline, induced a novel RNA modification response (via N4-acetylcytidine accumulation) that enhanced the synthesis of recalcitrant carbon-degrading enzymes. Crucially, these adaptations precipitated a significant decline in microbial carbon use efficiency (CUE), shifting the soil carbon cycle from an accumulation to an inefficient consumption phase. Our findings provide a mechanistic basis for using understory vegetation as a primary tool to align giant panda habitat conservation with climate-smart forestry goals.</p>

2025-12-02 | MTBLS13433 | MetaboLights

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

Differential expression for rice-gall midge interaction

Project description:We exposed Kavya rice seedlings to different gall midge biotypes, GMB1 and GMB4M, which exhibit incompatible and compatible interactions, respectively. Expression study in Kavya seedlings using pooled samples of stem meristematic tissues 24, 48, 96, and 120 hr after GMB1 and GMB4M infestation when compared with uninfested control. Three replicates each condition.

2011-11-16 | E-GEOD-22538 | biostudies-arrayexpress

Larval habitat determine the bacterial and fungal microbiota of the mosquito vector Aedes aegypti

Project description:Larval habitat determine the bacterial and fungal microbiota of the mosquito vector Aedes aegypti

| PRJEB45062 | ENA

Multi-omics deciphers details of chitin decomposition in soil by a model bacterial consortium.

Project description:Soil microorganisms carry out decomposition of complex organic carbon molecules, such as chitin. High diversity of the soil microbiome and complexity of the soil habitat has posed a challenge to elucidate specific interactions between soil microorganisms. Here, we overcame this challenge by studying a model soil consortium (MSC-2) that is composed of 8 species. The MSC-2 isolates were originally obtained from the same soil that was enriched with chitin as a substrate. Our aim was to elucidate specific roles of the 8 member species during chitin metabolism in soil. The 8 species were added to sterile soil with chitin and incubated for 3 months. Multi-omics was used to understand how the community composition, transcript and protein expression and chitin-related metabolites shifted during the incubation period. The data clearly and consistently revealed a temporal shift during chitin decomposition and defined contributions by individual species. A Streptomyces species was a key player in early steps of chitin decomposition, followed by other members of MSC-2. These results illustrate how multi-omics applied to a defined consortium untangles complex interactions between soil microorganisms.

2025-02-01 | GSE251759 | GEO

Coral larval microbiome ontogeny

Project description:Coral larval microbiome ontogeny Raw sequence reads

| PRJNA1113312 | ENA

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

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data