Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Rare biosphere texture

ABSTRACT: Probing the texture of the rare biosphere: We have bracketed the dimensions of the rare biosphere in two marine bacterial samples by comparing a deep (1 million sequences per sample) pyrosequencing analysis of the two samples and the cultures isolated from one of them.

PROVIDER: PRJEB9061 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	ERR852100.fastq.gz	Fastqsanger.gz
	ERR852101.fastq.gz	Fastqsanger.gz
	ERR852102.fastq.gz	Fastqsanger.gz
	ERR852103.fastq.gz	Fastqsanger.gz

Items per page:

1 - 4 of 4

Similar Datasets

Marine biosphere

Project description:Marine biosphere Targeted loci

| PRJNA761870 | ENA

Deep biosphere of El'gygytgyn Crater Lake Sediments

Project description:Analyzing the deep biosphere of up to 3.6 million years old El’gygytgyn Crater Lake sediments

| PRJEB9144 | ENA

Linking Lacustrine Deep Biosphere and Sediment Substrates along a Million-Year Ferruginous Archive

Project description:Lacustrine Deep Biosphere and Sediment Substrates along a Million-Year Ferruginous Archive

| PRJEB85713 | ENA

El Vizcaino Biosphere Reserve Goat Fecal Samples

Project description:El Vizcaino Biosphere Reserve Goat Fecal Samples Raw sequence reads

| PRJNA721080 | ENA

Transcriptome profiling of cultivar-specific apple fruit ripening and texture attributes

Project description:Molecular events regulating apple fruit ripening and sensory quality are largely unknown. Such knowledge is essential for genomic-assisted apple breeding and postharvest quality management. In this study, a parallel transcriptome profile analysis, scanning electron microscopic (SEM) examination and systematic physiological characterization were performed on two apple cultivars, Honeycrisp (HC) and Cripps Pink (CP), which have distinct ripening features and texture attributes. Systematic physiological characterization of fruit ripening based on weekly maturity data indicated substantial differences in fruit crispness and firmness at comparable ripening stages. SEM images of fruit cortex tissues prepared from fruits with equivalent maturity suggested that the cell wall thickness may contribute to the observed phenotypes of fruit firmness and crispness. A high-density long-oligo apple microarray consisting of duplex 190,135 cross-hybridization-free 50-70-mer isothermal probes, and representing 23,997 UniGene clusters, was manufactured on a Nimblegen array platform. Transcriptome profiling identified a total of 1793 and 1209 UniGene clusters differentially expressed during ripening from cortex tissues of HC and CP, respectively. UniGenes implicated in hormone metabolism and response, cell wall biosynthesis and modification and those encoding transcription factors were among the prominent functional groups. Between the two cultivars, most of the identified UniGenes were similarly regulated during fruit ripening; however, a short list of gene families or specific family members exhibited distinct expression patterns between the two cultivars, which may represent candidate genes regulating cultivar-specific apple fruit ripening patterns and quality attributes.

2010-11-05 | GSE24523 | GEO

Deep Biosphere - Beatrix 326 BH2 (270712)

Project description:This project aims to investigate the metabolic pathways expressed by the active microbial community occurring at the deep continental subsurface. Subsurface chemoLithoautotrophic Microbial Ecosystems (SLiMEs) under oligotrophic conditions are supported by H2; however, the overall ecological trophic structures of these communities are poorly understood. Some deep, fluid-filled fractures in the Witwatersrand Basin, South Africa appear to support inverted trophic pyramids wherein methanogens contributing <5% of the total DNA apparently produce CH4 that supports the rest of the community. Here we show the active metabolic relationships of one such trophic structure by combining metatranscriptomic assemblies, metaproteomic and stable isotopic data, and thermodynamic modeling. Four autotrophic β-proteobacteria genera that are capable of oxidizing sulfur by denitrification dominate. They co-occur with sulfate reducers, anaerobic methane oxidizers and methanogens, which each comprises <5% of the total community. Defining trophic levels of microbial chemolithoautotrophs by the number of transfers from the initial abiotic H2-driven CO2 fixation, we propose a top-down cascade influence of the metabolic consumers that enhances the fitness of the metabolic producers to explain the inverted biomass pyramid of a multitrophic SLiME. Symbiotic partnerships are pivotal in the deep biosphere on and potentially beyond the Earth.

2018-10-27 | PXD004634 | Pride

Whole-genome transcriptomic analysis in Sorghum bicolor variety CSV24SS

Project description:We report transcriptome profiling of middle internode tissues from four development stages and three soil moisture readings representing progressive drought stress in sweet sorghum. Sequencing of 14 libraries (two biological replicates for each stage). Each replicate yielded an average of 86 million reads per sample for developmental stages and drought stressed samples yielded an average of 74 million reads per sample .

2023-12-31 | GSE155194 | GEO

Whole-genome transcriptomic analysis from stem internodes in Sorghum bicolor variety ICSV12012

2023-12-31 | GSE178993 | GEO

Whole-genome transcriptomic analysis in Sorghum bicolor variety M35-1

Project description:We report transcriptome profiling of middle internode tissues from four development stages and three soil moisture readings representing progressive drought stress in grain sorghum. Sequencing of 14 libraries (two biological replicates for each stage). Each replicate yielded an average of 86 million reads per sample for developmental stages and drought stressed samples yielded an average of 74 million reads per sample .

2023-12-31 | GSE178603 | GEO

Integrating a genome-wide association study with a large-scale transcriptome analysis to predict genetic regions influencing the glycemic index and texture in rice

Project description:Reliably generating rice varieties with low glycemic index (GI) is an important nutritional intervention given the high rates of Type II diabetes incidences in Asia where rice is staple diet. We integrated a genome-wide association study (GWAS) with a transcriptome-wide association study (TWAS) to determine the genetic basis of the GI in rice. GWAS utilized 305 re-sequenced diverse indica panel comprising ~2.4 million single nucleotide polymorphisms (SNPs) enriched in genic regions. A novel association signal was detected at a synonymous SNP in exon 2 of LOC_Os05g03600 for intermediate-to-high GI phenotypic variation. Another major hotspot region was predicted for contributing intermediate-to-high GI variation, involves 26 genes on chromosome 6 (GI6.1). These set of genes included GBSSI, two hydrolase genes, genes involved in signalling and chromatin modification. The TWAS and methylome sequencing data revealed cis-acting functionally relevant genetic variants with differential methylation patterns in the hot spot GI6.1 region, narrowing the target to 13 genes. Conversely, the promoter region of GBSSI and its alternative splicing allele (G allele of Wxa) explained the intermediate-to-high GI variation. A SNP (C>T) at exon-10 was also highlighted in the preceding analyses to influence final viscosity (FV), which is independent of amylose content/GI. The low GI line with GC haplotype confirmed soft texture, while other two low GI lines with GT haplotype were characterized as hard and cohesive. The low GI lines were further confirmed through clinical in vivo studies. Gene regulatory network analysis highlighted the role of the non‑starch polysaccharide pathway in lowering GI.

2019-02-01 | GSE123616 | 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