Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Targeted amplicon sequencing of mixed microbial communities

ABSTRACT: The microbial community of liquid cultures, containing wheat straw as a sole carbon source, were investigated over eight weeks using ITS and 16S sequencing

PROVIDER: PRJEB38167 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	ERR5696870.fastq.gz	Fastqsanger.gz
	ERR5696871.fastq.gz	Fastqsanger.gz
	ERR5696872.fastq.gz	Fastqsanger.gz
	ERR5696873.fastq.gz	Fastqsanger.gz
	ERR5696874.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 12

Similar Datasets

Transcriptome Sequencing of Solid Fermentation under Different Induced Carbon Sources

Project description:Here comparative transcriptomic analyses of Penicillium oxalicum grown on wheat bran (WB), WB plus rice straw (WR) and WB plus Avicel (WA) as the sole carbon source under solid-state fermentation (SSF) revealed that most of differentially expressed genes (DEGs) were involved in metabolism specifically carbohydrate metabolism.

2019-10-15 | GSE131173 | GEO

Genome-wide transcriptional response of the filamentous fungus Trichoderma reesei to lignocellulose using RNA sequencing and comparison with Aspergillus niger

Project description:The induction of genes in response to exposure of T. reesei to wheat straw was explored using genome-wide RNA-seq and compared to published RNA-seq data and model of how A. niger senses and responds to the lignocellulose. After 24 h of exposure to straw, transcript levels of known and predicted lignocellulose-degrading enzymes increased to around 8% of total cellular mRNA in T. reesei, which was much less when compared to A. niger. The bulk of enzymes used to deconstruct wheat straw is similar in both fungi. Other, non-plant cell wall-degrading enzymes which may aid in lignocellulose degradation were also uncovered in T. reesei and similar to those described in A. niger. Antisense transcripts were also shown to be present in T. reesei and their expession can be regulated by the respective growth condition. Triplicate samples of T. reesei cultivated in each of the three following conditions were taken: 1) After 48 h growth in glucose-based minimal media; 2) After transfer of mycelia from glucose-based media into media containing wheat straw as a sole carbon source and 3) 5 h after addition of glucose to straw cultures.

2013-04-01 | E-GEOD-44648 | biostudies-arrayexpress

A transcriptomic analysis of Neurospora crassa using five major crop residues and the novel role of the sporulation regulator rca-1 in lignocellulase production

Project description:Comparative transcriptional profiling of N. crassa grown on five major crop straws of China (barley, corn, rice, soybean and wheat straws) revealed a highly overlapping group of 430 genes, the Biomass commonly Induced Core Set (BICS). A large proportion of induced carbohydrate-active-enzyme (CAZy) genes (82 out of 113) were also conserved across the five plant straws. Excluding 178 genes within the BICS that were also up-regulated under no-carbon conditions, the remaining 252 genes were defined as the Biomass Regulon (BR). Interestingly, 88 genes were only induced by plant biomass and not by three individual polysaccharides (Avicel, xylan, and pectin); these were denoted as the Biomass Unique Set (BUS). Deletion of one BUS gene, the transcriptional regulator rca-1, significantly improved lignocellulase production using plant biomass as the sole carbon source, possibly functioning via de-repression of the regulator clr-2. Thus, this result suggests that rca-1 is a potential engineering target for biorefineries, especially for plant biomass direct microbial conversion processes. Conidia of Neurospora crass wild type were inoculated at 10^6 conidia/mL into 100 mL 1×Vogel’s salts with 2% (w/w) ground crop straws, barley straw, corn straw, rice straw, soybean straw and wheat straw respectively for 30 h or 2% sucrose for 16 h. Then, mycelia were harvested through filtration and immediately frozen in liquid nitrogen.Total RNA from frozen sample was isolated with TRIzol reagent (Invitrogen) and further treated with DNase I (RNeasy Mini Kit, QIAGEN). The qualified RNA was prepared with standard protocol from Shenzhen BGI (China) and sequenced on the Illumina HiSeqTM 2000 platform.

2015-01-21 | E-GEOD-60986 | biostudies-arrayexpress

Genome-wide Transcriptional Responses of the Filamentous Fungus Aspergillus niger to Lignocellulose (Wheat straw) using RNA-sequencing

Project description:We have studied the physiological response of the fungus Aspergillus niger when exposed to wheat straw as a model lignocellulosic substrate. Using RNA-sequencing we showed that, 24 hours after exposure to straw, gene expression of known plant cell wall degrading enzymes represents a huge investment for the cells (about 20 % of the total mRNA). Our results also uncovered new esterases and surface interacting proteins that might form part of the fungal degradative arsenal. We also show that antisense transcripts are abundant and that their expression can be regulated by conditions. Triplicate samples of A. niger N402 taken at each of three timepoints: After 48 h growth in minimal media with Glucose as sole carbon source, After transfer to Wheat Straw media for 24 h and 5 h after after the exogenous addition of glucose to the wheat starw media.

2012-08-27 | E-GEOD-33852 | biostudies-arrayexpress

The role of carbon starvation in the induction of enzymes that degrade plant-derived carbohydrates in Aspergillus niger

Project description:Fungi are an important source of enzymes for saccharification of plant polysaccharides and production of biofuels. Understanding of the regulation and induction of expression of genes encoding these enzymes is still incomplete. To explore the induction mechanism, we analysed the response of the industrially important fungus Aspergillus niger to wheat straw, with a focus on events occurring shortly after exposure to the substrate. RNA sequencing showed that over a third of the genes induced after 6 h of exposure to wheat straw were also induced during 6 h of carbon starvation, indicating that carbon starvation is probably an important factor in the early response to wheat straw. The up-regulation of the expression of a high number of genes encoding CAZymes that are active on plant-derived carbohydrates during early carbon starvation suggests that these enzymes could be involved in a scouting role during starvation, releasing inducing sugars from complex plant polysaccharides. Eight samples in total consisting of duplicate shake flask Aspergillus niger cultures from four conditions: 48h glucose, 6 h starvation, 6 h wheat straw, 24 h starvation

2014-08-22 | E-GEOD-57315 | biostudies-arrayexpress

Measuring transcriptional differences between Caulobacter crescentus cultured in nitrate versus ammonium as the sole nitrogen source

Project description:This study is measuring the steady-state levels of mRNA in wild-type Caulobacter crescentus grown in M2 defined medium containing either ammonium or nitrate as the sole nitrogen source.

2010-06-21 | GSE21203 | GEO

Neosartorya fischeri Comparative Transcriptome when the fungi uses a differente carbon source, petroleum asphaltenes or glucose-peptona

Project description:Neosartorya fischeri is a fungi that is able to grow in petroleum asphaltenes as sole carbon source. Here, was investigated which enzymes were up regulated

2015-04-23 | GSE68146 | GEO

To identify novel targets of a zinc finger transcription factor, Mxr1p in Pichia pastoris cultured in medium containing ethanol

Project description:The role of transcription factor Mxr1p has so far been studied in methanol, amino acid and acetate metabolism. We have demonstrated a key role of Mxr1p in regulation of ethanol metabolism when cells are cultured in medium containing ethanol as sole carbon source. We employed RNA Seq to identify new targets of Mxr1p in medium containing ethanol.

2021-09-22 | GSE168677 | GEO

Gene expression for Escherichia coli BW25113 exponential growth on minimal medium with eight different carbon sources: Glucose, Galactose, Glycerol, Gluconate, Fructose, Pyruvate, Succinate, Acetate.

Project description:This dataset contains the gene expression signature in triplicates of Escherichia coli BW25113 growing exponentially on eight different environments: minimal medium supplemented with 5 g/L of Glucose, Galactose, Glycerol, Gluconate, Fructose, Pyruvate, Succinate or Acetate as the sole carbon source.

2015-10-07 | E-MTAB-3392 | biostudies-arrayexpress

Transcriptome analysis of Arabidopsis wild-type and NRT1.1-knockout mutant seedlings grown under 10 mM ammonium as sole nitrogen source

Project description:High levels of ammonium as the sole nitrogen source impairs plant growth, i.e. ammonium toxicity, the primary cause of which remains to be determined. To obtain a clue about the toxic mechanism, we compared genome-wide gene expression between the wild-type (Col) and NRT1.1-knockout mutant (chl1-5, nrt1.1) seedlings growing in media containing toxic levels of ammonium as the sole nitrogen source.

2023-10-31 | E-MTAB-13395 | biostudies-arrayexpress

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