CbStrStra4
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB71552 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Straminergon stramineum (straw spear-moss), genomic and transcriptomic data
| PRJEB70977 | ENA
Project description:High-throughput sequencing of endogenous small RNAs from the moss Physcomitrella patens. This dataset encompasses microRNAs and other small RNAs of ~20-24 nucleotides expressed in the moss P. patens. SAMPLES UPDATED JULY 9, 2007 TO INCLUDE DATA ON SEQUENCED SMALL RNAS THAT DO NOT MATCH THE P. PATENS GENOME Keywords: High throughput small RNA sequencing
2006-08-15 | GSE5103 | GEO
Project description:Spear-ATAC is a modified droplet-based single-cell ATAC-seq (scATAC-seq) protocol that enables simultaneous read-out of chromatin accessibility profiles and integrated sgRNA spacer sequences from thousands of individual cells at once. Spear-ATAC profiling of 104,592 cells representing 414 sgRNA knock-down populations across three experiments revealed the temporal dynamics of epigenetic responses to regulatory perturbations in cancer cells and the associations between transcription factor binding profiles, demonstrating a high-throughput method for perturbing and evaluating dynamic single-cell epigenetic states.
2021-03-14 | GSE168851 | GEO
Project description:To determine whether and how warming affects the functional capacities of the active microbial communities, GeoChip 5.0 microarray was used. Briefly, four fractions of each 13C-straw sample were selected and regarded as representative for the active bacterial community if 16S rRNA genes of the corresponding 12C-straw samples at the same density fraction were close to zero.
2023-12-30 | E-MTAB-13326 | biostudies-arrayexpress
Project description:4plex_physco_2014-05 - ppmax2 response to gr24 - How does the Ppmax2 moss mutant respond to Strigolactone (GR24)? - Two moss genotypes are used: WT and the Ppmax2 mutant. Moss tissues are fragmented, then plated on medium (Petri dish with cellophane disks) and cultivated for 3 weeks. Moss tissues are then transfered for 6 hours on acetone-containing medium (control treatment, for WT and Ppmax2) or GR24 (1 microM, in acetone)-containing medium (for Ppmax2). After 6 hours, the moss tissues are collected, quickly forzen in liquid nitrogen. RNA are isolated using the Quiagen RNeasy Plant mini kit (including a RNase-free DNase treatment on column). Two similar experiments (T1 and T2) have been led.
2017-04-22 | GSE80578 | GEO
Project description:<p>Background:</p><p>Primary succession is predicted to proceed through shifts from stress-tolerant to competitive to cooperative ecological strategies as resource availability increases, yet molecular evidence for these transitions in microbial systems remains limited. Here, we used an integrated multi-omics approach to investigate how microbial functional traits and chemical outputs change across early ecosystem development using experimental basaltic hillslopes spanning succession from bare rock through biocrust to moss-dominated communities.</p><p> </p><p>Results:</p><p>Genome-resolved analyses revealed stress-tolerant pioneer communities enriched in oxidative and temperature stress-response genes on nitrogen-limited and physically unstable basalt. These communities were replaced by competitive nitrogen-fixing cyanobacteria that formed biocrusts enriched in carbon and nitrogen fixation pathways while stabilizing substrates through exopolysaccharide production. This stabilization enabled the establishment of functionally diverse moss-associated communities characterized by complete biogeochemical cycling and cooperative metabolic interactions. Metabolomic profiling linked these functional transitions to distinct chemical signatures across succession. Early stages were enriched in organic nitrogen- and sulfur-containing compounds, intermediate stages accumulated nucleosides and organic acids, and later stages were characterized by complex lipids and secondary metabolites. Metabolites discriminated successional stages with substantially higher accuracy than taxonomic markers, indicating that functional outputs in this system more reliably capture ecosystem state than community composition. While microbial community assembly shifted from stochastic to deterministic processes over succession, metabolite assembly remained predominantly deterministic throughout.</p><p> </p><p>Conclusions:</p><p>Integration across genomic and metabolomic data demonstrates that cyanobacterial nitrogen fixation coupled with substrate stabilization alleviates nutrient limitation and modifies physical habitat conditions, driving successional progression through ecological strategy shifts. These results advance succession theory by showing that biogeochemical and physical processes operate in tandem rather than sequentially. These molecular insights provide the first comprehensive evidence for predicted ecological strategy shifts at the molecular level and offer a framework for ecosystem monitoring and restoration, with stage specific metabolic signatures serving as quantitative biomarkers for assessing recovery trajectories.</p>
2026-03-12 | MTBLS14041 | MetaboLights
Project description:Wheat straw grown cultures of T. reesei QM9414 were supplemented with 100 µM L-methionine and the genome wide gene expression monitored in order to find novel L-Methionine repressible genes.
2015-06-11 | GSE69745 | GEO
Project description:Ahmad2017 - Genome-scale metabolic model
(iGT736) of Geobacillus thermoglucosidasius (C56-YS93)
This model is described in the article:
A Genome Scale Model of
Geobacillus thermoglucosidasius (C56-YS93) reveals its
biotechnological potential on rice straw hydrolysate
Ahmad Ahmada, Hassan B. Hartmanb, S.
Krishnakumara, David A. Fellb, Mark G. Poolmanb, Shireesh
Srivastavaa
Journal of Biotechnology
Abstract:
Rice straw is a major crop residue which is burnt in many
countries, creating significant air pollution. Thus,
alternative routes for disposal of rice straw are needed.
Biotechnological treatment of rice straw hydrolysate has
potential to convert this agriculture waste into valuable
biofuel(s) and platform chemicals. Geobacillus
thermoglucosidasius is a thermophile with properties specially
suited for use as a biocatalyst in lignocellulosic
bioprocesses, such as high optimal temperature and tolerance to
high levels of ethanol. However, the capabilities of
Geobacillus thermoglucosidasius to utilize sugars in rice straw
hydrolysate for making bioethanol and other platform chemicals
have not been fully explored. In this work, we have created a
genome scale metabolic model (denoted iGT736) of the organism
containing 736 gene products, 1159 reactions and 1163
metabolites. The model was validated both by purely theoretical
approaches and by comparing the behaviour of the model to
previously published experimental results. The model was then
used to determine the yields of a variety of platform chemicals
from glucose and xylose — two primary sugars in rice
straw hydrolysate. A comparison with results from a model of
Escherichia coli shows that Geobacillus thermoglucosidasius is
capable of producing a wider range of products, and that for
the products also produced by Escherichia coli, the yields are
comparable. We also discuss strategies to utilise arabinose, a
minor component of rice straw hydrolysate, and propose
additional reactions to lead to the synthesis of xylitol, not
currently produced by Geobacillus thermoglucosidasius. Our
results provide additional motivation for the current
exploration of the industrial potential of Geobacillus
thermoglucosidasius and we make our model publicly available to
aid the development of metabolic engineering strategies for
this organism.
This model is hosted on
BioModels Database
and identified by:
MODEL1703060000.
To cite BioModels Database, please use:
BioModels Database:
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quantitative kinetic models.
To the extent possible under law, all copyright and related or
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Public Domain Dedication for more information.
2017-04-12 | MODEL1703060000 | BioModels
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.
2013-04-01 | GSE44648 | GEO