Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1086467 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR28325350_1.fastq.gz | Fastqsanger.gz | |||
| SRR28325350_2.fastq.gz | Fastqsanger.gz | |||
| SRR28325351_1.fastq.gz | Fastqsanger.gz | |||
| SRR28325351_2.fastq.gz | Fastqsanger.gz |
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Project description:Conditions of low organic matter content per gram of soil in the hyperarid core of the Atacama Desert, extreme temperatures and high UV radiation, makes it one of the best terrestrial analogue of Mars and one of the best scenarios for testing instrumentation devoted to in situ planetary exploration. We have remotely and automatically operated the SOLID-LDChip, an antibody microarray-based sensor instrument, as part of a rover payload during the 2019 NASA’s ASTEP ARADS Mars drilling simulating campaign. SOLID was loaded with a robotic arm with samples collected down to 80 cm depth and, after sample analysis with LDChip, sent results to a remote science team, to be validated by “omics” techniques.
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2012-05-31 | E-GEOD-37124 | biostudies-arrayexpress
Project description:Scaffold or matrix attachment regions (S/MARs) are found in all eukaryotes. The pattern of distribution and genomic context of S/MARs is thought to be important for processes such as chromatin organization and modulation of gene expression. Despite the importance of such processes, much is unknown about the large-scale distribution and sequence content of S/ MARs in vivo. Here, we report the use of tiling microarrays to map 1358 S/MARs on Arabidopsis thaliana chromosome 4 (chr4). S/MARs occur throughout chr4, spaced much more closely than in the large plant and animal genomes that have been studied to date. Arabidopsis S/MARs can be divided into five clusters based on their association with other genomic features, suggesting a diversity of functions. While some Arabidopsis S/MARs may define structural domains, most occur near the transcription start sites of genes. Genes associated with these S/MARs have an increased probability of expression, which is particularly pronounced in the case of transcription factor genes. Analysis of sequence motifs and 6-mer enrichment patterns show that S/MARs are preferentially enriched in poly(dA:dT) tracts, sequences that resist nucleosome formation, and the majority of S/MARs contain at least one nucleosome-depleted region. This global view of S/MARs provides a framework to begin evaluating genome-scale models for S/MAR function.
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Project description:Scaffold or matrix attachment regions (S/MARs) are found in all eukaryotes. The pattern of distribution and genomic context of S/MARs is thought to be important for processes such as chromatin organization and modulation of gene expression. Despite the importance of such processes, much is unknown about the large-scale distribution and sequence content of S/ MARs in vivo. Here, we report the use of tiling microarrays to map 1358 S/MARs on Arabidopsis thaliana chromosome 4 (chr4). S/MARs occur throughout chr4, spaced much more closely than in the large plant and animal genomes that have been studied to date. Arabidopsis S/MARs can be divided into five clusters based on their association with other genomic features, suggesting a diversity of functions. While some Arabidopsis S/MARs may define structural domains, most occur near the transcription start sites of genes. Genes associated with these S/MARs have an increased probability of expression, which is particularly pronounced in the case of transcription factor genes. Analysis of sequence motifs and 6-mer enrichment patterns show that S/MARs are preferentially enriched in poly(dA:dT) tracts, sequences that resist nucleosome formation, and the majority of S/MARs contain at least one nucleosome-depleted region. This global view of S/MARs provides a framework to begin evaluating genome-scale models for S/MAR function. Contrast between DNA bound to nuclear scaffold/matrix and total genomic DNA in Arabidopsis Chr4 excluding the constitutive heterochromatin. Total of three biological replicates with two independent hybridizations on custom-designed NimbleGen high-density microarrays that include duplicate spots for each probe.
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Project description:Ouyang2014 - photomorphogenic UV-B signalling
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This model is described in the article:
Coordinated photomorphogenic
UV-B signaling network captured by mathematical modeling.
Ouyang X, Huang X, Jin X, Chen Z,
Yang P, Ge H, Li S, Deng XW.
Proc. Natl. Acad. Sci. U.S.A. 2014 Aug;
111(31): 11539-11544
Abstract:
Long-wavelength and low-fluence UV-B light is an
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signaling have been experimentally characterized over the past
decade, including the UV-B light receptor UV resistance locus
8; the positive regulators constitutive photomorphogenesis 1
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these proteins function in either positive or negative
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transduction of photomorphogenic UV-B signal. Less is known,
however, regarding how these signaling events are
systematically linked. In our study, we use a systems biology
approach to investigate the dynamic behaviors and correlations
of multiple signaling components involved in Arabidopsis
UV-B-induced photomorphogenesis. We define a mathematical
representation of photomorphogenic UV-B signaling at a temporal
scale. Supplemented with experimental validation, our
computational modeling demonstrates the functional interaction
that occurs among different protein complexes in early and
prolonged response to photomorphogenic UV-B.
This model is hosted on
BioModels Database
and identified by:
BIOMD0000000545.
To cite BioModels Database, please use:
BioModels Database:
An enhanced, curated and annotated resource for published
quantitative kinetic models.
To the extent possible under law, all copyright and related or
neighbouring rights to this encoded model have been dedicated to
the public domain worldwide. Please refer to
CC0
Public Domain Dedication for more information.
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