Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1156782 | ENA |
REPOSITORIES: ENA
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Project description:Pseudo-nitzschia multiseries (Ps-n) is a toxigenic marine diatom that produces the neurotoxin, domoic acid. We screened for candidate genes that may be involved in domoic acid production by determining changes in transcript profiles in Ps-n cultures that were in late exponential (low-domoic-acid-producing) vs. stationary (high-domoic-acid-producing) growth states. We also identified a number of candidate reference genes for future RT-qPCR studies, based on their stability in this study. Ps-n RNA was extracted from late exponential and stationary phase cultures. Experiments included one axenic culture, and two non-axenic cultures. Experiments were dye-swapped to account for differences in dye labeling and detection efficiencies: a) the axenic culture experiment included 4 technical replicate arrays (i.e., 2 dye-swapped experiments = 4 total hybridizations), and b) the non-axenic culture experiments each included 6 technical replicate arrays (i.e., 3 dye-swapped experiments = 6 total hybridizations).
2013-09-08 | E-GEOD-46845 | biostudies-arrayexpress
Project description:Non-axenic microalgae culture Raw sequence reads
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Project description:Chronic non-healing venous leg ulcers (VLUs) are a widespread debilitating disease with high morbidity and associated costs, as approximately $15 billion annually are spent on the care of VLUs. Despite their socioeconomic burden, there is a paucity of novel treatments targeted towards healing VLUs, which can be attributed to both lack of pathophysiologic insight into VLU development as well as lack of knowledge regarding biologic actions of VLU-targeted therapies. Currently, the bioengineered bilayered living cellular construct (BLCC) skin substitute is the only FDA-approved biologic treatment for healing VLUs. To elucidate the mechanisms through which the BLCC promotes healing of chronic VLUs, we conducted a clinical trial (NCT01327937) in which patients with non-healing VLUs were treated with either standard care (compression therapy) or with BLCC together with standard care. Tissue was collected from the VLU edge before and 1 week after treatment, and samples underwent comprehensive microarray, mRNA and protein analyses. Ulcers treated with BLCC skin substitute displayed three distinct patterns suggesting the mechanisms by which BLCC shifted a non-healing into a healing tissue response: it modulated inflammatory and growth factor signaling; it activated keratinocytes; and it attenuated Wnt/β-catenin signaling. In these ways, BLCC application orchestrated a shift of the chronic non-healing ulcer microenvironment into a distinctive healing milieu resembling that of an acute, healing wound. Our findings also provide first patient-derived in vivo evidence of specific biologic processes that can be targeted in the design of therapies to promote healing of chronic VLUs.
2016-09-01 | GSE84571 | GEO
Project description:CACIAM 19 non-axenic culture genome sequencing and assembly
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Project description:Genome-wide expression analysis in C. Elegans grown in axenic media with low to toxic selenium concentrations We performed Affymetrix micorarray-based transcriptional profiling on wild-type C. Elegans Bristol N2 grown in low Se axenic media supplemented with five concentrations of selenium, from low to toxic, and harvested at the L4-larva stage. RNA was prepared for hybridization to Affy microarrays from synchronized cultures of wild-type C. elegans seeded in low Se axenic media, supplemented with graded 0, 0.05, 0.1, 0.2, and 0.4 mM Se added as sodium selenite, and harvested at the L4-larva stage (1 culture/sample per Se concentgration).
2014-07-03 | E-GEOD-54011 | biostudies-arrayexpress