Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1135455 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Soil microorganisms carry out decomposition of complex organic carbon molecules, such as chitin. High diversity of the soil microbiome and complexity of the soil habitat has posed a challenge to elucidate specific interactions between soil microorganisms. Here, we overcame this challenge by studying a model soil consortium (MSC-2) that is composed of 8 species. The MSC-2 isolates were originally obtained from the same soil that was enriched with chitin as a substrate. Our aim was to elucidate specific roles of the 8 member species during chitin metabolism in soil. The 8 species were added to sterile soil with chitin and incubated for 3 months. Multi-omics was used to understand how the community composition, transcript and protein expression and chitin-related metabolites shifted during the incubation period. The data clearly and consistently revealed a temporal shift during chitin decomposition and defined contributions by individual species. A Streptomyces species was a key player in early steps of chitin decomposition, followed by other members of MSC-2. These results illustrate how multi-omics applied to a defined consortium untangles complex interactions between soil microorganisms.
2025-02-01 | GSE251759 | GEO
Project description:This study tested the effects of repeated social defeat (RSD) on gene expression in peripheral blood monocytes and examined the extent to which these effects were abrogated by the beta-adrenergic antagonist propranolol. Study Type: Risk prediction Gene expression profiling was carried out on peripheral blood monocyte mRNA samples collected from 36 mice randomized to either 6 cycles of repeated social defeat (RSD, n=18) or to parallel home cage control (HCC, n=18) conditions. Within each condition (RSD vs HCC), 9 animals were treated with the beta-adrenergic antagonist propranolol and 9 were treated with an equivalent volume of vehicle. After 6 cycles of RSD or parallel HCC, blood samples were pooled into groups of n=3 samples in each condition, and Illumina Mouse Ref-8 BeadArray assays were performed on RNA from approximately 1 million CD11b+ peripheral blood mononuclear cells (i.e., monocytes) which were immunomagnetically isolated by MACS. The primary research questions are 1) whether expression of pro-inflammatory genes is altered by RSD, and 2) whether treatment with propranolol abrogates these effects.
2013-11-04 | E-GEOD-47153 | biostudies-arrayexpress
Project description:Investigation of whole genome gene expression level changes in early generation Caenorhabditis elegans Bristol N2 rsd-2 and Bristol N2 rsd-6 single mutants, compared to late-generation strains at 25°C and 20°C A six chip study using total RNA recovered from two separate alleles of Caenorhabditis elegans Bristol N2 rsd-2 and one allele Bristol N2 rsd-6 , in which the effects of transgeneration aging are studied in early generation animals and late generation animals at the restrictive temperature of 25°C and the permissive temperature, 20°C.
2013-06-01 | E-GEOD-40459 | biostudies-arrayexpress
Project description:Attempt to identify progressive changes in small non-coding RNA levels in C.elegans lacking RSD-2 or RSD-6.
2013-06-01 | GSE40457 | GEO
Project description:The gene expression profile of MC4100 delta rsd with pACYC Rsd and pACYC delta BS plasmids has been analysed using whole genome oligonucleotide microarrays. Control RNA was isolated from 50ml LB cultures of MC4100 delta rsd strain with pACYC delta BS. Experimental RNA was isolated from 50ml LB cultures of MC4100 delta rsd with pACYC Rsd, for each growth condition (OD600 = 0.4: log phase, 0.9: late log phase, 1.1: transition phase, ST(OD600 = >2.0): stationary phase). The experiments performed replicate. Keywords: timecourse (overproduction of Rsd)
2007-10-22 | GSE5981 | GEO
Project description:This study tested the effects of repeated social defeat (RSD) on gene expression in peripheral blood mononuclear cells (PBMC), and examined the extent to which these effects were abrogated by depletion of CD11b+ cells (monocytes). Study Type: Risk prediction Gene expression profiling was carried out on peripheral blood mononuclear cell (PBMC) mRNA samples collected from 18 mice randomized to either 6 cycles of repeated social defeat (RSD, n=9) or to home cage control (HCC, n=9) conditions. PBMC samples were pooled into 3 groups of n=3 samples in each condition, and Illumina Mouse Ref-8 BeadArray assays were performed on approximately 1 million total PBMC and 1 million PBMC from which CD11b+ cells were immunomagnetically depleted by MACS. The primary research questions are 1) whether expression of pro-inflammatory genes is altered by RSD, and 2) whether depletion of CD11b+ cells (monocytes) abrogates these effects.
2013-11-04 | E-GEOD-47154 | biostudies-arrayexpress
Project description:This study tested the effects of repeated social defeat (RSD) on gene expression in peripheral blood monocytes and examined the extent to which these effects were abrogated by the beta-adrenergic antagonist propranolol. Study Type: Risk prediction
2013-11-04 | GSE47153 | GEO
Project description:This study tested the effects of repeated social defeat (RSD) on gene expression in peripheral blood mononuclear cells (PBMC), and examined the extent to which these effects were abrogated by depletion of CD11b+ cells (monocytes). Study Type: Risk prediction
2013-11-04 | GSE47154 | GEO
Project description:Stress is associated with an increased prevalence of anxiety and depression. Repeated social defeat (RSD) stress in mice increases the release of monocytes from the bone marrow that are recruited to the brain by microglia. These monocytes enhance inflammatory signaling and augment anxiety. Moreover, RSD promotes stress sensitization, in which exposure to acute stress 24 days after cessation of RSD causes anxiety recurrence. The purpose of this study was to determine whether microglia were critical to stress sensitization and exhibited altered gene expression 24 days after RSD.
2018-12-21 | GSE124169 | GEO