Mus musculus
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA139629 | ENA |
REPOSITORIES: ENA
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Project description:Microarray analysis was used to identify the differentially expressed genes. Bioinformatics analyses integrated with databases and text-mined gene network were conducted to understand irradiation-related hub genes, pathways and biological processes. Our hypothesis in these paper are: 1) the expression profiles of irradiation damaged bone marrow tissue are not identical in injury phase and recovery phase; and 2) some hub genes potentially vital to BM recovery can be screened out by means of microarray analysis and bioinformatics analysis. The results provide basic information to explain the radiation-related biological processes and hub genes. The five mRNA samples in total bone marrow cells were profiled by using gene chip at 3, 7, 11 and 21 days after irradiation and 0 day (sham-irradiation) as control. Each time point contains one sample.
2013-06-17 | E-GEOD-28195 | biostudies-arrayexpress
Project description:Microarray analysis was used to identify the differentially expressed genes. Bioinformatics analyses integrated with databases and text-mined gene network were conducted to understand irradiation-related hub genes, pathways and biological processes. Our hypothesis in these paper are: 1) the expression profiles of irradiation damaged bone marrow tissue are not identical in injury phase and recovery phase; and 2) some hub genes potentially vital to BM recovery can be screened out by means of microarray analysis and bioinformatics analysis. The results provide basic information to explain the radiation-related biological processes and hub genes.
2013-06-17 | GSE28195 | GEO
Project description:Retrograde signaling from axon to soma activates intrinsic regeneration mechanisms in lesioned peripheral sensory neurons; however, the links between axonal injury signaling and the cell body response are not well understood. Here, we used phosphoproteomics and microarrays to implicate ~900 phosphoproteins in retrograde injury signaling in rat sciatic nerve axons in vivo and ~4500 transcripts in the in vivo response to injury in the dorsal root ganglia. Computational analyses of these data sets identified ~400 redundant axonal signaling networks connected to 39 transcription factors implicated in the sensory neuron response to axonal injury. Experimental perturbation of individual overrepresented signaling hub proteins, including Abl, AKT, p38, and protein kinase C, affected neurite outgrowth in sensory neurons. Paradoxically, however, combined perturbation of Abl together with other hub proteins had a reduced effect relative to perturbation of individual proteins. Our data indicate that nerve injury responses are controlled by multiple regulatory components, and suggest that network redundancies provide robustness to the injury response Microarrays were run on mRNA extracted from adult rat L4 and L5 DRGs cells after 1,3,8,12,16,18,24, and 28 hours after a sciatic nerve (proximal and distal) lesion.
2010-12-29 | E-GEOD-26350 | biostudies-arrayexpress
Project description:Aromatase, a member of the cytochrome P450 superfamily, is a key enzyme in estrogen synthesis and is responsible for the aromatization of androgens into estrogens. Here, we used an integrated approach to better understand the effects of aromatase inhibition as well as the mechanisms involved in the adaptation and recovery process. We exposed female fathead minnows (Pimephales promelas) to 30 μg/L of a model aromatase inhibitor, fadrozole, during 8 days (exposure phase). Fish were then held in clean water for 8 more days (recovery phase). Samples were collected at 1, 2, 4, and 8 days of both the exposure and the recovery phase. We used transcriptomics, metabolomics, and network inference to understand changes and infer connections at the transcript and metabolite level in the ovary. Other apical endpoints such as plasma estradiol, testosterone, and vitellogenin levels were also measured. An integrated analysis of the data revealed changes in gene expression consistent with increased testosterone. Metabolites such as glycogen and taurine were strongly correlated with increased testosterone levels. Comparison of in vivo and ex vivo data suggested the accumulation of steroidogenic enzymes, including aromatase, as a mechanism to compensate for aromatase inhibition. We exposed female fathead minnows (Pimephales promelas) to 30 μg/L of a model aromatase inhibitor, fadrozole, during 8 days (exposure phase). Fish were then held in clean water for 8 more days (recovery phase). Samples were collected at 1, 2, 4, and 8 days of both the exposure and the recovery phase.
2013-11-01 | E-GEOD-51961 | biostudies-arrayexpress
Project description:Retrograde signaling from axon to soma activates intrinsic regeneration mechanisms in lesioned peripheral sensory neurons; however, the links between axonal injury signaling and the cell body response are not well understood. Here, we used phosphoproteomics and microarrays to implicate ~900 phosphoproteins in retrograde injury signaling in rat sciatic nerve axons in vivo and ~4500 transcripts in the in vivo response to injury in the dorsal root ganglia. Computational analyses of these data sets identified ~400 redundant axonal signaling networks connected to 39 transcription factors implicated in the sensory neuron response to axonal injury. Experimental perturbation of individual overrepresented signaling hub proteins, including Abl, AKT, p38, and protein kinase C, affected neurite outgrowth in sensory neurons. Paradoxically, however, combined perturbation of Abl together with other hub proteins had a reduced effect relative to perturbation of individual proteins. Our data indicate that nerve injury responses are controlled by multiple regulatory components, and suggest that network redundancies provide robustness to the injury response
2010-12-29 | GSE26350 | GEO
Project description:T cells undergo autoimmunization following spinal cord injury (SCI) and play both protective and destructive roles during the recovery process. T-cell deficient athymic nude (AN) rats recover better than immunocompetent Sprague-Dawley (SD) rats following spinal cord transection. In the present study, we evaluated locomotor recovery in SD and AN rats following moderate spinal cord contusion. To explain variable locomotor outcome, we assessed whole-genome expression using RNA sequencing, in the acute (1 week post-injury) and chronic (8 weeks post-injury) phases of recovery. AN rats demonstrated greater locomotor function than SD rats only at 1 week post-injury, coinciding with peak T cell infiltration in immunocompetent rats. Genetic markers for T cells and helper T cells were acutely enriched in SD rats, while AN rats expressed genes for Th2 cells, cytotoxic T cells, NK cells, mast cells, IL-1a, and IL-6 at higher levels. Acute enrichment of cell death-related genes suggested that SD rats undergo secondary tissue damage from T cells. Additionally, SD rats exhibited increased acute expression of voltage-gated potassium (Kv) channel-related genes. However, AN rats demonstrated greater chronic expression of cell death-associated genes and less expression of axon-related genes. We put forth a model in which T cells facilitate early tissue damage, demyelination, and Kv channel dysregulation in SD rats following contusion SCI. However, compensatory features of the immune response in AN rats cause delayed tissue death and limit long-term recovery. T cell inhibition combined with other neuroprotective treatment may thus be a promising therapeutic avenue. 2x2 model with 4 groups and 12 total samples. 2 rat strains (athymic nude [AN] and Sprague-Dawley [SD]) and 2 time points (1 week post-injury [acute] and 8 weeks post-injury [chronic]). 3 samples per group, for a total of 12 samples. No technical replicates were performed. Acute SD group = rats 618, 619, and 620. Chronic SD group = rats 605, 606, and 608. Acute AN group = rats 714, 715, and 717. Chronic AN group = rats 707, 712, and 713.
2015-10-26 | E-GEOD-62760 | biostudies-arrayexpress
Project description:Aromatase, a member of the cytochrome P450 superfamily, is a key enzyme in estrogen synthesis and is responsible for the aromatization of androgens into estrogens. Here, we used an integrated approach to better understand the effects of aromatase inhibition as well as the mechanisms involved in the adaptation and recovery process. We exposed female fathead minnows (Pimephales promelas) to 30 μg/L of a model aromatase inhibitor, fadrozole, during 8 days (exposure phase). Fish were then held in clean water for 8 more days (recovery phase). Samples were collected at 1, 2, 4, and 8 days of both the exposure and the recovery phase. We used transcriptomics, metabolomics, and network inference to understand changes and infer connections at the transcript and metabolite level in the ovary. Other apical endpoints such as plasma estradiol, testosterone, and vitellogenin levels were also measured. An integrated analysis of the data revealed changes in gene expression consistent with increased testosterone. Metabolites such as glycogen and taurine were strongly correlated with increased testosterone levels. Comparison of in vivo and ex vivo data suggested the accumulation of steroidogenic enzymes, including aromatase, as a mechanism to compensate for aromatase inhibition.
2013-11-01 | GSE51961 | GEO
Project description:Anterior cruciate ligament (ACL) tears occur in isolation or in combination with other intra-articular injuries such as meniscus tears. The impact of injury pattern on the molecular biology of the injured ACL is unknown. Here, we tested the hypothesis that the biological response of the ACL to injury varies based on the presence or absence of concomitant meniscus tear. RNA-seq analysis was performed on 28 ACL tears remnants (12 isolated, 16 combined). 16,654 transcripts were differentially-expressed between isolated and combined injury groups at false-discovery-rate of 0.05. Due to the large number of differentially expressed transcripts, we undertook an Ensembl approach to discover features that acted as hub-genes that did not necessarily have large fold-changes or high statistical significance, but instead had high biological significance. Our data revealed a negatively-correlated turquoise-module containing 5960 transcripts (down-regulated in combined injury) and a positively-correlated blue-module containing 2260 transcripts (up-regulated in combined injury). TNS1, MEF2D, NOTCH3, SOGA1, and MLXIP were highly-connected hub-genes in the turquoise-module and SCN2A, CSMD3, LRC44, USH2A, and LRP1B were critical hub-genes in the blue-module. Transcripts in the turquoise-module were associated with biological-adhesion, actin-filament organization, cell-junction assembly, and cell-matrix adhesion. The blue-module transcripts were enriched for neuron-migration and exocytosis-regulation. These findings indicate a loss of healing and gain of neurogenic signaling in combined ACL and meniscus tears, suggesting they have diminished potential for repair. The biological response of the ACL to injury could have implications for the healing potential of the ligament and the long-term health of the knee.
2018-01-23 | GSE109419 | GEO
Project description:The zebrafish has the capacity to regenerate its heart after severe injury. While the function of a few genes during this process has been studied, we are far from fully understanding how genes interact to coordinate heart regeneration. To enable systematic insights into this phenomenon, we generated and integrated a dynamic co-expression network of heart regeneration in the zebrafish and linked systems-level properties to the underlying molecular events. Across multiple post-injury time points, the network displays topological attributes of biological relevance. We show that regeneration steps are mediated by modules of transcriptionally coordinated genes, and by genes acting as network hubs. We also established direct associations between hubs and validated drivers of heart regeneration with murine and human orthologs. The resulting models and interactive analysis tools are available at http://infused.vital-it.ch. Using a worked example, we demonstrate the usefulness of this unique open resource for hypothesis generation and in silico screening for genes involved in heart regeneration. In order to monitor the whole regeneration process, we recovered samples at different time points post-injury: 4 h, 1 day, 3 days, 7 days, 14 days and 90 days (respectively 4 hpi, 1 dpi, 3 dpi, 7 dpi, 14 dpi and 90 dpi). Cryoinjured hearts were compared to healthy hearts from control fish in 3 independent experiments.
2016-06-01 | E-GEOD-67665 | biostudies-arrayexpress
Project description:UV crosslinking can be used to identify precise RNA targets for individual proteins, transcriptome-wide. We sought to develop a technique to generate reciprocal data, identifying precise sites of RNA-binding proteome-wide. The resulting technique, total RNA-associated protein purification (TRAPP), was applied to yeast (S. cerevisiae ) and bacteria (E. coli). In all analyses, SILAC labeling was used to quantify protein recovery in the presence and absence of irradiation. For S.cerevisiae, we also compared crosslinking using 254nm (UVC) irradiation (TRAPP) with 4-thiouracil (4SU) labeling combined with 350nm (UVA) irradiation (PAR-TRAPP). Recovery of proteins not anticipated to show RNA-binding activity was significantly higher in TRAPP compared to PAR-TRAPP. As an example of preferential TRAPP-crosslinking, we tested enolase (Eno1) and demonstrated its strong, but largely sequence independent, binding to RNA in vivo. We speculate that many protein-RNA interactions have biophysical effects on localization and/or accessibility, by opposing or promoting phase separation. Homologous metabolic enzymes showed RNA crosslinking in S. cerevisiae and E. coli, indicating conservation of this property. TRAPP allows alterations in RNA interactions to be followed and we initially analyzed the effects of weak acid stress. This revealed specific alterations in RNA-protein interactions; for example, during late 60S ribosome subunit maturation. Precise sites of crosslinking at the level of individual amino acids (iTRAPP) were identified following phospho-peptide enrichment combined with a bioinformatic pipeline (Xi). TRAPP is quick, simple and scalable, allowing rapid characterization of the RNA-bound proteome in many systems.
2018-09-13 | GSE119867 | GEO