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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Transcription profiling of olfactory epithelium isolated from wild type and SR-A mutant mice at different time points after bilateral olfactory bulbectomy to understand the temporal gene expression patterns.

ABSTRACT: Sham and bilateral OBX were performed on wild-type and SR-A mutant mice. Tissue collected 2, 8, 16, and 48 hours following OBX. Expression profiles were determined using Affynetrix MG U74Av2 chips. Experiment Overall Design: olfactory epithelium from 3 wild type 6 week old mice and 3 SR-A 6 week old mutant mice

ORGANISM(S): Mus musculus

SUBMITTER: Marilyn Getchell

PROVIDER: E-GEOD-3455 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Temporal gene expression profiles of target-ablated olfactory epithelium in mice with disrupted expression of scavenger receptor A: impact on macrophages.

Getchell M L ML Li H H Vaishnav R A RA Borders A S AS Witta J J Subhedar N N de Villiers W W Stromberg A J AJ Getchell T V TV

Physiological genomics 20060801 3

Target ablation [removal of the olfactory bulb (OBX)] induces apoptotic death of olfactory sensory neurons (OSNs) and an immune response in which activation and recruitment of macrophages (ms) into the olfactory epithelium (OE) occupy a central role. Ms phagocytose apoptotic neurons and secrete cytokines/growth factors that regulate subsequent progenitor cell proliferation and neurogenesis. Scavenger receptor A (SR-A) is a pattern recognition receptor that mediates binding of ms to apoptotic cel ...[more]

PMID: 16882882

Similar Datasets

Olfactory epithelium of SR-A mutant mice following bilateral olfactory bulbectomy

Project description:Sham and bilateral OBX were performed on wild-type and SR-A mutant mice. Tissue collected 2, 8, 16, and 48 hours following OBX. Expression profiles were determined using Affynetrix MG U74Av2 chips. Keywords: repeat

2006-10-14 | GSE3455 | GEO

RNA sequencing analysis of unilateral orchidectomy, bilateral orchidectomy, and Nell2 knockout initial segment-caput epididymis.

Project description:Purpose: The purpose of this study is to characterize genes whose expressions in the initial segment (IS)-caput epididymis were affected by unilateral orchidectomy (UOD), bilateral orchidectomy (BOD), and Nell2 gene ablation. Methods: The unilateral or bilateral orchidectomy of WT mice was performed from 8 weeks old and continued for 4 weeks until tissue sampling at 12 weeks old. Contralateral epididymis was used as a control for UOD. Sham operation was also done as a control for BOD. Nell2-/- mice and their control WT mice were used wthen they were 14-week-old. IS-caput epididymal mRNA profiles were generated by deep sequencing, in triplicate, using Illumina NovaSeq6000. Results: RNA-seq data identified differentially expressed transcripts. Conclusions: Our results show that the expression of many genes was affected by UOD, BOD, and Nell2 ablation.

2023-11-19 | GSE247764 | GEO

Transcription profiling of murine olfactory epithelium during neuronal death and replacement to study adult neurogenesis in the olfactory epithelium

Project description:Expression profiling of mRNA abundance in the adult mouse olfactory epithelium during replacement of OSNs forced by the bilateral ablation of the olfactory bulbs. The experiment was done on 6 week old male C57Bl/6 mice. Olfactory epithelium tissue samples were collected on days 1, 5, and 7 after bulbectomy. The cellular processes activated by bulbectomy include apoptosis of mature olfactory sensory neurons, infiltration of macrophages and dendritic cells, stimulation of proliferation of basal cell progenitors, and differentation of new sensory neurons.

2007-09-04 | E-GEOD-2437 | biostudies-arrayexpress

Transcriptional changes during neuronal death and replacement in the adult olfactory epithelium

2005-08-01 | GSE2437 | GEO

Transcription profiling of mouse liver to understand the regulation of hepatic gene expression by dwarfism and caloric restriction

Project description:Mice were killed between 24 to 26 months of age, tissues removed, rapidly frozen on dry ice, and stored in liquid nitrogen. Total liver RNA was isolated from frozen tissue as described (T. Tsuchiya, J.M. Dhahbi, X. Cui, P.L. Mote, A. Bartke, S.R. Spindler, Physiological Genomics, Submitted). mRNA levels were measured using the Affymetrix mouse U74Av2 array according to standard protocols. After hybridization, arrays were scanned using a Hewlett-Packard GeneArray Scanner. Image analysis was performed as described (Cao SX, Dhahbi JM, Mote PL, and Spindler SR. Genomic profiling of short- and long-term caloric restriction effects in the liver of aging mice. Proc Natl Acad Sci U S A 98: 10630-10635, 2001). A more detailed description of the methods can be found in (T. Tsuchiya, J.M. Dhahbi, X. Cui, P.L. Mote, A. Bartke, S.R. Spindler, Physiological Genomics, Submitted). This SuperSeries is composed of the following subset Series: GSE1086: Dwarf Ad libitum; GSE1087: Dwarf Calorie Restricted; GSE1088: Normal Ad Libitum; GSE1089: Normal Calorie Restricted Experiment Overall Design: Refer to individual Series

2007-10-06 | E-GEOD-1093 | biostudies-arrayexpress

TCR repertoire analysis revealed the highly conserved TCR repertoire in the bilateral tumor in mice

Project description:Temporal analysis of T-cell receptor (TCR) repertoire has been used to monitor treatment-induced changes in antigen-specific T cells in patients with cancer. However, lack of experimental model that allows the temporal analysis of TCR repertoire in same individual in homogeneous population limit the understanding of causal relationship between changes in TCR repertoire and antitumor responses. A bilateral tumor model, in which tumor cells were inoculated into the bilateral backs of mice, can be used for temporal analysis in TCR repertoire. In this study, we examined the prerequisite for this strategy: TCR repertoire are conserved between the bilateral tumor with same growth rate. The bilateral tumors with equivalent tumor size and draining lymph nodes (dLN) were collected 13 days after the tumor inoculation to analyze the TCR repertoire of CD4+ and CD8+ T cells. Most of the tumor-infiltrating T-cell clones were highly conserved between the bilateral tumors, and the extent of clonal expansion was equivalent. In addition, the similarity between bilateral tumors were equivalent to the heterogeneity in one side of the tumor. The similarity of TCR repertoire in the bilateral dLN was markedly lower than that of the tumor, suggesting that tumor-reactive T-cell clones induced independently in each dLN were integrated during recirculation and then infiltrated the tumor. These findings suggest that our bilateral tumor model is suitable for temporal monitoring of TCR repertoire to evaluate temporal and treatment-induced changes in tumor-reactive T-cell clones.

2021-05-12 | GSE174225 | GEO

Expression data from RH30 vector and RH30 IκBα SR cells

Project description:Classical NF-κB activity can be inhibited by overexpression of the IκBα super repressor (SR). To determine the role of NF-κB in rhabdomyosarcoma cells, we overexpressed the IκBα SR in RH30 rhabdomyosarcoma cells. IκBα SR was overexpressed in RH30 cells. RH30 vector cells were used as control group.

2018-03-30 | GSE112119 | GEO

Genome-wide Analysis Reveals SR Protein Cooperation and Competition in Regulated Splicing

Project description:SR proteins are well-characterized RNA binding proteins that promote exon inclusion by binding to exonic splicing enhancers (ESEs). However, it has been unclear whether regulatory rules deduced on model genes apply generally to activities of SR proteins in the cell. Here, we report global analyses of two prototypical SR proteins SRSF1 (SF2/ASF) and SRSF2 (SC35) using splicing-sensitive arrays and CLIP-seq on mouse embryo fibroblasts (MEFs). Unexpectedly, we find that these SR proteins promote both inclusion and skipping of exons in vivo, but their binding patterns do not explain such opposite responses. Further analyses reveal that loss of one SR protein is accompanied by coordinated loss or compensatory gain in the interaction of other SR proteins at the affected exons. Therefore, specific effects on regulated splicing by one SR protein actually depend on a complex set of relationships with multiple other SR proteins in mammalian genomes.

2013-04-05 | GSE44591 | GEO

Genome-wide Analysis Reveals SR Protein Cooperation and Competition in Regulated Splicing

2013-04-05 | E-GEOD-44591 | biostudies-arrayexpress

Developmental dynamics of the postsynaptic proteome to understand synaptic maturation and dysmaturation

Project description:The postsynaptic density (PSD) is a protein condensate composed of ~1,000 proteins beneath the postsynaptic membrane of excitatory synapses. The number, shape, and plasticity of synapses are altered during development. However, the dynamics of synaptic protein composition across development have not been fully understood. Here we show alterations of PSD protein composition in mouse and primate brains during development. Proteins involved in synapse regulation are enriched in the differentially expressed (288 decreased and 267 increased) proteins on mouse PSD after a 2-week-old, which may be involved in changes of synaptic signal transduction. We find that the changes in PSD protein abundance in mouse brains correlate with gene expression levels in postnatal mice and perinatal primates. Proteome analysis of PSD from developing common marmosets (Callithrix jacchus) shows that the changes of PSD composition in mouse brain after 2-week-old occur in the marmoset brain mainly during the neonatal period and continue until adulthood. We also describe the changes of PSD proteome at the late developmental stage of marmoset, which may be involved in synaptic pruning observed in primate brains. The maturation of PSD composition is likely defective in autism spectrum disorder (ASD). Our results provide a comprehensive architecture of the remodeling of PSD composition across development, which may explain the molecular basics of synapse maturation and the pathology of psychiatric disorders, such as ASD.

2024-01-17 | PXD048549 | Pride

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