Gene expression analysis of genes differentially expressed between CD93-ko mice and wild-type mice in post ischemic mice brain tissue
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ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE21002 | GEO | 2010/03/23
SECONDARY ACCESSION(S): PRJNA125749
REPOSITORIES: GEO
Similar Datasets
Project description:To further decipher CD93-dependent pathways, we compared global expression profiles of ischemic (ipsilateral) hemispheres of CD93-deficient mice (CD93-ko) with expression profiles of wild-type mice. Total RNA obtained from CD93-ko and WT mice at different time points after cerebral ischemia and from untreated brain tissue
2010-03-23 | E-GEOD-21002 | biostudies-arrayexpress
Project description:TNF/TNFRI signaling has previously been shown to exert neuroprotective effects after brain ischemic injury. However, the detailed pathways involved remain unidentified. This study aims to identify key neuroprotective molecules activated by TNFRI after permanent ischemic injury in mice. Microarray analysis of the ipsilateral hemispheres of WT and TNFRI knockout at early time points (3 and 6 hours) after the middle cerebral artery occlusion mice were chosen to study the CNS response to injury without significant immune infiltration. Using the ATLAS mouse cDNA arrays that include known genes representative of multiple pathways, we identify novel protective pathways triggered by TNFRI signaling after ischemia. Keywords: brain, ischemic lesion, comparison between WT and TNFRI knockout mice, cDNA array, two different time points (3 and 6 h)
2007-09-05 | GSE8886 | GEO
Project description:TNF/TNFRI signaling has previously been shown to exert neuroprotective effects after brain ischemic injury. However, the detailed pathways involved remain unidentified. This study aims to identify key neuroprotective molecules activated by TNFRI after permanent ischemic injury in mice. Microarray analysis of the ipsilateral hemispheres of WT and TNFRI knockout at early time points (3 and 6 hours) after the middle cerebral artery occlusion mice were chosen to study the CNS response to injury without significant immune infiltration. Using the ATLAS mouse cDNA arrays that include known genes representative of multiple pathways, we identify novel protective pathways triggered by TNFRI signaling after ischemia. Keywords: brain, ischemic lesion, comparison between WT and TNFRI knockout mice, cDNA array, two different time points (3 and 6 h) RNA was extracted from WT (n=2) and TNFRI KO (n=2) mice at each time point studied (3 and 6 h after ischemia). For each individual sample two hybridisations were performed.
2007-09-04 | E-GEOD-8886 | biostudies-arrayexpress
Project description:CD93+ and CD93- HSCs comparison
| PRJNA701025 | ENA
Project description:CD93+ and CD93- HSCs comparison [RNA-Seq]
| PRJNA701026 | ENA
Project description:CD93+ and CD93- HSCs comparison [ATAC-Seq]
| PRJNA701027 | ENA
Project description:Our group has been systematically investigating effects of the neuropeptide pituitary adenylate-cyclase activating polypeptide (PACAP) on the ischemic brain. To do so, we have established and utilizing the permanent middle cerebral artery occlusion (PMCAO) mouse model, where PACAP38 (1 pmol) injection is given intracerebroventrically in comparison to a control saline (0.9% NaCl) injection, in conjunction with high-throughput DNA microarray analysis. In previous studies, we have accumulated a large volume of data (gene inventory) from the whole brain (ipsilateral and contralateral hemispheres) by this approach. In our latest research, we have targeted specifically infract/ischemic core (hereafter IC) and the penumbra (hereafter P) post-PACA38 injection, for re-examining the transcriptome at 6 and 24 h post-treatment. The aim of the current study is simple M-bM-^@M-^S to delineate the specificity of expression and localization of differentially expressed molecular factors influenced by PACAP38. Prior to this highly expensive and time-consuming omic analysis, we checked the validity of our hypothesis and experimental strategy wherein, ischemic core and penumbra were carefully sampled and compared to the corresponding contralateral (healthy) IC and P regions at 6 and 24 h, post PACAP38 or saline injections to reveal expected differences in gene and protein expression by traditional reverse transcriptase-polymerase chain reaction (RT-PCR) and Western blot analyses, respectively (Hori et al., 2014). Our present results using the mouse 4x44K whole genome DNA chip reveal numerous changes (M-bM-^IM-'/M-bM-^IM-& 1.5/0.75-fold) at both 6 h (654 and 456, and 522 and 449 up- and down-regulated genes for IC and P, respectively; and 24 h (2568 and 2684, and 1947 and 1592 up- and down-regulated genes for IC and P, respectively) after PACAP38 treatment. Using bioinformatics analysis by pathway- or specific-disease-state focused gene classifications and Ingenuity Pathway Analysis (IPA), these genes were functionally classified and discussed. Taken together, the DNA microarray analysis provides not only a great resource for further study, but also reinforces the importance of region-specific analyses in genome-wide identification of target molecular factors that might play a role in the neuroprotective function of PACAP38. In the present study, we used three mice each in PMCAO groups for PACAP38 and saline injections, respectively, that exhibited neurological grades G1 and G2 for the subsequent downstream analysis. Six or 24 h post-injection of PACAP38 or saline, the mice were removed from their cages, decapitated, and their brains carefully removed on ice. The right (ipsilateral; ischemic) and left (contralateral) hemispheres were dissected, and from each hemisphere the ischemic core and penumbra regions and corresponding healthy core and penumbra were carefully removed with a sterile scalpel, and placed in 2 ml Eppendorf tubes. The samples were then quickly immersed in liquid nitrogen and stored in -80 M-BM-:C prior to further analysis. Effect of the intracerebroventricular PACAP38 administration into ischemic mouse brain was evaluated at the molecular level in the ischemic core and penumbra of ipsilateral (right) hemisphere over the saline injection by whole genome DNA microarray analysis (4x44K, Agilent).
2014-10-31 | E-GEOD-62884 | biostudies-arrayexpress
Project description:IL-17D/CD93 axis was essential for ILC3s hemostasis. In order to further understand how IL-17D-CD93 axis regulate ILC3s function, we conducted RNA-seq analysis of ILC3s.
2021-05-20 | GSE165788 | GEO
Project description:Ischemic tolerance can be induced by numerous preconditioning stimuli, including various Toll-like receptor (TLR) ligands. We have shown previously that systemic administration of the TLR4 ligand, lipopolysaccharide (LPS) or the TLR9 ligand, unmethylated CpG ODNs prior to transient brain ischemia in mice confers substantial protection against ischemic damage. To elucidate the molecular mechanisms of preconditioning, we compared brain and blood genomic profiles in response to preconditioning with these TLR ligands and to preconditioning via exposure to brief ischemia. The experiment is a comparison of multiple treatment groups with sampling at multiple time points. The objective is to identify differentially regulated genes associated with preconditioning. Time points are examined both following preconditioning alone and following subsequent ischemic challenge (middle cerebral artery occlusion (MCAO)). Brain ipsilateral cortex tissue and blood were collected and processed from each animal. 6 experimental conditions: (n=3-4 mice/condition) LPS treated (i.p. 0.2mg/kg) + ischemic challenge (45min MCAO) CpG treated (i.p. 0.8mg/kg) + ischemic challenge (45min MCAO) Saline treated (i.p.) + ischemic challenge (45min MCAO) brief ischemia (12 min MCAO) + ischemic challenge (45min MCAO) Sham of brief ischemia (12 min) + ischemic challenge (45min MCAO) Non-treated + ischemic challenge (45min MCAO) Time points: Pre-ischemic challenge 3hr 24hr 72hr Post-ischemic challenge 3hr 24hr Unhandled (6 mice)-BASELINE
2011-10-04 | E-GEOD-32529 | biostudies-arrayexpress
Project description:The neuropeptide pituitary adenylate cyclase-activating polypeptide (PACAP) is considered to be a potential therapeutic agent for prevention of cerebral ischemia. Ischemia is a most common cause of death after heart attack and cancer causing major negative social and economic consequences. - This study was designed to investigate the effect of PACAP38 injection intracerebroventrically in a mouse model of permanent middle cerebral artery occlusion (PMCAO) along with corresponding sham control that used 0.9% saline injection. Ischemic and non-ischemic brain tissues were sampled at 6 and 24 hours post-treatment. - Following behavioral analyses to confirm whether the ischemia has occurred, we investigated the genome-wide changes in gene and protein expresison using DNA microarray chip (4x44K, Agilent) and one-/two-dimensional gel electrophoresis (1-/2-DGE) coupled with matrix assisted laser desorption/ionization-time of flight-mass spectrometry (MALDI-TOF-MS), respectively. - Our results revealed numerous changes in the transcriptome of ischemic (ipsilateral) hemisphere treated with PACAP38 over the saline-injected SHAM control hemisphere. In parallel, 2-DGE analysis revealed a highly expressed protein spot in the ischemic region that was identified as dihydropyrimidinase-related protein 2 (DPYL2). The DPYL2, also known as Crmp2, is a marker for the activated neuronal defense mechanisms, and interestingly, PACAP strongly suppresed this induction. - This study provides the first inventory of PACAP influenced gene and protein targets in ischemic hemisphere, and provides new targets for thereaupetic interventions. The PMCAO model mice were generated as described previously. Briefly, the mice were anesthetized with 4% sevoflurane (induction) and 2% sevoflurane (maintenance) in a 30% O2 and 70% N2O gas mixture via a face mask. An incision was then made in the cervical skin followed by opening of the salivary gland, and the right common carotid artery was visualized. A midline cervical incision was made to expose the external carotid artery. The intraluminal filament technique was used, to generate the PMCAO model. - The PACAP38 (1 M-BM-5l containing 1 pmol) or 1 M-BM-5l of saline (0.9% NaCl) was injected intracerebroventrically, immediately after PMCAO. PACAP38 (Peptide Institute Inc., Osaka, Japan; supplier temperature was -20M-BM-:C and was stored at -80M-BM-:C) was dissolved in, and diluted M-CM-^W10 times with 0.9% NaCl just before use. - In the sham control animals, following exposure of the external carotid artery, the wound was sutured. The PACAP38 or saline was injected intracerebroventrically in the same concentrations as above. After injections, the animals were returned to their cages. - A total of eight groups were prepared: four groups of three, seven, four and five mice in the PMCAO plus PACAP38 and PMCAO plus saline cohorts at 6 and 24 h after operation, respectively, and five mice each in the control (sham) plus PACAP and saline groups at 6 and 24 h after operation, respectively. - We used three mice each in PMCAO groups that exhibited neurological grades G1 and G2 and three mice each at random in sham groups for the subsequent downstream analysis. Six or 24 hours post-injection of PACAP38 or saline, the mice were removed from their cages, decapitated, and their brains carefully removed on ice. The left (contralateral) and right (ipsilateral; ischemic) hemispheres were dissected and placed in 2 mL Eppendorf tubes, which were then quickly immersed in liquid nitrogen before being stored in -80M-BM-:C prior to further analysis. - For analysis of gene components, the tissues were ground to a very fine powder with liquid nitrogen, used for total RNA extraction, quantity and quality check, followed by cDNA synthesis, and RT-PCR. A mouse 4 x 44K whole genome oligo DNA microarray chip (G4122F, Agilent Technologies, Palo Alto, CA, USA) was used for global gene expression analysis using the ipsilateral (ischemic) hemisphere. Briefly, total RNA (900 ng; 300 ng each replicate pooled together) was labeled with either Cy3 or Cy5 dye using an Agilent Low RNA Input Fluorescent Linear Amplification Kit (Agilent). Fluorescently labeled targets of control (sham) as well as treated (PMCAO) samples with PACAP38 or without PACAP38 (saline) were hybridized to the same microarray slide with 60-mer probes. - Here, we compared the PMCAO plus PACAP38 injected mice to PMCAO plus saline, i.e. the ipsilateral brain region of the PMCAO mice was compared with the same right hemisphere of the control mice. Similarly, Sham control plus PACAP38 injected mice to Sham control plus saline were analyzed to identify only the PACAP38 influenced genes. A flip labeling (dye-swap or reverse labeling with Cy3 and Cy5 dyes) procedure was followed to nullify the dye bias associated with unequal incorporation of the two Cy dyes into cDNA.
2012-04-30 | E-GEOD-37565 | biostudies-arrayexpress