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Whole-genome gene expression profiling of Pik3cg-depleted mice

ABSTRACT: We performed whole-genome gene expression profiling in Pik3cg-/- mice and subsequent gene ontology clustering of differentially expressed genes compared to wild type mice, in order to investigate the role of Pik3cg in platelet membrane biogenesis and blood coagulation. Pik3cg-deficient mice were obtained from sources previously described (T. Sasaki et al, 2000, Science 287, 1040-1046), backcrossed onto the C57BL/6J Jax genetic background for eight generations (B6J;129-Pik3cg-tm1Pngr) and then maintained as a closed colony by intercrossing from within the colony (C57BL/6J Jax contribution: 99.6%). Whole blood from three Pik3cg-/- and three C57BL/6J Jax wild type mice (all females, age: 13-16 weeks, Mouse Breeders Diet (Lab Diets 5021-3)) was collected from terminally anaesthetized mice via the retro-orbital sinus. For each RNA extraction, in vitro transcription (IVT) reactions were performed in duplicates.

ORGANISM(S): Mus musculus

SUBMITTER: Dirk Paul

PROVIDER: E-GEOD-26111 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Whole-genome gene expression profiling of Pik3cg-depleted mice

Project description:We performed whole-genome gene expression profiling in Pik3cg-/- mice and subsequent gene ontology clustering of differentially expressed genes compared to wild type mice, in order to investigate the role of Pik3cg in platelet membrane biogenesis and blood coagulation. Pik3cg-deficient mice were obtained from sources previously described (T. Sasaki et al, 2000, Science 287, 1040-1046), backcrossed onto the C57BL/6J Jax genetic background for eight generations (B6J;129-Pik3cg-tm1Pngr) and then maintained as a closed colony by intercrossing from within the colony (C57BL/6J Jax contribution: 99.6%).

2011-07-01 | GSE26111 | GEO

Mus musculus

Project description:RNA sequencing of C57BL/6NJ (B6NJ) x C57BL/6J (B6J) - F2 mice

| PRJNA328473 | ENA

C57BL/6 substrain differences in inflammatory and neuropathic nociception and genetic mapping of a major quantitative trait locus underlying acute thermal nociception

Project description:Sensitivity to different pain modalities has a genetic basis that remains largely unknown. The use of closely related inbred mouse strains can facilitate gene mapping of nociceptive behaviors in preclinical pain models. We previously reported enhanced sensitivity to acute thermal nociception in C57BL/6J (B6J) versus C57BL/6N (B6N) substrains. Here, we expanded on pain phenotypes and observed an increase in inflammatory nociceptive behaviors induced by hindpaw formalin injections in B6J versus B6N mice (Charles River Laboratories). No strain differences were observed in mechanical or thermal hypersensitivity or in paw diameter following the Complete Freund s Adjuvant (CFA) model of inflammatory pain, indicating specificity in the inflammatory nociceptive stimulus. In the chronic nerve constriction injury (CCI), a model of neuropathic pain, no strain differences were observed in baseline mechanical threshold or in mechanical hypersensitivity up to one month post-CCI. We replicated the enhanced thermal nociception in B6J mice in the 52.5 C hot plate test relative to B6N mice from The Jackson Laboratory. Using a B6J x B6N-F2 cross (N=164), we mapped a major QTL underlying hot plate sensitivity to chromosome 7 that peaked at 26 Mb (LOD = 3.81, 8.74 Mb-36.50 Mb) that was more pronounced in males. Genes containing expression QTLs (eQTLs) associated with the peak nociceptive marker that have been implicated in pain and inflammation include Ryr1, Cyp2a5, Pou2f2, Clip3, Sirt2, Actn4, and Ltbp4 (FDR < 0.05). Future studies involving positional cloning and gene editing will determine the quantitative trait gene(s) and potential pleiotropy of this locus across other pain modalities. RNA-seq data and genotype information from striatum punches of F2 C57BL/6J (B6J) cross C57BL/NJ (B6NJ) oxycodone-treated mice. Genotypes are given relative to B6J allele, eg 0 = homozygous B6J.

2018-11-26 | GSE119719 | GEO

Examination of gene expression in cerebellum of mouse strains B6J, B6J-nmf205-/-, B6J-Gcn2-/- and B6J-nmf205-/-;Gcn2-/-.

Project description:Ribosome stalling during translation has recently been shown to cause neurodegeneration, yet the signaling pathways triggered by stalled elongation complexes are unknown. To investigate these pathways we analyzed the brain of B6J-nmf205-/- mice in which neuronal elongation complexes are stalled at AGA codons due to deficiencies in a tRNA Arg(UCU) tRNA and GTPBP2, a mammalian ribosome rescue factor. Increased levels of phosphorylation of eIF2Î± (Ser51) were detected prior to neurodegeneration in these mice and transcriptome analysis demonstrated activation of ATF4, a key transcription factor in the integrated stress response (ISR) pathway. Genetic experiments showed that this pathway was activated by the eIF2alpha kinase, GCN2, in an apparent deacylated tRNA-independent fashion. Further we found that the ISR attenuates neurodegeneration in B6J-nmf205-/- mice, underscoring the importance of cellular and stress context on the outcome of activation of this pathway. These results demonstrate the critical interplay between translation elongation and initiation in regulating neuron survival during cellular stress. Examination of gene expression in cerebellum and hippocampus for 4 mice strains derived from C57BL/6J (B6J) strain. Microarray data was performed for 3 week and 5 week old mice in both cerebellum and hippocampus for B6J and B6J-nmf205-/- three replicates each. RNA-Seq data was perform on cerebellum of mice 3 weeks old, three replicates for each genotype: B6J, B6J-nmf205-/-, B6J-Gcn2-/- and B6J-nmf205-/-;Gcn2-/-.

2016-06-15 | E-GEOD-79929 | biostudies-arrayexpress

Examination of gene expression in cerebellum and hippocampus for mouse C57BL/6J WT and nmf205-/-

Project description:Ribosome stalling during translation has recently been shown to cause neurodegeneration, yet the signaling pathways triggered by stalled elongation complexes are unknown. To investigate these pathways we analyzed the brain of B6J-nmf205-/- mice in which neuronal elongation complexes are stalled at AGA codons due to deficiencies in a tRNA Arg(UCU) tRNA and GTPBP2, a mammalian ribosome rescue factor. Increased levels of phosphorylation of eIF2Î± (Ser51) were detected prior to neurodegeneration in these mice and transcriptome analysis demonstrated activation of ATF4, a key transcription factor in the integrated stress response (ISR) pathway. Genetic experiments showed that this pathway was activated by the eIF2Î± kinase, GCN2, in an apparent deacylated tRNA-independent fashion. Further we found that the ISR attenuates neurodegeneration in B6J-nmf205-/- mice, underscoring the importance of cellular and stress context on the outcome of activation of this pathway. These results demonstrate the critical interplay between translation elongation and initiation in regulating neuron survival during cellular stress. Examination of gene expression in cerebellum and hippocampus for 4 mice strains derived from C57BL/6J (B6J) strain. Microarray data was performed for 3 week and 5 week old mice in both cerebellum and hippocampus for B6J and B6J-nmf205-/- three replicates each. RNA-Seq data was perform on cerebellum of mice 3 weeks old, three replicates for each genotype: B6J, B6J-nmf205-/-, B6J-Gcn2-/- and B6J-nmf205-/-;Gcn2-/-.

2016-06-15 | E-GEOD-79926 | biostudies-arrayexpress

Homo sapiens

Project description:c57bl/6j mice

| PRJNA900002 | ENA

R_HAN_01.05 Mice sera fed with prebiotic or antibiotics

Project description:Control diet for C57Bl/6j Mice and effect on microbiota and immunity. Metabolome content of blood of these mice. LC-HRMS/MS C18+.

2019-07-05 | MSV000084062 | MassIVE

Mitochondria proteomics of murine kidney podocytes

Project description:To understand how diabetes alters the protein subunits of mitochondrial Electron Transfer Chain (ETC) in the podocytes, we performed a proteomic analysis of mitochondrial proteins isolated from primary kidney podocytes of WT (C57BL/6J background) and Ins2Akita/+ diabetic (C57BL/6J background) mice.

2024-02-08 | PXD045828 | Pride

Mitochondria proteomics of murine kidney podocytes

2024-02-08 | PXD041202 | Pride

Expression profiling of Brain tissue from C57BL/6J X C3H/HeJ)F2 and (C3H/HeJ X C57BL/6J)F2

Project description:The purpose of this experiment was to determine the expression traits in animals from F2 intercross of inbred strains C57BL/6J, C3H/HeJ. (N=309, 164 males and 145 females). Brain from 292 F2 female and male mice were generated by intercrossing F1 mice. Mice were fed chow diet containing 4% fat (Ralston-Purina Co., St. Louis, MO) until 8 weeks of age and then were placed on a high-fat "Western" diet containing 42% fat and 0.15%cholesterol (Teklad 88137, Harlan Teklad, Madison WI) for 12 weeks. At 20 weeks mice were sacrificed, after a 12-hour fast Brain tissues were dissected and flash frozen in LN2 and stored at -80Â°C.

2009-08-09 | E-GEOD-12798 | biostudies-arrayexpress

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