Mus musculus
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA219453 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Genome-wide expression data can provide important insights into normal and pathological cellular processes. However, the ability to use gene expression data to quantitatively assess the activation state of a given signaling pathway or transcriptional network in a sensitive and specific manner remains an important unmet goal. We now describe a computational algorithm, energy-paired scoring (EPS), that satisfies these criteria by predicting pathway activity using gene-gene interactions within a pathway signature in a manner analogous to the estimation of energy generated by two charged particles, as described by Coulomb’s law. We demonstrate the ability of EPS to: quantitatively assess pathway activation levels in vivo and in vitro; accurately estimate the extent of pathway inhibition achieved by gene knockdown; sensitively detect crosstalk between endogenous signaling pathways in vivo; and accurately identify compounds capable of inhibiting selected signaling pathways. Our findings indicate that EPS can accurately predict pathway activity over a wide dynamic range based upon gene expression data sets derived from multiple profiling platforms, as well as different species, tissues and cell types in both in vitro and in vivo contexts Four timepoints (0h, 24h, 48h and 96h) with 3 replicates per timepoint of doxycycline induction for MTB (Control), MTB/TAN, MTB/TOM and MTB/TWNT1
2013-09-18 | E-GEOD-50969 | biostudies-arrayexpress
Project description:To test whether SVD regression is sufficiently sensitive to detect activation of a secondary, endogenous pathway as it occurs following ectopic manipulation of a strong primary pathway by focusing on the relationship between the Ras and TGFβ signaling pathways. Experiment Overall Design: Bitransgenic MTB/TRAS mice in an FVB/N background were generated by crossing MTB and TRAS mice. To induce oncogenic v-H-Ras expression, 6-week old MTB/TRAS female mice were administered 2 mg/ml doxycycline with 5% sucrose in their drinking water. Mammary tissue was harvested at different post-induction time points and snap frozen. To generate Ras-driven tumors, MTB/TRAS mice were administered 0.012 mg/ml doxycycline in their drinking water and monitored for tumor formation. Mice were sacrificed when tumors reached ~1 cm and tissue was snap frozen. The non-transformed murine mammary epithelial cell line, NMuMG, was cultured in Dulbeccoâs modified Eagleâs medium (DMEM) supplemented with 10% bovine calf serum, 1% penicillin/streptomycin, and 2 mM L-glutamine. For TGFβ treatment, cells were cultured in low serum medium (0.5%) overnight followed by treatment with 5 ng/ml TGF-β1 or TGF-β3 (Sigma). After 24 hr, RNA and protein were harvested for microarray hybridization or biochemical analysis.
2009-01-13 | E-GEOD-13986 | biostudies-arrayexpress
Project description:Baseline gene expression for two primary and two recurrent tumor cell lines derived from MTB;TAN transgenic mice. Microarrays were performed in biological duplicate to determine differential gene expression between primary and recurrent tumor cell cohorts.
2018-07-03 | GSE116513 | GEO
Project description:Response of dox-inducible, bitransgenic Ccsp-rtta x Teto-fgf7 mice to 1 and 3 days of doxycycline treatment
2022-11-22 | E-MEXP-644 | biostudies-arrayexpress
Project description:The aim of this experiment is to determine microRNAs that are diffferentially regulated in allergic airway inflammation. MicroRNA expression profile between untreated and doxycycline treated CC10-IL13 bitransgenic mice
2009-04-15 | E-MEXP-1992 | biostudies-arrayexpress
Project description:Analysis of mammary glands from tet-inducible(rtTA) transgenic mice expressing cyclin D1 using Affymetrix Mouse Gene 1.0 ST GeneChip arrays. MMTV-rtTA transgenic mice (MMTV-Mouse Mammary Tumor Virus promoter) were cross-mated to cyclin D1 transgenic mice under control of tet operon. 8-week-old tetracycline-inducible cyclin D1/rtTA bi-transgenic pregnant female mice (12 days postcoitus) were treated with doxycycline through drinking water supplementation at a final concentration of 2 mg/ml. Control mice were rtTA transgenics alone and treated in the same manner. After 7 days of doxycycline treatment, the mice were sacrificed and mammary glands taken for RNA isolation. Results provide insight into the in vivo gene expression pattern regulated by cyclin D1 through acute induction. Analysis of mammary glands from MMTV-cyclin D1/WT and MMTV-cyclin D1/KE using Affymetrix Mouse 430A v2.0 GeneChip arrays. Cyclin D1 point mutant, cyclin D1/KE K112E (K112E) contains a lysine to glutamine substitution at amino acid position 112. cyclin D1. The cyclin D1/KE mutant fails to induce cyclin D1-dependent kinase activity. Female MFD1, MFD1-KE, and WT mice were monitored twice weekly, up to 760 days, for the development of palpable tumors. Those developing palpable tumors were sacrificed within a week of tumor detection. Tumors were dissected and portions snap frozen for RNA isolation. Results provide insight into the in vivo gene expression pattern regulated by cyclin D1 that is kinase independent. Two separate control mice were positive for MMTV-rtTA transgene compared to 3 separate cyclin D1/rtTA bitransgenic female mice and 3 separate cyclin D1 KE mutant/rtTA bitransgenic female mice (Mouse Gene 1.0 ST arrays). Three separate control WT FvBmice were compared to three MMTV-cyclin D1/WT and 3 MMTV-cyclin D1/KE mice (Mouse 430A v2.0 arrays).
2013-12-31 | E-GEOD-43216 | biostudies-arrayexpress
Project description:Control of Mycobacterium tuberculosis infection requires generation of T cells that migrate to granulomas, complex immune structures surrounding sites of bacterial replication. Here we compared the gene expression profiles of T cells in pulmonary granulomas, bronchoalveolar lavage and blood of Mtb-infected rhesus macaques to identify granuloma-enriched T cell genes. TNFRSF8/CD30 was among the top genes that was upregulated in both CD4 and CD8 granuloma T cells and independent of bacterial loads. Transcriptomic profiling of lung T cells from Mtb-infected mixed bone marrow chimeric mice showed that CD30 directly promotes CD4 T cell differentiation and effector molecule expression. Moreover, in mice CD30 expression on CD4 T cells is required for survival of Mtb infection. These results show the CD30 co-stimulatory axis is highly upregulated on granuloma T cells and is critical for the generation of protective T cell responses against Mtb infection.
2023-03-24 | GSE228113 | GEO
Project description:Over-expression of Stat3C in lung alveolar type II epithelial cells of CCSP-rtTA/(teto)7Stat3C bitransgenic mice leads to severe pulmonary inflammation in the lung. As a consequence, spontaneous lung bronchoalveolar adenocarcinoma was observed in bitransgenic mice. Aberrantly expressed genes in the bitransgenic model were identified by Affymetrix GeneChip Microarray. Lungs were isolated from 4 individual mice in each group after 9 months of doxycycline-treatment. To eliminate sample differences generated by individual mice, the lung tissues were combined in each group and homogenized for RNA isolation. The total lung RNAs were purified using the QIAGEN total RNA purification kit as recommended by the manufacturer. The Affymetrix GeneChip assay was performed in duplicate. Briefly, the same amounts (10 ug) of total RNAs from the lungs of doxycycline not treated and treated mice was subject to reverse transcription using oligo dT with T7 promoter sequences attached, followed by second strand cDNA synthesis. Antisense cRNA was then amplified and biotinylated using T7 RNA polymerase, prior to hybridization to the Mouse 430A GeneChip (Affymetrix Inc) using the Affymetrix recommended protocol. Affymetrix MicroArray Suite version 5.0 was used to scan and quantitate the Genechips using default scan settings. Intensity data was collected from each chip, scaled to a target intensity of 1500 and the results were analyzed using GeneSpring 5.0 (Silicon Genetics, Inc.) and JMP4 (SAS Institute, Inc.). Hybridization data were sequentially subject to normalization, transformation, filtering and functional classification. Genes differentially expressed between doxycycline treated and not treated mice were identified by Student t-test at p value < 0.05 and fold change > 2. To evaluate data consistency and reproducibility, coefficiency of variation among replicates were calculated with the maximal cutoff line as 98%.
2008-05-07 | E-MEXP-1137 | biostudies-arrayexpress
Project description:Purpose: The goal of this study was to characterize the atrial and ventricular transcriptomic changes in a cardiac mouse model of myotonic dystrophy. The mouse model utilizes a bitransgenic system for doxycycline (dox) inducible and cardiomyocyte specific expression of pathogenic RNA containing 960 CUG repeats. Bitransgenic animals (called CUG960 mice) homozygous for the TREDT960I transgene (containing 960 interrupted CTG repeats) and hemizygous for reverse transactivator (rtTA) transgene containing a cardiomyocyte-specific alpha myosin heavy chain promoter are given dox food for expression of CUG repeat RNA. Mice hemizygous for rtTA transgene (MHCrtTA) given dox food were used as controls. Methods:We performed RNA-seq for high-resolution analysis of transcriptomic alterations in atria and ventricles of CUG960 experimental and MHCrtTA control mice given dox chow since postnatal day 1 (PN1) for a period of 10 weeks. Results: We identified pathogenic CUG repeat RNA induced gene expression and alternative splicing changes in ion transport genes that are associated with inherited cardiac conduction diseases, including a subset of genes involved in calcium handling. Conclusions: We identified potential tissue-specific mechanisms contributing to the cardiac disease relevant phenotypes in an animal model of DM1.
2021-01-15 | GSE164825 | GEO
Project description:We use bulk RNA sequencing of sorted cells to characterize the gene expression profiles of splenic TOM+ cDC2 and TOM- DC2 from 1 week-old mice as well and of TOM+ cDC2 from adult mice. We aim to reveal transcriptional differences based on ontogeny and developmental age. Sequencing results revealed that the developmental age rather than cell origin is a major determinantof the transcriptomic differences observed between young and adult cDC2.
2020-11-06 | GSE151593 | GEO