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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Murine forestomach epithelial sheets: Controls vs. Sox2 overexpression mutants

ABSTRACT: Transcriptional profiling of adult forestomach epithelium comparing K5-CreER controsl with K5-CreER;Rosa26Sox2/Sox2 mutants. Two doses of tamoxifen were given and four weeks later the epithelal sheets were harvested for RNA extraction. Goal was to determine the effects of Sox2 overexpression on epithelial phenotypic changes. Two-condition experiment, wildtype Vs Sox2 overexpression mutant. Biological replicates: 3 control replicates, 3 mutant replicates.

ORGANISM(S): Mus musculus

SUBMITTER: Hao Chen

PROVIDER: E-GEOD-37857 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Murine forestomach epithelial sheets: Controls vs. Sox2 overexpression mutants

Project description:Transcriptional profiling of adult forestomach epithelium comparing K5-CreER controsl with K5-CreER;Rosa26Sox2/Sox2 mutants. Two doses of tamoxifen were given and four weeks later the epithelal sheets were harvested for RNA extraction. Goal was to determine the effects of Sox2 overexpression on epithelial phenotypic changes.

2012-05-09 | GSE37857 | GEO

Mus musculus

Project description:Murine forestomach epithelial sheets: Controls vs. Sox2 overexpression mutants

| PRJNA164691 | ENA

Transcriptional analysis of apoptotic cerebellar granule neurons following rescue by Gip, Sp, Pacap and Igf1

Project description:Primary cultures of Cerebellar Granule Neurons (CGNs) have been extensively utilized to examine the signal transduction mechanisms underlying neuronal apoptosis. We conducted whole-genome expression profiling to decipher the transcriptional program controlling the apoptotic/survival switch in cerebellar granule neurons (CGNs) following the induction of apoptosis by serum and potassium deprivation and their rescue by gastric inhibitory polypeptide (Gip), substance p (Sp), insulin-like growth factor-1 (Igf1) or pituitary adenylyl cyclase-activating polypeptide (Pacap). Our results reveal the transcriptional changes intersecting neuronal apoptosis and survival and form the basis for further functional analyses and pharmacological exploitation to identify neuroprotective drugs. After six days âin vitroâ (DIV), extracellular KCl of CGNs was shifted from 25 to 5 mM for neuronal apoptotic death induction. After two washes with serum-free BME containing 5 mM KCl, neurons were incubated with the same medium for 6 h (K5), while control neurons were incubated with serum free medium supplemented with 25 mM KCl (K25). K5 neurons were also treated with a maximal effective dose of Gip, Sp, Igf1 and Pacap. Four biological replicates (derived from the same litter) for each of the experimental conditions (K25, K5, K5 + Gip; K25, K5, K5 + Sp; K25, K5, K5 + Igf1; K25, K5, K5 + Pacap) were analyzed.

2016-07-03 | E-GEOD-67788 | biostudies-arrayexpress

Transcription profiling of mouse model of Epidermolysis bullosa simplex keratin5 knockout epidermis response to doxycycline treatment

Project description:Epidermolysis bullosa simplex (EBS) is a skin disorder caused by mutations in keratin (K) 5 or K14 genes. Little effect therapy is available.Following clinical reports, we applied the small molecule doxycycline to K5-/- mice. We demonstrate that doxycycline extended the survival of neonatal K5-/- mice from less than 1 to up to 8 hours. Microarray and TaqMan real-time PCR showed a downregulation of MMP-13 and IL-1ï¢, indicating an effect of doxycycline on transcription. Our data offer a novel small molecule based therapy approach for EBS. Experiment Overall Design: doxycycline (50 Âµg/mlwith 5 % sucrose) was administered by oral route to pregnant K5+/- females (mated to K5+/- males) starting from E13.5. 5 % sucrose solution was administered to the control group.

2008-06-15 | E-GEOD-7662 | biostudies-arrayexpress

Transcription profiling of mouse medulloblastoma

Project description:Dysregulatio of Hh signaling has been shown to be involved in the formation of human medulloblastoma. We generated a mouse model (CAGGS-CreER;R26-SmoM2) of Hh related tumors. We used microarray to profile gene expression in Hh induced mouse medulloblastoma and identified distinct classes of up-regulated or down-regulated genes during Hh dependent tumorigenesis . Experiment Overall Design: Medulloblastoma samples and adjacent wild type cerebellar tissue from CAGGS-CreER;R26-SmoM2 mice were isolated for RNA extraction and hybridization on Affymetrix microarrays.

2008-06-16 | E-GEOD-9299 | biostudies-arrayexpress

Comparison of the transcripts in control and Blimp-1-deficient keratinocytes

Project description:We performed microarray analysis to examine the differential gene expression profiles between Prdm1 (Blimp-1)-deleted and control keratinocytes. Keratinocytes isolated from Prdm1-floxed K5-CreER positive (CKO) mice were cultured in the presence of 4OHT to induce deletion of the Prdm1 allele in vitro. Prdm1-floxed K5-CreER positive (CKO) keratinocytes treated with the ethanol solvent control (EtOH) or Prdm1-floxed K5-CreER negative (control) keratinocytes treated with 4OHT or EtOH served as controls. Microarray analyses revealed that there were 93 genes up-regulated and 109 genes down-regulated by more than 2-fold in the CKO + 4OHT group in comparison with the CKO + EtOH, Ctrl + 4OHT or Ctrl + EtOH groups. Several corneocytes-related genes, including Rptn, Lce1f, Krt1 and Lce1d, are significantly down-regulated and several cytokines/chemokines, including Cxcl1, Cxcl2, Cxcl5 and Il24, are significantly up-regulated upon the deletion of Prdm1 in vitro.

2013-04-02 | GSE34586 | GEO

Gene expression changes in Apc-mutant mouse intestinal organoids with and without deleting the Prox1 transcription factor

Project description:We isolated and selected intestinal adenoma organoids from villin-CreER; Apcflox/flox and villin-CreER; Apcflox/flox; Prox1flox/flox mice and added tamoxifen to induce the deletion of the Apc and Prox1 genes in the intestinal epitheliul ex vivo. Microarray experiments were carried out 7 days after the addition of tamoxifen. Total RNA obtained from villin-CreER; Apcflox/flox and villin-CreER; Apcflox/flox; Prox1flox/flox organoids were compared 7 days after the addition of tamoxifen and 5 days after the selection for Apc-mutant organoids in the absence of the Wnt-agonist R-Spondin1.

2014-08-15 | E-GEOD-47568 | biostudies-arrayexpress

Comparison of the transcripts in control and Blimp-1-deficient keratinocytes

2013-04-02 | E-GEOD-34586 | biostudies-arrayexpress

mRNA profiling of Pontin depleted ES cells and Oct4 depleted ES cells

Project description:In order to investigate the cooperative roles of Pontin and Oct4 for self-renewal and pluripotency in mouse ES cells, we performed mRNA-sequencing analysis from mRNAs isolated from Pontin- and Oct4-depleted ES cells. This analysis provides insight into molecular mechanisms for maintaining ES cell identity. mRNA expression profiles of Pontinf/f; CreER ES cells at 0, 3, or 4 days post-treatment with OHT (wild type and Pontin-depleted ES cells) and ZHBTc4 ES cells at 2 days post-treatment with tetracycline (Oct4-depleted ESE cells) were examined by Illumina Hiseq2000.

2015-10-16 | E-MTAB-1953 | biostudies-arrayexpress

FAM3C/ILEI protein is elevated in psoriatic lesions and triggers psoriasiform hyperproliferation in mice

Project description:Inducible keratinocyte-specific ILEI overexpression in mice (K5-ILEIind) recapitulates many aspects of psoriasis following TPA challenge, primarily manifested by impaired epidermal differentiation and increased neutrophil recruitment. Mechanistically, ILEI triggers Erk and Akt signaling, which then activate STAT3 via Ser727 phosphorylation. Keratinocyte-specific ILEI deletion ameliorates TPA-induced skin inflammation. A transcriptomic ILEI signature obtained from the K5-ILEIind model shows enrichment in several signaling pathways also found in psoriasis and identifies urokinase as a targetable enzyme to counteract ILEI activity. Pharmacological inhibition of urokinase in TPA-induced K5-ILEIind mice results in significant improvement of psoriasiform symptoms by reducing ILEI secretion. The ILEI signature distinguishes psoriasis from healthy skin with uPA ranking among the top “separator” genes. Our study identifies ILEI as a key driver in psoriasis, indicates the relevance of ILEI-regulated genes for disease manifestation and shows the clinical impact of ILEI and urokinase as novel potential therapeutic targets in psoriasis.

2023-04-12 | E-MTAB-12849 | biostudies-arrayexpress

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