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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Expression data from post natal mouse aortic heart valves treated with all-trans retinoic acid or a retinoic acid receptor antagonist (LE540) relative to DMSO treated controls

ABSTRACT: Our lab has previously shown that treatment of murine heart valve explants with ATRA promotes calcification in vitro. In order to fully explore gene expression changes in the valve in response to ATRA or LE540, a high throughput microarray was performed. In this data set, we include expression data from dissected murine post natal aortic valve explants treated with ATRA or DMSO as a vehicle control. These data are used to obtain 432 probe sets that are differentially expressed in response to ATRA treatment, with 118 being downregulated and 314 increased. A total of 9 samples were analyzed; 3 DMSO treated controls, 3 LE540 and 3 ATRA treated experimental samples. Differential expression of probe sets were ranked based on false discovery rate (<0.1) and fold change (>2).

ORGANISM(S): Mus musculus

SUBMITTER: Joy Lincoln

PROVIDER: E-GEOD-40491 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Expression data from post natal mouse aortic heart valves treated with all-trans retinoic acid or a retinoic acid receptor antagonist (LE540) relative to DMSO treated controls

Project description:Our lab has previously shown that treatment of murine heart valve explants with ATRA promotes calcification in vitro. In order to fully explore gene expression changes in the valve in response to ATRA or LE540, a high throughput microarray was performed. In this data set, we include expression data from dissected murine post natal aortic valve explants treated with ATRA or DMSO as a vehicle control. These data are used to obtain 432 probe sets that are differentially expressed in response to ATRA treatment, with 118 being downregulated and 314 increased.

2012-08-31 | GSE40491 | GEO

The effect of a novel form of macrophage colony-stimulating factor (CSF1-Fc) on gene expression in the liver.

Project description:Treatment of mice with daily injections of CSF1-Fc produce a 50% increase in the size of the liver within 5 days. There was extensive proliferation of hepatocytes, similar to that seen following partial hepatectomy. Comparative gene expression profiles of the treated and control livers, alongside macrophages grown in CSF1, indicate extensive infiltration by macrophages in response to CSF1-Fc, and demonstrate that infiltrating macrophages produced several candidate mediators of hepatocyte proliferation.

2013-12-31 | E-GEOD-52636 | biostudies-arrayexpress

Expression data comparing dp53R-shSCR and dp53R-shARF mouse embryonic fibroblasts

Project description:Mouse embryonic fibroblasts deficient for p53 and expressing mutant RasV12 were infected with lentiviral constructs carrying short hairpin RNAs targeting ARF or a scrambled control. Four days post infection, cells were harvested for microarray analysis. 6 Total samples were analyzed. Arrays were downloaded from Washington University bioinformatics web site and processed in Affymetrix Expression Console (Affymetrix, Version) using RMA (Robust Multi-chip Average)algorithm. Only core probesets were used for the analysis. Control probesets as well as those interrogating probesets that are absent across all 12 arrays were filtered out. We considered those probesets as 'Present' while their signal intensity exceeded Mean (negative control signal intensity) +2 X Standard deviations (negative control signal intensity).Hierarchical cluster map was plotted using Partek Genomic suite to visualize the sample quality and differential expression analysis was performed using Significant Analysis of Microarrays (SAM) and list of differentially expressed genes were generated.

2013-06-27 | E-GEOD-48315 | biostudies-arrayexpress

Whole-genome microarray analysis of primary, secondary, tertiary and quaternary memory CD8 T cells

Project description:The transcriptome of naive OT-I T cells was compared to memory CD8 T cells after 1, 2, 3, or 4 infection with ovalbumin expressing Listeria monocytogenes (LM-OVA). Naive Thy1.1 OT-I T cells were adoptively transferred into Thy1.2 naive hosts prior to infection with LM-OVA. The resulting memory CD8 T cell population was again adoptively transferred into naive hosts and the recipient mice were again infected with LM-OVA. The adoptive transfer was repeated up to four times to generate memory CD8 T cells with up to four consecutive antigen stimulations. Three individual mice were analyzed for each group. For quaternary memory CD8 T cells, spleens from two to three mice were pooled for each sample. Naive OT-I T cells served as control samples. http://dx.doi.org/10.1016/j.immuni.2010.06.014

2010-07-09 | E-GEOD-21360 | biostudies-arrayexpress

Expression data from WT DN3, TCF-1-deficient DN3 thymocytes, and T cell lymphomas in TCF-1-deficient animals.

Project description:TCF-1 is an HMG family transcription factor which is known to be critical for T cell development. We discovered that it has a unique role in suppressing malignant transformation of developing thymocytes at early stages. We identified ID2 and LEF-1 as key TCF-1 target genens in tumor suppression. We used microarrays to detect gene expression changes in WT and TCF-1 deficient DN3 thymocytes as well as T cell lymphoma cells developed in TCF-1 KO mice. DN3 thymocytes were directly sorted from WT or TCF-1 KO mice. T cell lymphoma blast cells were also sorted from TCF-1 KO mice that developed the disease. RNA was extracted and hybridized to GeneChip Mouse GENE 1.0 ST arrays (Affymetrix).

2012-10-25 | E-GEOD-33292 | biostudies-arrayexpress

Expression data from WT and TCF-1-deficient memory CD8 T cells

Project description:TCF-1 is an HMG family transcription factor which is known to be activated by the canonical Wnt signaling pathway and modulated by other signals such as those derived from T cell receptor. We found that during CD8 T cell responses, TCF-1 deficiency impaired long-term maintenance of antigen-specific memory CD8 T cells. We used microarrays to detect gene expression changes in memory CD8 T cells caused by TCF-1 deficiency. Host mice that received WT or TCF-1-deficient OT-I CD8 T cells were infected with attenuated Listeria monocytogenes expressing Ova peptide. In memory phase (i.e., more than 80 days post infection), antigen-specific T cells were ioslated by cell sorting. RNA was extracted and hybridized to GeneChip Mouse GENE 1.0 ST arrays (Affymetrix).

2010-10-04 | E-GEOD-20754 | biostudies-arrayexpress

Expression data from Tcf1 deficient and Tcf1 wildtype cultured bone marrow lymphoid primed progenitors after four days on Notch ligand expressing stroma (OP9-DL4).

Project description:Tcf1 is necessary for optimal T lineage development. Tcf1 deficient progenitors fail to initiate the T lineage program in vitro and development is severely defective in vivo. We used microarrays to assess the overal global gene expression differences from Tcf1 wildtype and deficient lymphoid biased progenitors cultures on Notch-ligand expressing stroma to determine if Tcf1 deficient progenitors are able to intiate the T lineage specification program. Abstract of manuscript: The thymus imposes the T cell fate on incoming multipotent progenitors, but the molecular mechanisms are poorly understood. We show that transcription factor Tcf1 initiates T-lineage-specific gene expression. Tcf1 is downstream of Notch1 signaling and expressed in early T-cell progenitors. Progenitors deficient for Tcf1 are unable to initiate normal T-lineage specification. Conversely, ectopic expression of Tcf1 in hematopoietic progenitors is sufficient to induce expression of T-lineage specific genes in vitro. Thus, our study identifies Tcf1 as critically involved in the establishment T cell identity. Tcf1 wildtype and deficient bone marrow lymphoid primed progenitors (LMPPs, Lineage marker- Sca+kit+Flt3high) were harvested in triplicate and seeded onto OP9-DL4 expressing stroma for 4 days upon which highly pure lineage negative and Thy1+CD25+ T cells were cell sorted for expression analysis. The lineage negative populations represent three seperate mice from each genotype and the Thy1+CD25+T lineage population represents two replicates from the Tcf1 wildtype group. No Thy1+CD25+ T lineage cells develop from Tcf1 deficient progentiors.

2011-08-03 | E-GEOD-26559 | biostudies-arrayexpress

Hemangioblast skewing from embryonic stem(ES) cells by defined factors

Project description:Successful derivation of a specific cell lineage from pluripotent stem cells will tremendously facilitate the clinical usage of pluripotent stem derived somatic cells. Herein, we demonstrate that ER71/Etv2, GATA2 and Scl form a core network in hemangioblast development and that transient co-expression of these three factors robustly induced hemangioblasts from ES cells. Such induced hemangioblasts potently generated hematopoietic and endothelial cells in culture as well as in vivo, warranting the evaluation of these cells in the future for repairing and/or regenerating hematopoietic and/or angiogenic defects. We have established a doxycycline inducible ES cell, iEGS, in which ER71/Etv2, GATA2 three transcription factors can be transiently co-expressed by doxycycline induction. We further analyzed the downstream target genes and signaling pathways at 6, 12 and 24hrs after ER71/Etv2, GATA2 induction. These data were obtained from three independent experiments.

2014-02-03 | E-GEOD-45147 | biostudies-arrayexpress

Expression data from WT and GABPalpha-deficient Flt3(-) LSK cells

Project description:GABPalpha is an Ets family transcription factor and involved in regulation of both basic cellular functions such as cell cycle progression and tissue-specific biological processes. We found that GABPalpha is critically required for survival and differentiation of hematopoietic stem cells. We used microarrays to detect gene expression changes in Flt3(-) LSK cells (which contains both long-term and short-term hematopoietic stem cells) by GABPalpha deficiency. Mx1Cre-GABPa(FL/+) and Mx1Cre-GABPa(FL/-) mice were treated with pIpC to induce inactivation of GABPalpha in bone marrow cells. Four days after last treatment of pIpC, the bone marrow cells were isolated and the Flt3(-)LSK subset was purified by cell sorting. RNA was extracted and hybridized to GeneChip Mouse GENE 1.0 ST arrays (Affymetrix).

2011-07-27 | E-GEOD-23341 | biostudies-arrayexpress

Regulatory RNA Apela Is a Component of a Negative Feedback Loop Regulating p53-Mediated Apoptosis in Embryonic Stem Cells (I)

Project description:p53-repressed transcripts have recently been shown to play important roles in various biological processes, such as stem cell differentiation and cancer. We identified a transcript named Apela that is repressed by p53 and highly expressed in mouse ES cells. To see which transcripts are affected by Apela knockdown, we performed gene expression microarray using Affymetrix Gene ST 1.0 array. Two short hairpin RNAs (shRNAs) targeting Apela were used to decrease the RNA levels of Apela to about 20% of the control (a shRNA target luciferase, shLuc). We designed two lentivirus-based shRNAs against Apela and used shRNA against luciferase as a control. Lentiviruses were made and used to transduced mouse ES cells. For each shRNA, three repeats were done.

2015-06-05 | E-GEOD-54355 | biostudies-arrayexpress

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