Genome-wide analysis of transcription factor PPARγ-responsive gene expression in the nodose ganglion (NG)
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ABSTRACT: Analysis of gene expression regulated by PPARγ in the nodose ganglion of Phox2b::Cre; PPARγ fl/+ and Phox2b::Cre; PPARγ fl/fl mice. Resutls demonstrate potential PPARγ transcriptional targets in neurons RNA was purified from laser-captured nodose neurons. Three independent biological replicates were prepared by pooling RNA of nodose neurons from multiple animals of the same genotypes. Genomics and Microarray Core Facility at UT Southwestern ( http://microarray.swmed.edu/) checked RNA quality and performed the hybridization with a Mouse-6 V2 BeadChip (Illumina Inc.). We used Partek Genomics Suite 6.5 (Partek Inc.) and Ingenuity Pathway Analysis (Ingenuity Systems Inc.) for data and pathway analysis respectively.
Project description:Analysis of gene expression regulated by PPARγ in the nodose ganglion of Phox2b::Cre; PPARγ fl/+ and Phox2b::Cre; PPARγ fl/fl mice. Resutls demonstrate potential PPARγ transcriptional targets in neurons
Project description:Analysis of gene expression regulated by FoxO1 in the ventromedial hypothalamus (VMH) of wildtype and knockout mice. Results provide important information of gene expression in the VMH. The transcription factor FoxO1 contributes to leptin and insulin action, including cells in the brain. However, the neurons mediating these effects and the identity of the molecular targets through which FoxO1 exerts metabolic actions remains to be defined. For the gene expression profiling, total RNA was obtained from the VMH of WT and VMH-specific FoxO1 KO mice using Qiagen RNeasy Lipid Tissue Mini Kit (Qiagen Sciences, Maryland) and Phase Lock Gel (5 Prime Inc., Gaithersburg, MD). To make sure reproducibility and biological significance, triple hybridizations were performed for each genotype with the RNA from three independent VMH samples, each sample contains RNA from three animals (biological replicates). Genomics and Microarray Core Facility at UT-Southwestern (http://microarray.swmed.edu/) checked RNA quality with Bioanalyzer Chip and processed the samples for hybridization with Illumina Mouse-6 V2 BeadChip (Illumina Inc., San Diego, CA). We used Partek Genomics Suite 6.5 (Partek Inc., St Louis, MO) and Ingenuity Pathway Analysis (Ingenuity Systems, Inc., Redwood City, CA) for data analysis.
Project description:Five HCMV (+) CRC tissues detected by PCR were selected for RNA-seq. GEPs were pre-processed by Cutadapter and FastQC to remove jointed reads and low-quality reads. Tophat (v.2.0.0) was used to compare the sequences with Homo sapiens and HCMV genomes. The GEPs of HCMV was determined by Integrated Genomics Viewer (IGV) and Partek® Genomics Suite™ (version 6.5 beta, Partek Inc., St. Louis, MO, USA).
Project description:We are using genome-wide ChIP-seq with isoform-specific antibodies and chromatin from select tissues of mice challenged with different dietary conditions that enrich for specific SREBPs. We show that hepatic SREBP-2 binds preferentially to two different gene-proximal motifs as well as SREBP-2 directly activates autophagy genes during cell sterol depletion, conditions known to induce both autophagy and nuclear SREBP-2 levels. Gene expression profiling was carried out using the Mouse Gene 1.0 OST (Affymetrix) by hybridizing RNA from LE and Ch livers in triplicate at the Sanford-Burnham Genomics Core facility in Lake Nona Fl. Differential expression was then assessed using the Partek Genomics Suite (Partek Inc.) and cyberT.
Project description:RNA was extracted from cells using Aurum Total RNA kit from Bio-Rad Laboratories, Inc., Hercules, CA following the manufacturer’s recommendations. Gene expression profiling was performed using the BeadChip HumanHT-12 v4 Expression kit from Illumina®, which contains 47,231 gene-probes (Illumina® Inc., San Diego, CA). The raw signal intensities were imported and analyzed using the GenomeStudio® data software. After background subtraction and normalization, the signal intensity values were exported to the Partek® genomics expression analysis suite using “Partek's Report Plug-in” option in the GenomeStudio® software. Differentially expressed genes in the dox- versus vehicle-treated samples were identified using the “gene expression” workflow in the Partek® software.
Project description:Branchiomotor neurons are an important class of cranial motor neurons that innervate the branchial-arch-derived muscles of the face, jaw and neck. They arise in the ventralmost progenitor domain of the rhombencephalon characterized by expression of the homeodomain transcription factors Nkx2.2 and Phox2b. Phox2b in particular plays a key role in the specification of branchiomotor neurons. In its absence, generic neuronal differentiation is defective in the progenitor domain, and no branchiomotor neurons are produced. Conversely, ectopic expression of Phox2b in spinal regions of the neural tube promotes cell cycle exit and neuronal differentiation and at the same time induces genes and an axonal phenotype characteristic for branchiomotor neurons. How Phox2b exerts its pleiotropic functions, both as a proneural gene and a neuronal subtype determinant, has remained unknown. To gain further insight into the genetic programme downstream of Phox2b we searched for novel Phox2b-regulated genes by cDNA microarray (here NIA 15k slides) analysis of facial branchiomotor neuron precursors from heterozygous and homozygous Phox2b mutant embryos. Keywords: Phox2b-regulated genes identification Four biological replicates each in dye swap
Project description:Branchiomotor neurons are an important class of cranial motor neurons that innervate the branchial-arch-derived muscles of the face, jaw and neck. They arise in the ventralmost progenitor domain of the rhombencephalon characterized by expression of the homeodomain transcription factors Nkx2.2 and Phox2b. Phox2b in particular plays a key role in the specification of branchiomotor neurons. In its absence, generic neuronal differentiation is defective in the progenitor domain, and no branchiomotor neurons are produced. Conversely, ectopic expression of Phox2b in spinal regions of the neural tube promotes cell cycle exit and neuronal differentiation and at the same time induces genes and an axonal phenotype characteristic for branchiomotor neurons. How Phox2b exerts its pleiotropic functions, both as a proneural gene and a neuronal subtype determinant, has remained unknown. To gain further insight into the genetic programme downstream of Phox2b we searched for novel Phox2b-regulated genes by cDNA microarray (here NeuroDev slides) analysis of facial branchiomotor neuron precursors from heterozygous and homozygous Phox2b mutant embryos. Keywords: Phox2b-regulated genes identification Four biological replicates each in dye swap
Project description:Dhps<fl/fl> mice and Dhps<fl/fl>;Vil1<cre/+> mice were infected or not with Citrobacter rodentium (10^9 bacteria/mouse) for 14 days, and cell lysates were prepared for analysis. A total of 4 mice per group were used for the following groups: (1) Vil1<+> no C. Rod; (2) Vil1<cre> no C. Rod; (3) Vil1<+> with C. Rod; (4) Vil1<cre> with C. Rod
Project description:This study (McConnell, et al. Science 2012) used both SNP array and sequencing data to examine copy number variation in neuronal genomes. Encolsed here are the SNP Array data from the 42 fibroblasts, 19 human induced pluripotent stem cell (hiPSC)-derived neural progenitor cells (NPCs), and 40 hiPSC-derived neurons that were reported in the manuscript. Copy number analysis was performed on .CEL files using Partek Genomics Suite with a custom single cell reference file.