Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Murine Adult Cortex: Gtf2i (+/Δex2 ) VS WT (+/+)

ABSTRACT: Transcriptional profiling of mouse cortex tissue comparing control animals with Gtf2i-mutated mouse (Gtf2i+/Δex2 ). Goal was to determine the specific deregulated genes in the cortex of mutated animals. Pools of total RNA derived from five-three mice of each genotype were subjected to microarray analysis. We compared pools instead of single individuals in order to minimize individual and technically-related variation. The original raw data file (i.e. Agilent feature extraction files) are not available. The modified raw data files are provided along with the file contents description (raw_data_readme.txt available on Series records).

ORGANISM(S): Mus musculus

SUBMITTER: Victoria Campuzano

PROVIDER: E-GEOD-41251 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

TFII-I regulates target genes in the PI-3K and TGF-β signaling pathways through a novel DNA binding motif.

Segura-Puimedon Maria M Borralleras Cristina C Pérez-Jurado Luis A LA Campuzano Victoria V

Gene 20130703 2

General transcription factor (TFII-I) is a multi-functional protein involved in the transcriptional regulation of critical developmental genes, encoded by the GTF2I gene located on chromosome 7q11.23. Haploinsufficiency at GTF2I has been shown to play a major role in the neurodevelopmental features of Williams-Beuren syndrome (WBS). Identification of genes regulated by TFII-I is thus critical to detect molecular determinants of WBS as well as to identify potential new targets for specific pharma ...[more]

PMID: 23831514

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Project description:Recombinant baculoviral vectors efficiently transduce several types of cells in the brain. To characterize host responses to viral challenge, thus verifying the suitability of using the virus for the development of gene therapy strategies in the central nervous system, we used cDNA microarray technology to examine in vitro and in vivo global cellular gene expression profiles after viral transduction. We demonstrated that the transduction induced host antiviral responses as a major reaction in all three types of samples profiled, including the rat brain, cultured human astrocytes and human neuronal cells. The related genes were mainly those associated with innate immunity. Several genes of the major histocompatibility complex molecules, an important component of the host adaptive immunity to exogenous pathogens, were up-regulated in the rat brain and human astrocytes, but not in neuronal cells. We also observed that genes related to cell death and apoptosis were up-regulated and genes related cell cycle regulation were down-regulated in neuronal cells, but not obviously affected in astrocytes. These findings should be useful in understating the molecular basis for neural cell response to baculoviral transduction and guiding rational applications of baculoviral vectors in the central nervous systems Experiment Overall Design: For in vivo viral inoculation, adult male Wistar rats (weighing 250â300 g) were used. Five Î¼l of baculovirus vectors (5 x 107 viral particles) was injected stereotaxically into the striatum at two injection sites (AP Â±1.0mm, ML +2.5mm, and DV -5.0mm from bregma and dura) using a 10 Î¼l Hamilton syringe connected with a 30-gauge needle, at a speed of 0.5 Î¼l/min. The needle remained in place for another 5 min before being slowly retracted. Rats were sacrificed and the brain tissues were collected 48 hours later for analysis. Five Î¼l of PBS was injection into the contralateral striatum and the tissues were collected and used as controls. Experiment Overall Design: Seven rats were used for the study. Experiment Overall Design: Total RNA was isolated using TrizolÂ® (Invitrogen, Carlsbad,CA) according to the manufacturerâs instruction. RNA was further cleaned up using RNeasy mini kit (Qiagen). Total RNA was quantified using a Nanodrop spectrophotometer and its quality was further assessed using an RNA nanochip on a Bioanalyzer. One to 10 ïg of good quality RNA (i.e. A260/A280 > 2.0 and A230/A260 > 2.1) was used to prepare labeled cRNA using either Affymetrixâs One-Cycle Target Labeling and Control Reagents or Kreatechâs RNA ampULSe amplification and labeling kit (Kreatech, Amsterdam, The Netherlands). Hybridization mixes with 15 ïg of fragmented cRNA previously checked on the bioanalyzer were prepared according to Affymetrixâs GeneChipÂ® Hybridization, Wash, and Stain Kitâs instruction and used to hybridize the human GeneChipï¢ Human Genome U133 Plus 2.0 or GeneChipï¢ Rat Genome 230 2.0 for 16 hours at 45ÂºC. The arrays were washed and stained with phycoerythrin according to the manufacturerâs instructions. Chips were scanned using GeneChipÂ® Scanner 3000 and data acquired using the GCOS software. Experiment Overall Design: Data obtained from GCOS was exported using the Data Transfer Tool and transferred to GeneSpring and Genedata software respectively. The GC-RMA preprocessor file was used to re-process imported CEL files and to normalize the data at the probe level. Replicates (at least 3 per experiment) were grouped and data normalized using the default setting of Genespring (Data transformation: values less than 0.01 to 0.001; Global normalization function: Per Chip normalization to median or a percentile; Gene normalization function: normalize to median was used. The Genedataâs Refiner function was used to assess the overall quality of the hybridization. To analyze the data, the genes were grouped according to the cellsâ or brainâs treatment (Non- infected/infected) and the log of normalized values were taken for further analysis. Data was filtered according to their flags in such a way that at least 5 out of 7 brain samples or 2 out of 3 cell replicates had a present call and that at least one of the groups of replicates (non-infected/infected) fulfilled this condition. The volcano plot was sometime used to filter the data further with the following cut-off (2-fold difference in expression level and t-test p-value of less than 0.05). Further data manipulation for comparison purposes are described in the text.

Dataset Information

Murine Adult Cortex: Gtf2i (+/Δex2 ) VS WT (+/+)

Publications

TFII-I regulates target genes in the PI-3K and TGF-β signaling pathways through a novel DNA binding motif.

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