The study of the differential expression profile in bone tissues between Tnni2del175k mutant mice and their wild-type littermates using mRNA array.
Ontology highlight
ABSTRACT:
ORGANISM(S): Mus musculus
SUBMITTER: xiaoquan zhu
PROVIDER: E-GEOD-32163 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series
2013-09-01 | E-GEOD-32401 | biostudies-arrayexpress
Project description:Alpha synuclein (SNCA) has been linked to neurodegenerative diseases (synucleinopathies) that include Parkinson’s disease (PD). Although the primary neurodegeneration in PD involves nigrostriatal dopaminergic neurons, more extensive yet regionally selective neurodegeneration is observed in other synucleinopathies. Furthermore, SNCA is ubiquitously expressed in neurons and numerous neuronal systems are dysfunctional in PD. Therefore it is of interest to understand how overexpression of SNCA affects neuronal function in regions not directly targeted for neurodegeneration in PD. To gain a better understanding of the consequences of excessive SNCA expression on basal ganglia function, we performed transcriptome analysis of striatal tissue from male Thy1-aSyn-mice and wt littermates. The present study investigated the consequences of SNCA overexpression on cellular processes and functions in the striatum of mice overexpressing wild-type, human SNCA under the Thy1 promoter (Thy1-aSyn mice) by transcriptome analysis. The analysis revealed alterations in multiple biological processes in the striatum of Thy1-aSyn mice, including synaptic plasticity, signaling, transcription, apoptosis, and neurogenesis. The present study investigated the consequences of SNCA overexpression on cellular processes and functions in the striatum of mice overexpressing wild-type, human SNCA under the Thy1 promoter (Thy1-aSyn mice) by transcriptome analysis. The analysis revealed alterations in multiple biological processes in the striatum of Thy1-aSyn mice, including synaptic plasticity, signaling, transcription, apoptosis, and neurogenesis. Animal care was conducted in accordance with the U. S. Public Health Service Guide for the Care and Use of Laboratory Animals and procedures were approved by the University of California, Los Angeles (UCLA), I.A.C.U. Committee. Transgenic (tg) mice overexpressing human wt SNCA under the Thy-1 promoter (Thy1-aSyn) created previously in a mixed C57BL/6-DBA background were kept in this background by breeding mutant females with wt males. Only male mice were used in the study. The genotype of all tg and wt mice was verified by PCR analysis of tail DNA. Animals were maintained on a 12 hr light/dark cycle with free access to water and food. Six-month old male Thy1-aSyn and wt littermates were sacrificed by decapitation. For microarray analysis, whole striata from each hemisphere were immediately dissected and pooled for each brain. Tissue was permeated in RNAlater (Qiagen, Valencia, CA), frozen in liquid nitrogen, and stored at - 80º C until used for RNA preparation. For PCR verification of transcriptional changes and for protein extracts preparation, brains from 5 male Thy1-aSyn and 5 wt littermates were obtained as above but then the brains were placed in a metal brain mold with grooves to ensure reproducible cutting of thick brain slices. A first coronal cut was made with a razor blade to remove the frontal part of the brain (at bregma + 1mm, at the anterior level of striatum). The following 1mm coronal slice (including the striatum but no globus pallidus) was used to dissect out striatal tissue. A horizontal cut was made through the anterior commissures to exclude the nucleus accumbens. One cube of striatum was dissected out from each hemisphere, taking care not to include any corpus callosum, choroid plexus, or subventricular zone. Samples were stored at -80º C until further processing. Total RNA was extracted from striata of Thy1-aSyn and wt littermates (all males) with Trizol (Invitrogen, Carlsbad, CA), followed by a clean-up step with RNeasy columns (Qiagen) and RNA integrity check using a Bioanalyzer (Agilent Tech., Foster city, CA). RNA samples were pooled, one pool representing the six control wt mice and the other representing the six SNCA overexpressing animals. After synthesis, using Superscript (Invitrogen) and labeling using the ENZO labeling kit (Affymetrix Inc., Santa Clara, CA), cRNA probes were hybridized to mouse MOE-430A GeneChip arrays (Affymetrix) following the manufacturer’s protocol at the UCLA microarray core facility. Significant differential gene expression between pooled tg and wt samples was ascertained by estimation of signal log2 ratios (or fold changes in expression values), after quality control checks, data normalization and estimating expression values using the Affymetrix Microarray Suite 5.0 Software (MAS 5.0). After pairwise comparisons and filtering of this gene list using the following criteria: change p-value <0.005 for induce genes, change p-value > 0.995 for decreased genes, signal log2 ratio > 0.6 (> 1.52 fold change), excluding probes called absent in both groups, a list of differentially expressed genes was generated. We used various statistical softwares and databases to ascertain pathways affected by overexpression of SNCA that are associated with overrepresented genes in this gene list, including, the functional annotation tools accessible through DAVID (Database for Annotation, Visualization and Integrated Discovery, http://david.abcc.ncifcrf.gov )
2012-02-11 | E-GEOD-35723 | biostudies-arrayexpress
Project description:Diabetic retinopathy is one of the leading causes of blindness in diabetic patients. Emerging evidence suggests that retinal neurodegeneration is an early event in the pathogenesis of diabetic retinopathy, but the underlying causes of neuronal loss are unknown. To unravel potential mechanisms underlying early retinal neurodegeneration in diabetic retinopathy, a gene expression profiling study was undertaken to compare the gene expression in retinas of 8-week db/db diabetic mice with that of lean non-diabetic littermates. Retinas were obtained from 8-week db/db diabetic mice and age-matched lean non-diabetic controls. Total RNA was extracted and processed for being hybridized onto affymetrix DNA microarrays.
2014-02-27 | E-GEOD-55389 | biostudies-arrayexpress
Project description:Periphilin is a protein which is involved in multiple processes in vivo, including terminal differentiation of keratinozytes as well as cell-cycle and cancer related functions. Here we generated mice with a targeted disruption of the periphilin-1 gene to explore its physiological role from an organismic perspective. In accordance with a ubiquitous expression of periphilin in the murine embryo, the homozygous deficiency of periphilin is lethal in early embryogenesis. We therefore characterized mice with a disruption of only one periphilin allele. As heterozygous periphilin knockout mice show no obvious histological alterations and have no apparent behavioural phenotypes, we compared whole transcriptome RNA expression profiles of total brain tissue of periphilin+/- knockout mice and wild type littermates for an in-depth analysis of heterozygous animals. In periphilin+/- knockout mice, 3 probe sets were indicative of significant differential expression (p ⤠0.05, SLR ⥠1 which is equivalent to 2 fold). Two of these probe sets (1438864_at and 1439170_at) refer to unannotated or unclassifiable genes. According to the NetAffx⢠Analysis Center, the third probe set (1447831_s_at) is assigned to myotubularin related protein 7 (Mtmr7). The probe set, however, lies upstream of the Mtmr7 gene (Ensembl gene ENSMUSG00000039431), and its signal is therefore not representative for the Mtmr7 gene. Quantitative RT-PCR (qRT-PCR) analysis with a primer set specific for Mtmr7 confirmed that its expression is not altered in periphilin+/- knockout mice (relative expression compared to wild type: 0.924; p = 0.419). In summary, none of more than 45.000 covered transcripts is differentially expressed in periphilin+/- knockout mice in comparison to wild type littermates. Experiment Overall Design: Whole brains of three male 2-months-old periphilin+/-knockout mice and three C57BL/6-wild type littermates
2009-04-12 | E-GEOD-14059 | biostudies-arrayexpress
Project description:SREBF-1c is a transcription factor regulating fatty acid biosynthesis. We have charaterized the impact of the abcence of SREBF-1c on the development of peripheral neuropathy In this dataset we included expression data from dissected sciatic nerve from 10 months old SREBF-1c KO mice and relative littermates. 6 total samples were analyzed (3 wild type and 3 SREBF-1c KO). Data handling was mainly done using TAC and Partek Genomic Suite software. The Robust Multichip Average (RMA) method was employed to calculate probe set intensity. RMA is a robust multi-chip average expression method that estimates the probe-level data from a set of chips: the perfect-match (PM) values are background-corrected, normalized and finally summarized resulting in a set of expression measures. The identification of differentially expressed genes was addressed using Fold Change (FC) and ANOVA. For each experimental condition the probesets whose fold change are higher or equal than 1.5 with an ANOVA unadjusted p-value lower than 0,05 are selected as significantly modulated.
2015-02-10 | E-GEOD-65754 | biostudies-arrayexpress
Project description:Gastrointestinal content of mice fed high or low fiber diets was labeled with the GH2c-ABP. 3x replicates of each diet, 2x littermates per diet. 12 total mice.
2022-08-11 | PXD018644 | Pride
Project description:Transcriptome analysis of nucleus accumbens shell samples from RARβ-null mutant mice and their wild type littermates The active vitamin A derivative retinoic acid (RA) is an important regulator of adult brain functions. How these regulations are achieved is poorly known, partly due to the paucity of information on RA molecular targets. The striatum, the region involved in control of motor, cognitive and affective functions, may be particularly prone to such regulation as it displays the highest levels of RA and its receptors (RARs). We report the first genome-wide analysis of RAR-binding sites in the brain. Using chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq), as well as transcriptomic analysis of RARβ-null mutant mice, we identified genomic transcriptional targets of RARβ in the striatum. Our data point to a strong contribution of RARβ in controlling neurotransmission, energy metabolism, and transcription, with a particular involvement of G-protein, cAMP and calcium signaling. Quantitative PCR analysis of striatal subregions revealed a higher sensitivity of ventral structures (nucleus accumbens) to lack of RARβ signaling. There is a high overlap of transcriptional targets of RARβ and genes affected in expression in Huntingtonâs disease (HD), and we observed a decrease of RARβ expression in the striatum of R6/2 transgenic mice, a murine model of HD. A large number of genes bearing RARβ binding sites have also been implicated in Alzheimerâs and Parkinsonâs diseases, raising the possibility that compromised RA signaling in striatum may be a mechanistic link explaining the similar affective and cognitive symptoms of these diseases. Globally, our data point to a possibility of a neuroprotective function of RARβ in the striatum. We analyzed nucleus accumbens from 11 mice (6 WT, 5 RARβ-null mutant mice) using the Affymetrix GeneChip Mouse Gene 1.0 ST arrays.
2016-07-26 | E-GEOD-67761 | biostudies-arrayexpress
Project description:To investigate the role of the circadian clock gene Bmal1 in skeletal muscle, we compared the circadian transcriptomes of fast tibialis anterior (TA) and slow soleus (SOL) skeletal muscles from muscle-specific Bmal1 KO (mKO) and their control Cre- littermates (Ctrl). Keyword: Circadian Transcriptome, time course 72 samples were analyzed, comprised of 4 experimental groups (Ctrl SOL, mKO SOL, Ctrl TA, mKO TA), with 3 biological replicates for each time point sampled every 4 hours for 24 hours. SOL and TA muscles were collected from the same animals, as indicated by Source Animal ID data column
2014-01-01 | E-GEOD-43071 | biostudies-arrayexpress
Project description:Livers from three SRSF3HKO mice and 3 wild-tyope littermates were used to analyze changes in exon utilization and gene expression. two genotypes, three replicates each
2012-12-01 | E-GEOD-35686 | biostudies-arrayexpress
Project description:Ptprq is one of the genes markedly downregulated in the diminuendo mouse, which carries a mutation in the microRNA miR-96. We carried out microarrays on mice homozygous for a functional null allele of Ptprq and their wildtype littermates to compare expression changes to those seen in diminuendo homozygotes and examine how much, if any, of the diminuendo transcriptional phenotype can be explained by the downregulation of Ptprq.
2014-01-27 | E-MTAB-1785 | biostudies-arrayexpress