RNA-seq profiling of Hoxa2/Hoxb2 mutants versus wild type in Math1 positive cells from the Cochlear Nucleus
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ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE64092 | GEO | 2016/11/23
SECONDARY ACCESSION(S): PRJNA270100
REPOSITORIES: GEO
Similar Datasets
Project description:The cochlear nucleus is the first central pathway involved in the processing of peripheral auditory activity. It is heterogeneous in neuronal populations and physiologic responses and is organized in three major subdivisions: the anterior ventral cochlear nucleus (AVCN), the posterior ventral cochlear nucleus (PVCN) and the dorsal cochlear nucleus (DCN). Although each region demonstrates multiple cell types and functions, there are predominant populations of neurons in each region that underlie the principal role each subdivision plays in auditory processing. Little is known of the underlying genetic contribution to these properties. This study sought to identify genes expressed in the subdivisions of the cochlear nucleus that may account for the anatomical and physiological characteristics of each subdivision. These data provide a genetic basis for understanding normal auditory processing in the cochlear nucleus and a template for investigating changes that may occur with hearing loss, the generation and percept of tinnitus, and central processing disorders. Keywords: normal, comparative Brown Norway rats (n=40, female, 45days) were anesthetized and decapitated. Brains were rapidly removed and the subdivisions of the cochlear nucleus (AVCN, PVCN and DCN) dissected on dry ice. Total RNA was extracted and tested for concentration and purity by spectrophotometry and integrity by gel electrophoresis. SAGE was performed using the NlaIII enzyme and Invitrogen SAGE kit. Concatemers were commercially sequenced and imported into eSAGE (Margulies and Innis, 2000) for tag extraction and frequency.
2005-12-31 | E-GEOD-3628 | biostudies-arrayexpress
Project description:The cochlear nucleus is the first central pathway involved in the processing of peripheral auditory activity. It is heterogeneous in neuronal populations and physiologic responses and is organized in three major subdivisions: the anterior ventral cochlear nucleus (AVCN), the posterior ventral cochlear nucleus (PVCN) and the dorsal cochlear nucleus (DCN). Although each region demonstrates multiple cell types and functions, there are predominant populations of neurons in each region that underlie the principal role each subdivision plays in auditory processing. Little is known of the underlying genetic contribution to these properties. This study sought to identify genes expressed in the subdivisions of the cochlear nucleus that may account for the anatomical and physiological characteristics of each subdivision. These data provide a genetic basis for understanding normal auditory processing in the cochlear nucleus and a template for investigating changes that may occur with hearing loss, the generation and percept of tinnitus, and central processing disorders. Keywords: normal, comparative
2006-01-01 | GSE3628 | GEO
Project description:P3 Math1-nGFP mouse cochlear sensory epithelia, consisting of greater and lesser epithelial ridges (GER & LER) including the organ of Corti with nGFP-positive hair cells, were dissected, dissociated into single cells, and labeled with propidium iodide and three CD marker antibodies. The cell suspension was subjected to FACS purification. 83.6 ±2.8% of the total input of cells were viable, determined by exclusion of propidium iodide. Only viable cells were collected into 5 distinct populations: GFP+ cells (Samples HC_A-D), GFP?/CD271High (Samples Mac_A-C), as well as GFP?/CD271Low/CD326+/CD146Low (Samples SC_A-B), GFP?/CD271Low/CD326+/CD146Hig (Samples GER_A-B), and GFP?/CD271Low/CD326? (Sample BM_B). Please see Sinkkonen et al 2011 PMID: 22355545 Total RNA was isolated from 5 different FACS sorted cell poulations from P3 Math1-nGFP cochlea.
2014-10-22 | E-GEOD-62582 | biostudies-arrayexpress
Project description:Deprivation of peripheral nerve input by cochlear removal in young mice results in dramatic neuron death in the cochlear nucleus (CN). The same manipulation in older mice does not result in significant loss. The molecular basis of this critical period of vulnerability remains largely unknown. Here we identified genes regulated at early time points after cochlear removal at ages when neurons are vulnerable (postnatal day (P)7) or invulnerable (P21) to this challenge. Afferent deprivation regulated very different sets of genes at P7 and P21. These genes showed a variety of functions at both ages, but surprisingly there was no net increase in pro-apoptotic genes at P7. A large set of upregulated immune-related genes was identified at P21. Experiment Overall Design: Mice received unilateral cochlear removals. At 6, 12, 24, and 48 hours after surgery, the CN ipsilateral and contralateral were removed, and RNA isolated from separate pools of tissue for each replicate. Deafferented CN were compared to age-matched and time-matched contralateral, control CN to identify genes regulated by cochlear removal at age P7 and P21.
2008-06-13 | E-GEOD-5394 | biostudies-arrayexpress
Project description:Deprivation of peripheral nerve input by cochlear removal in young mice results in dramatic neuron death in the cochlear nucleus (CN). The same manipulation in older mice does not result in significant loss. The molecular basis of this critical period of vulnerability remains largely unknown. Here we identified genes regulated at early time points after cochlear removal at ages when neurons are vulnerable (postnatal day (P)7) or invulnerable (P21) to this challenge. Afferent deprivation regulated very different sets of genes at P7 and P21. These genes showed a variety of functions at both ages, but surprisingly there was no net increase in pro-apoptotic genes at P7. A large set of upregulated immune-related genes was identified at P21. Keywords: Time Course after Cochlear Removal, Age Comparison
2007-12-26 | GSE5394 | GEO
Project description:C57B6J mice carrying a LacZ allele at the Math1 locus (Math1-LacZ/+) were backcrossed at least 10 generations. The LacZ allele phenocopies a null allele. A total of 5 heterozygous and 5 homozygous null spinal cords were collected (staged at embryonic day 12.5) and individually processed (i.e. not pooled). RNA was extracted and prepared for hybridization to Affymetrix MOE430v2.0 chips under standard conditions (www.affymetrix.com)
2008-03-13 | E-MEXP-1492 | biostudies-arrayexpress
Project description:We analyzed whether cochlear removal-induced transcriptional changes in the cochlear nucleus (CN) were due to loss of electrical activity in the 8th nerve. Pharmacological activity blockade of the auditory nerve for 24 h resulted in similar expression changes for only a subset of genes. Thus, an additional factor not dependent on action potential-mediated signaling must also regulate transcriptional responses to deafferentation in the CN. Experiment Overall Design: TTX was infused into the cochlea unilaterally via osmotic pumps to block activity in the 8th nerve. CN tissue was dissected out from 10-12 mice per replicate and pooled. Three biological replicates were performed. Gene expression was compared between the ipsilateral and contralateral CN tissue to identify genes transcriptionally regulated after activity deprivation.
2008-10-25 | E-GEOD-11726 | biostudies-arrayexpress
Project description:Developmental differences in gene expression in the postnatal mouse cochlear nucleus was analyzed at two or three ages using two different array platforms, the Affymetrix Mouse 430A GeneChip or the NIA 15K mouse cDNA microarray. These ages, P7, P14, and P21 parallel a critical period of neuron survival dependent on input from the auditory nerve. Keywords: parallel sample
2005-10-15 | GSE2390 | GEO
Project description:We analyzed whether cochlear removal-induced transcriptional changes in the cochlear nucleus (CN) were due to loss of electrical activity in the 8th nerve. Pharmacological activity blockade of the auditory nerve for 24 h resulted in similar expression changes for only a subset of genes. Thus, an additional factor not dependent on action potential-mediated signaling must also regulate transcriptional responses to deafferentation in the CN.
2008-08-30 | GSE11726 | GEO
Project description:P3 Math1-nGFP mouse cochlear sensory epithelia, consisting of greater and lesser epithelial ridges (GER & LER) including the organ of Corti with nGFP-positive hair cells, were dissected, dissociated into single cells, and labeled with propidium iodide and three CD marker antibodies. The cell suspension was subjected to FACS purification. 83.6 ±2.8% of the total input of cells were viable, determined by exclusion of propidium iodide. Only viable cells were collected into 5 distinct populations: GFP+ cells (Samples HC_A-D), GFP−/CD271High (Samples Mac_A-C), as well as GFP−/CD271Low/CD326+/CD146Low (Samples SC_A-B), GFP−/CD271Low/CD326+/CD146Hig (Samples GER_A-B), and GFP−/CD271Low/CD326− (Sample BM_B). Please see Sinkkonen et al 2011 PMID: 22355545
2014-10-22 | GSE62582 | GEO