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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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MiR-7 blockade alters E12.5 mouse cortical mRNA levels

ABSTRACT: Purpose: To assess changes in mRNA levels due to in vivo blockade of microRNA miR-7 with a miR-7 sponge in the E12.5 mouse neocortex Methods: total RNA was isolated and sequenced from the dorsal cortex of wild-type or Emx1-Cre:miR-7-sponge transgenic mice in triplicate using an Illumina high-seq 1000. Raw data was analyzed using Gobyweb v1.7. Genes were considered changed which demonstrated expression level>1RPKM, fold-change>1.25, and FDR-qvalue <0.25. Changed genes were then filtered by prediction of miR-7 targeting to reveal predicted miR-7 targets which were altered in vivo due to miR-7 sponge expression. Results: 419 cortically expressed genes were significantly increased in expression level due to miR-7 sponge expression. Of these, 162 are predicted to be targets of miR-7. total RNA was isolated and sequenced from the dorsal cortex of wild-type or Emx1-Cre:miR-7-sponge transgenic mice in triplicate using an Illumina high-seq 1000.

ORGANISM(S): Mus musculus

SUBMITTER: Andrew Pollock

PROVIDER: E-GEOD-59204 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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miR-7 blockade alters E12.5 mouse cortical mRNA levels

Project description:Purpose: To assess changes in mRNA levels due to in vivo blockade of microRNA miR-7 with a miR-7 sponge in the E12.5 mouse neocortex Methods: total RNA was isolated and sequenced from the dorsal cortex of wild-type or Emx1-Cre:miR-7-sponge transgenic mice in triplicate using an Illumina high-seq 1000. Raw data was analyzed using Gobyweb v1.7. Genes were considered changed which demonstrated expression level>1RPKM, fold-change>1.25, and FDR-qvalue <0.25. Changed genes were then filtered by prediction of miR-7 targeting to reveal predicted miR-7 targets which were altered in vivo due to miR-7 sponge expression. Results: 419 cortically expressed genes were significantly increased in expression level due to miR-7 sponge expression. Of these, 162 are predicted to be targets of miR-7.

2014-07-09 | GSE59204 | GEO

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gene expression analysis in Pbx1; Emx1-cre mutant cortex at embryonic day 15.5

Project description:the goal of the study was to compare gene expression between control and Pbx1; Emx1-cre mutant corteces at e15.5 E15.5 whole cortex was dissected for the analysis. Control embryo genotype was Pbx1F/+. Mutant embryo genotype was Pbx1F/-; Emx1-cre. 4 corteces of each genotype were used for the analysis: 4 controls and 4 mutants, 8 samples total.

2015-11-10 | E-GEOD-73287 | biostudies-arrayexpress

gene expression analysis in Pbx1; Emx1-cre mutant cortex at embryonic day 12.5

Project description:the goal of the study was to compare gene expression between control and Pbx1; Emx1-cre mutant corteces at e12.5 E12.5 whole cortex was dissected for the analysis. Control embryo genotype was Pbx1F/+. Mutant embryo genotype was Pbx1F/-; Emx1-cre. 4 corteces of each genotype were used for the analysis: 4 controls and 4 mutants, 8 samples total.

2015-11-10 | E-GEOD-73286 | biostudies-arrayexpress

p53-mediated neurodegeneration in the absence of the nuclear protein Akirin2

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2016-02-27 | E-GEOD-78720 | biostudies-arrayexpress

Genome-wide distribution of Pbx1/2/3 in mouse cortex at embryonic day 15.5 [ChIP-seq]

Project description:We demonstrate using conditional mutagenesis that Pbx1, with and without Pbx2+/ sensitization, regulates regional identity and laminar patterning of the developing mouse neocortex in cortical progenitors (Emx1-Cre) and in newly generated neurons (Nex1-Cre). Pbx1/2 mutants have three salient molecular phenotypes of cortical regional and laminar organization: hypoplasia of the frontal cortex, ventral expansion of the dorsomedial cortex, and ventral expansion of Reelin expression in the cortical plate of the frontal cortex, concomitant with an inversion of cortical layering in the rostral cortex. Molecular analyses, including PBX ChIP-seq, provide evidence that PBX promotes frontal cortex identity by repressing genes that promote dorsocaudal fate. Chromatin immunoprecipitation was performed using antibody against Pbx1/2/3 (sc-888, Santa Cruz). Wild type E15.5 mouse whole cortex was used for the analysis.

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