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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Wnt/b-catenin signaling regulates sequential fate decisions of murine cortical precursor cells

ABSTRACT: In order to compare expression changes upon Wnt/b-catenin signaling inactivation in the forebrain of mouse embryos, we have isolated dorso-medial pallium from E11.5 mutant and control embryos and performed microarray analysis. Dorso-medial pallium from E11.5 control and mutant embryos was dissected and snap-frozen. RNA isolation on single embryo brains was performed with RNAeasy kit with on-column Dnase digestion.

ORGANISM(S): Mus musculus

SUBMITTER: Lukas Sommer

PROVIDER: E-GEOD-70134 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Wnt/β-catenin signaling regulates sequential fate decisions of murine cortical precursor cells.

Draganova Kalina K Zemke Martina M Zurkirchen Luis L Valenta Tomas T Cantù Claudio C Okoniewski Michal M Schmid Marie-Theres MT Hoffmans Raymond R Götz Magdalena M Basler Konrad K Sommer Lukas L

Stem cells (Dayton, Ohio) 20150101 1

The fate of neural progenitor cells (NPCs) is determined by a complex interplay of intrinsic programs and extrinsic signals, very few of which are known. β-Catenin transduces extracellular Wnt signals, but also maintains adherens junctions integrity. Here, we identify for the first time the contribution of β-catenin transcriptional activity as opposed to its adhesion role in the development of the cerebral cortex by combining a novel β-catenin mutant allele with conditional inactivation approach ...[more]

PMID: 25182747

Similar Datasets

Wnt/b-catenin signaling regulates sequential fate decisions of murine cortical precursor cells

Project description:In order to compare expression changes upon Wnt/b-catenin signaling inactivation in the forebrain of mouse embryos, we have isolated dorso-medial pallium from E11.5 mutant and control embryos and performed microarray analysis.

2015-06-23 | GSE70134 | GEO

MicroRNA expression signatures for developing tongue primordia in mouse embryos

Project description:We aimed to understand the molecular basis of muscular development in tongue. We focused on the critical stages of tongue myogenesis, namely, E10.5 (settlement of myogenic progenitors in tongue primordium), E11.5 (initiation of myoblast differentiation with the development of lateral lingual swellings). We conducted miRNA microarray analysis of the tongue primordia at E10.5 and E11.5, during which myoblast differentiation was induced as a result of the activation of muscle regulatory gene expression. The medial part of the fused mandibular prominences that corresponds to a tongue primordium were collected from E10.5 and E11.5 mouse embryos. Forty embryos for each time-point were used to obtain a pool of total RNA.

2014-03-11 | E-GEOD-51364 | biostudies-arrayexpress

The SET-2/SET1 histone H3K4 methyltransferase maintains pluripotency in the caenorhabditis elegans germline.

Project description:Histone H3 Lys 4 methylation (H3K4me) is deposited by the conserved SET1/MLL methyltransferases acting in multiprotein complexes including Ash2 and Wdr5. While individual subunits contribute to complex activity, how they influence gene expression in a specific tissue remains largely unknown. In caenorhabditis elegans, SET-2/SET1, WDR-5.1 and ASH-2 are differentially required for germline H3K4 methylation. Using expression profiling on germlines from animals lacking set-2, ash-2 or wdr-5.1, we show that these subunits play unique and redundant functions to promote expression of germline genes and repress somatic genes. We further show that in set-2 and wdr-5.1 deficient germlines, somatic gene misexpression is associated with conversion of germ cells into somatic cells, and that nuclear RNAi acts in parallel with SET-2 and WDR-5.1 to maintain germline identity. These findings uncover a unique role for SET-2 and WDR-5.1 in preserving germline pluripotency, and underline the complexity of the cellular network regulating this process. Gene misregulation in SET1/set-2, wdr-5.1 and ash-2 defective germlines

2014-09-04 | E-GEOD-61094 | biostudies-arrayexpress

Adenosine deaminases that act on RNA induce reproducible changes in abundance and sequence of embryonic miRNAs

Project description:We used transgenic mouse embryos that are deficient in the two enzymatically active RNA editing enzymes ADAR1 and ADAR2 to compare relative frequencies but also sequence composition of mature miRNAs in these genetically modified backgrounds to wild-type mice by Illumina next gen sequencing. Deficiency of ADAR2 leads to a reproducible change in abundance of specific miRNAs and their predicted targets. Changes in miRNA abundance seem unrelated to editing events. Additional deletion of ADAR1 has surprisingly little impact on the mature miRNA repertoire, indicating that miRNA expression is primarily dependent on ADAR2. A to G transitions reflecting A to I editing events can be detected at few sites and at low frequency during the early embryonic stage investigated. Again, most editing events are ADAR2 dependent with only few editing sites being specifically edited by ADAR1. Besides known editing events in miRNAs a few novel, previously unknown editing events were identified. Some editing events are located to the seed region of miRNAs opening the possibility that editing leads to their retargeting. GSM852140-8: sequencing of mature miRNAs of wt, ADAR2-/- and ADAR1-/-/ADAR2-/- female mouse embryos at E11.5 GSM863778-81: Gene expression was measured in wiltype, ADAR2-/- and ADAR1-/-/ADAR2-/- E11.5 whole female mouse embryos using Agilent Whole Mouse Genome Oligo Microarrays 8x60K.

2012-02-02 | E-GEOD-34626 | biostudies-arrayexpress

Transcriptomic analysis of prefrontal medial cortex, hippocampus and nucleus accumbens of alcohol-preferring and nonpreferring rats

Project description:Animal models provide opportunity to study neurobiological aspects of human alcoholism. Changes in gene expression have been implicated in mediating brain function, including reward system and addiction. The current study aimed to identify novel genes that may underlie ethanol preference. Microarray analysis comparing gene expression in nucleus accumbens (NAc), hippocampus (HP) and prefrontal medial cortex (mPFC) was performed in two rat strains selected for extreme levels of ethanol preference - Warsaw High Preferring (WHP) and Warsaw Low Preferring (WLP). The identified candidate genes may underlie differential ethanol preference in rat model of alcoholism. This is analysis of 18 RNA samples, including 9 technical replicates. Two strains of rats selected for extreme levels of ethanol preference (low preferring WLP and high preferring WHP) were compared. Three brain areas (nucleus accumbens, prefrontal medial cortex and hippocampus) were studied. For each brain area, 6 RNA samples (including 3 technical replicates) were analyzed. Each RNA sample consist of of equal amounts of total RNA from 3 male rats. Comparisons: Nucleus accumbens of WHP vs. Nucleus accumbens of WLP; Prefrontal medial cortex of WHP vs. Prefrontal medial cortex of WLP; Hippocampus of WHP vs. Hippocampus of WLP. 3 biological replicates in each comparison.

2015-01-17 | E-GEOD-65064 | biostudies-arrayexpress

Expression data from mandibular arches in mouse embryos

Project description:Fusion of branchial arch derivatives is an essential event in the development of craniofacial architecture. A unique feature of the mandibular arch development is medial/lateral compartmentalization for the molecular networks. Those networks give rise to multiple region-specific organs, namely teeth, a tongue, salivary glands, and the supporting matrices such as bones and cartilages. We aimed to investigate molecular networks that govern the fusion process during mouse mandibular development. To this end, cDNA microarray technology was employed for screening of spatio-temporal gene expression in developing mandibular arch from E9.7 through E11.5. We conducted to divide a mandibular arch medially and laterally to compare both gene expression. From an embryo at E10.5, a medial (M) sample of the mandibular arch was dissected out -at just the distal end of opposed lateral lingual swellings-, and the bulk of remnant lateral region was collected as (L) sample under a stereomicroscope. Forty embryos for each time-point were used to obtain a pool of total RNA.

2012-07-12 | E-GEOD-35091 | biostudies-arrayexpress

Drosophila PTB regulates dorso-ventral patterning genes in embryos

Project description:Drosophila PTB (Polypyrimidine Tract-binding protein dmPTB) regulates dorso-ventral patterning genes in embryos

2014-05-10 | GSE57517 | GEO

Gene expression profiles of E8.5, E9.5 and E11.5 kidney precursors

Project description:Understanding processes how the early stage kidney precursor gives rise to metanephric mesenchyme, which is a committed progenitor cells of adult kidney is important for the regeneration of kidney in vitro. The combination of fluorescent activated cell sorting (FACS) plus microarray analysis offers a powerful, efficient and effective method for the creation of global gene expression profiles of the developing kidney precursors. Those gene expression data provides insights into not only the stage specific marker genes but also the signals working in each population, which should be informative for the directed differentiation of pluripotent stem cells in vitro. Osr1-GFP knock-in mice were used to isolate kidney precursor cells from embryos at E8.5, E9.5 and E11.5. At E9.5 and E11.5 embryos, to identify the differences between nephron progenitors and surrounding mesenchyme, nephron progenitor populations were further enriched by gating Osr1-GFP positive Integrin alpha8 positive Pdgfr alpha negative population and compared with Osr1-GFP positive cells other than that gate. RNA was isolated from cells and the gene expression profiles were determined by microarrays.

2015-01-13 | E-GEOD-51054 | biostudies-arrayexpress

Technical variation between RNA isolations from individual embryos

Project description:Transcriptome analysis during embryogenesis usually requires pooling of embryos to obtain sufficient RNA. Hence, the measured levels of gene-expression represent the average mRNA levels of pooled samples and the biological variation among individuals is lost for inclusion into statistical models used to analyze transcriptome data. This can irreversibly reduce the robustness, resolution and expressiveness of the experiment. Therefore, we developed a robust method to isolate abundant high-quality RNA from individual embryos to perform single embryo transcriptome analyses using the zebrafish as a model. Zebrafish embryos were selected from the germ ring stage. RNA from 4 individual embryos and RNA from 4 pooled embryos and afterwards splitted material was isolated. These 8 samples were hybridized against a common reference made from a pool of 20 embryos.

2010-04-01 | E-GEOD-17738 | biostudies-arrayexpress

Embryonic and adolescent forelimbs, brains, whole embryos, Aha-enrichment forelimbs, Mus musculus (wild-type, C57BlJ6/J; OIM, B6C3Fe a/a-Col1a2oim/J), proteomic dataset

Project description:Embryonic day (E)12.5 whole murine embryos, E11.5 - E14.5 whole murine embryos, E11.5 - E14.5, post-natal day (P)3 and P35 murine forelimbs, E14.5 brains, and COL1A2-mutant and COL1A2-WT forelimbs were fractionated and specific fractions were analyzed via LC-MS/MS. Aha-enrichment experiments consisted of in vivo protein labeling with azidohomoalanine (Aha) followed by tissue fractionation of the forelimbs and enrichment of labeled ECM proteins from the final IN pellet ('enriched'). 'Unenriched samples', or the background from which newly synthesized proteins were enriched from, were also analyzed via LC-MS/MS.

2020-06-05 | MSV000085556 | MassIVE

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