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Identification of neural genes using Xenopus DNA microarrays

ABSTRACT: In order to isolate novel genes regulating neural induction, we utilized a DNA microarray approach. As neural induction is thought to occur via the inhibition of BMP signaling, BMP signaling was inhibited in ectodermal cells by overexpression of a dominant-negative receptor. RNAs were isolated from control animal cap explants and from dominant-negative BMP receptor expressing animal caps and subjected to a microarray experiment using newly generated high-density Xenopus DNA microarray chips. Keywords = neural induction Keywords = BMP Keywords = nervous system Keywords = Xenopus Keywords = microarray Keywords: parallel sample

ORGANISM(S): Xenopus laevis

PROVIDER: GSE2266 | GEO | 2005/03/05

SECONDARY ACCESSION(S): PRJNA91381

REPOSITORIES: GEO

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Identification of neural genes using Xenopus DNA microarrays

Project description:In order to isolate novel genes regulating neural induction, we utilized a DNA microarray approach. As neural induction is thought to occur via the inhibition of BMP signaling, BMP signaling was inhibited in ectodermal cells by overexpression of a dominant-negative receptor. RNAs were isolated from control animal cap explants and from dominant-negative BMP receptor expressing animal caps and subjected to a microarray experiment using newly generated high-density Xenopus DNA microarray chips. Keywords = neural induction Keywords = BMP Keywords = nervous system Keywords = Xenopus Keywords = microarray

2010-06-10 | E-GEOD-2266 | biostudies-arrayexpress

Multicilin drives centriole biogenesis via E2f proteins

Project description:Biochemistry suggests e2f4 forms a complex with the coiled-coiled protein multicilin (MCIDAS), a protein that is necessary and sufficient to specify multiciliated cells in vertebrates. Here, we performed RNAseq on Xenopus laevis ectoderm in the presence of multicilin alone or multicilin and a dominant-negative e2f4 construct. We also performed ChIPseq on e2f4 in the presence or absence of multicilin. Taken together, these data demonstrate how multicilin affects e2f4 genomic targets and their downstream transcription. RNAseq: misexpression of multicilin-HGR +/- dominant-negative e2f4 messenger RNAs in X. laevis animal caps, multicilin induced with dexamethasone at mid-stage 11 and harvested at 3 timepoints (3, 6, and 9 hours after induction, roughly corresponding to stages 13, 16, and 18) with 3 biological replicates. ChIPseq: misexpression of e2f4-GFP +/- multicilin-HGR messenger RNAs in X. laevis animal caps, multicilin induced at mid-stage 11 and harvested at one timepoint (6 hours after induction, roughly corresponding to stage 16), immunoprecipitated with anti-GFP and sequenced; 2 biological replicates. Background was input prior to IP.

2014-07-10 | E-GEOD-59309 | biostudies-arrayexpress

Identification of Kctd15 target genes in Xenopus animal caps injected with wnt3a and chordin

Project description:We aimed to identify genes that are inhibited by Kctd15 overexpression during neural crest (NC) induction. Injection of RNAs encoding Wnt3a and chordin into the embryo followed by animal cap explant culture leads to the induction of NC marker genes as well as additional genes expressed in the neural plate border. Our previous study indicated that co-injection of kctd15 inhibits the induction of these markers. We injected four sets of RNAs, lacZ as control (L), wnt3a+chd (WC), wnt3a+chd+kctd15 (WCK), and kctd15 (K). After evaluation of marker gene expression with RT-PCR, we prepared probes with same RNA extract for Affymetrix DNA microarray. The hybridization, washing and scanning were perfomed following the manual from Affymetrix. Partek Genomics Suite was employed for data analysis. Xenopus embryos were injected with mRNAs at two-cell stage. When developing to stage 9, the animal caps were dissected for RNA extraction and hybridization on Affymetrix microarrays. According to the mRNAs injected, the animal caps (AC) were divided into four groups, including (1) AC injected with lacZ; (2) AC injected with kctd15; (3) AC injected with chordin and wnt3a; (4) AC injected with chordin, wnt3a and kctd15. The injected animal caps were cultured till stage 15 and then collected for RT-PCR and microarray assay. Each group had three repeats.

2015-08-26 | E-GEOD-72391 | biostudies-arrayexpress

EFTF vs GFP Experiment

2009-08-19 | GSE9173 | GEO

A Xenopus DNA microarray approach to identify novel direct BMP target genes involved in early embryonic development

Project description:Bone Morphogenetic Proteins (BMPs), a subgroup of the TGF-beta superfamily, were originally isolated from bone on the basis of their ability to induce ectopic bone development. While BMPs are involved in a wide range of developmental and physiological functions, very few vertebrate target genes in this pathway have been identified. To identify target genes regulated by the BMP growth factor family in Xenopus, large-scale microarray analyses were conducted to discover genes directly activated by this factor in dissociated animal cap tissues treated with a combination of the protein synthesis inhibitor cycloheximide and BMP2. Keywords = Xenopus Keywords = BMP Keywords = microarray Keywords = development Keywords = target genes Keywords: parallel sample

2005-03-05 | GSE2274 | GEO

Identification of genes regulated by XOct-25 overexpression in Xenopus ectoderm

Project description:The Xenopus POU class V transcription factor XOct-25 has been shown to inhibit BMP-dependent epidermal differentiation and promote neural induction in the ectoderm during early embryogenesis. In order to identify genes that act downstream of XOct-25, transcriptional profile of Xenopus ectodermal cells overexpressing XOct-25 was compared with control cells by using a DNA microarray method.

2012-10-05 | GSE24562 | GEO

A Xenopus DNA microarray approach to identify novel direct BMP target genes involved in early embryonic development

Project description:Bone Morphogenetic Proteins (BMPs), a subgroup of the TGF-ï¢ superfamily, were originally isolated from bone on the basis of their ability to induce ectopic bone development. While BMPs are involved in a wide range of developmental and physiological functions, very few vertebrate target genes in this pathway have been identified. To identify target genes regulated by the BMP growth factor family in Xenopus, large-scale microarray analyses were conducted to discover genes directly activated by this factor in dissociated animal cap tissues treated with a combination of the protein synthesis inhibitor cycloheximide and BMP2. Keywords = Xenopus Keywords = BMP Keywords = microarray Keywords = development Keywords = target genes

2010-06-10 | E-GEOD-2274 | biostudies-arrayexpress

Transcription profiling of Xenopus embryos

Project description:Xenopus laevis embryos were injected with mRNA for EFTFs at 2-cell stage. Animal caps collected at stage 9, cultured to the equivalent of stage 15 and RNA extracted. Four biological replicates of the EFTF-injected and GFP-injected (control) caps were used to profile transcript expression patterns using Affymetrix Xenopus Laevis GeneChip microarrays. Experiment Overall Design: Xenopus laevis embryos were injected with mRNA for EFTFs at 2-cell stage. Animal caps collected at stage 9, cultured to the equivalent of stage 15 and RNA extracted. Four biological replicates of the EFTF-injected and GFP-injected (control) caps were used to profile transcript expression patterns using Affymetrix Xenopus Laevis GeneChip microarrays.

2009-09-15 | E-GEOD-9173 | biostudies-arrayexpress

Xenopus laevis embryos and animal caps: Control vs PouV morpholino

Project description:Transcriptional profiling of Xenopus laevis embryos and ectoderm (animal caps) comparing embryos injected with control morpholino with embryos injected with the morpholino mixture PVD2, which knocks down all three Xenopus PouV proteins. Whole embryos (WE) or animal caps (AC) were collected at late blastula (9) or early gastrula (10) stages from Control and PVD2 morphants.

2013-11-12 | GSE47578 | GEO

Identification of microRNAs and microRNA targets in Xenopus ectoderm

Project description:Purpose: The establishment of cell lineages occurs via a dynamic progression of gene regulatory networks that underlie developmental commitment and differentiation. To investigate how microRNAs (miRs) function in this process, we compared miRs and miR targets at the initiation of the two major ectodermal lineages in Xenopus. Methods: We injected Xenopus laevis embryos with noggin or constitutively active BMP4 receptor (CABR) at two-cell stage and cut animal caps at stg. 8. Isolated animal caps were grown separately till mid gastrula and processed for either RNA isolation or immunoprecipitation. Results: We have identified over 400 miRNAs in early neural and epidermal ectoderm. The Ago-RNP RNAs from these tissues represent overlapping, yet distinct, subsets of genes. Moreover, the profile of Ago-RNP associated genes differs substantially from the profile of total RNAs in these tissues. Identification of microRNAs and microRNA targets in establishment of early ectodermal tissues in Xenopus.

2016-06-28 | E-GEOD-83784 | biostudies-arrayexpress

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