Transcription profiling of Xenopus pole tissue explants from Notch treated embryos vs. controls
Ontology highlight
ABSTRACT:
ORGANISM(S): Xenopus laevis
SUBMITTER: Curtis Altmann
PROVIDER: E-GEOD-5564 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:Animal pole tissue explants were dissected from either untreated embryos or embryos injected with 1 ng of Notch Intracellular Domain RNA (NICD) at the two cell stage. Tissue explants were dissected and cultured until sibling embryos reached embryonic stage 20. Each array hybridization represents a biological replicate containing approximately 100 tissue explants. Expression profiles were determined using Affymetrix Xenopus Genechip 1 arrays. Keywords: repeat
2008-01-18 | GSE5564 | GEO
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2008-06-12 | E-GEOD-3712 | biostudies-arrayexpress
Project description:The goal of this study is to investigate the molecular mechanism of lhx1 on regulation of pronephros formation during the early embryonic development. In the vertebrate embryo the kidney is derived from the intermediate mesoderm. The LIM-class homeobox transcription factor lhx1 is expressed early in the intermediate mesoderm and is one of the first genes to be expressed in the nephric mesenchyme. The animal cap cells can be induced by treatment of activin and retinoic acid to differentiate into pronephros tissue. In this study we investigated the role of Lhx1 in differentiation of pronephros by depleting lhx1 in the organ culture system. We generated the gene expression profile of early pronephros tissue, and demonstrated that expression of genes from all the kidney domains is affected by the absence of lhx1. Taken together our results highlight an essential role for Lhx1 in pronephros formation. lhx1 is involved in driving specification of intermediate mesoderm into nephrogenic mesenchyme. Lhx1 is initially expressed throughout the entire intermediate mesoderm. To determine the role of lhx1 pronephros formation, we performed a microarray analysis using an explant culture system. Xenopus tissue explants can be surgically isolated and cultured under specific conditions to be driven towards many distinct tissue types. Formation of pronephric cell fates is induced by culturing isolated explants in the presence of Activin and RA (AcRA). Treatment of dissected explants of stage 9 blastulae embryos with 10ng/ml Activin and 1x10-4 M retinoic acid can induce differentiation of the pluripotent ectoderm into pan-kidney tissue. For this experiment, both blastomeres of 2-cell embryos were injected with a total of 800pg lhx1 DEED-AS. Explants were dissected and treated with AcRA and expression of pax8 at stage 15 (based on timing of paired control whole embryos) was analyzed. We observed a lack of induction of pax8 expression in lhx1-depleted explants under AcRA treatment conditions in which expression of this gene is normally induced. Based on this observation, microarray analysis was carried out to identify genes whose expression is affected by the absence of lhx1. Explants of injected embryos with 800pg of lhx1 DEED-AS were dissected, treated with pronephric tissue inductive conditions (AcRA) and harvested after 24 hours incubation at 14C (Fig. S5B). The sibling control embryos reached stage 12.5. Explants from uninjected embryos +AcRA and -AcRA as well as explants from DEED injected embryos -AcRA were also harvested. Approximately 12 caps were pooled for each RNA preparation and the analysis was performed using triplicates.
2010-09-29 | E-GEOD-24392 | biostudies-arrayexpress
Project description:The response of ectodermal explants, neuralized by noggin and treated with cycloheximide, following activation of hormone-inducible zic1 injected into the parent embryos compared to those from beta globin injected embryos as controls, is expected to provide information on the direct targets of the Zic1 transcription factor. Experiment Overall Design: Activation of zic1 in ectodermal explants following inhibition of new protein synthesis allowed the direct targets of zic1 to be identified by comparison with controls. After RNA extraction, purification and checks with PCR with actin primers for any mesoderm contamination samples were prepared for hybridization to Xenopus laevis Affymetrix GeneChip arrays.
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Project description:Animal poles of 1 to 2-cell stage embryos were injected with a cocktail containing 5pg of Fgf4 and 50pg wnt8 mRNA. Embryos were grown alongside batch controls to NF stage 8/9. Animal cap explants were dissected from the embryos and grown overnight in NAM alongside whole embryo controls as a means of staging. At NF stage 25, caps were collected for microarray analysis. Custom microarrays containing sequences for Xenopus tRNA and RNA Polymerase III gene families as well as selected mRNAs were used to detect changes in transcription at this stage in response to induction of myogenic differentiation. We aimed to use this data to investigate the relationship between any codon bias in highly expressed mRNAs with expression of their matching tRNA isoacceptors in response to a specific differentiation programme.
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Project description:Sox9 acts together with Sox5 or Sox6 as a master regulator for chondrocyte differentiation; however, how these transcription factors functionally interact and collaborate to regulate chondrogenesis remains unclear. Here we show that the protein kinase MLTK plays an essential role in the onset of chondrogenesis through triggering the induction of Sox6 by Sox9. Knockdown of MLTK in Xenopus embryos results in drastic loss of craniofacial cartilages without defects in neural crest formation. We also find that Sox6 is specifically induced during craniofacial chondrogenesis and this induction is inhibited by MLTK knockdown. Remarkably, Sox6-knockdown embryos display essentially the same phenotype as the MLTK-knockdown embryos; the drastic loss of cartilages and the marked down-regulation of genes involved in chondrogenesis. Microarray analysis reveals a remarkable similarity between Sox6-depleted and MLTK-depleted embryos in their gene expression pattern. Moreover, we find that ectopic expression of MLTK can induce Sox6 expression in a Sox9-dependent manner. These results identify a novel, key regulator for chondrogenesis. We used microarrays to describe the genome-wide gene expression profiles of xMLTK-depleted and xSox6-depleted embryos. CoMO, xMLTK-MO, or xSox6-MO was injected into the animal pole of all blastomeres (10 ng/cell) at the four-cell stage. The heads of embryos were cut out and harvested at 72 hours after fertilization (corresponding to about stage 41). Total RNA was extracted using TRIsol reagent, treated with DNase (TURBO DNase, Ambion), and then purified using RNeasy Mini Kit (QIAGEN) according to the manufacturerM-bM-^@M-^Ys instruction. The quality of total RNA was assessed using the Agilent 2100 BioAnalyzer. Reverse transcription to synthesize first-strand cDNA, second-strand cDNA synthesis, in vitro transcription to synthesize Biotin-modified aRNA, aRNA purification and fragmentation of the labeled aRNA were performed using the GeneChip 3M-bM-^@M-^Y IVT Express Kit and hybridization to the Affymetrix GeneChip Xenopus laevis Genome 2.0 Array was performed using the GeneChip Hybridization Wash and Stain Kit according to the manufacturerM-bM-^@M-^Ys instruction. Hybridized arrays were scanned using an Affymetrix GeneChip Scanner. Scanned Chip images were analyzed with GeneChip operating Software v.1.4 (GCOS) and GeneSpring GX 11.0.2. (Agilent technologies).
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