Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

13 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcription profiling of Xenopus tropicalis tadpole tail tissue regeneration following removal

ABSTRACT: In this experiment, we show transcription profiling of the Xenopus tropicalis tadpole tail tissue regeneration following removal. The tail tissues include its spinal cord, notochord, muscle, and dorsal aorta. We characterized the early, intermediate, and late stages of Xenopus tropicalis tail regeneration using the Xenopus tropicalis Affymetrix genome array in biological replicate.

ORGANISM(S): Xenopus tropicalis

SUBMITTER: Leo Zeef

PROVIDER: E-MEXP-2420 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Mapping gene expression in two Xenopus: evolutionary constraints and developmental flexibility

Project description:Variation in gene expression is known to be important for morphological evolution, however little is known about its general propensity. Here we examine a pair of frogs M-bM-^@M-^S Xenopus laevis and Xenopus tropicalis M-bM-^@M-^S with highly similar embryology, and ask how their transcriptomes compare. Despite separation for over ~30-90 million years we found a strong conservation in gene expression in the vast majority of the expressed orthologs. There were a significant number of changes in the level of expression of genes. Changes in timing of expression, heterochrony, were much less common, and were often found in genes and pathways that reflect responses to selective features of the environment. Differences in gene expression levels were concentrated in the earliest embryonic stages. We propose that different evolutionary rates across developmental stages may be explained by the stabilization of cell fate determination pathways in later stages. 96 microarrays, across developmental stages in Xenopus laevis and Xenopus tropicalis in wildtype embryos. For each of the two timecourse indepenent triplicates (clutches) were generated.

2011-06-01 | E-GEOD-27227 | biostudies-arrayexpress

High-throughput sequencing of small RNAs from Xenopus tropicalis

Project description:High-throughput sequencing of small RNAs from Xenopus tropicalis (adult liver, adult skin, oocytes stage I, II, III, IV, V, VI). total RNA, ~18-42 nt RNAs isolated using PAGE, ligation to adapters requires 5' monophosphate and 3' OH Illumina/Solexa sequencing of adult liver, adult skin, oocytes stage I, II, III, IV, V, VI

2009-07-09 | E-GEOD-14952 | biostudies-arrayexpress

RNA-seq of a time course of spinal cord regeneration following tail amputation in Xenopus tropicalis tadpoles at stage 50

Project description:The tails of stage NF50 Xenopus tropicalis were amputated and samples were collected at 0, 1 and 3 days post amputation. About 20 spinal cords were isolated manually and pooled for each sample. in biological triplicates at each time point.

2020-02-26 | E-MTAB-8785 | biostudies-arrayexpress

Identification of candidate genes for morph-biased expression using heterlogous hybridization

Project description:This series represents the 16 arrays that were used to identify expression differences between the alternative morphs of Spadefoot toads (Spea bombifrons). We used Affymetrix GeneChip Xenopus tropicalis genome arrays, 8 biological replicates for two ecotypes (morphs).

2011-12-31 | E-MEXP-3324 | biostudies-arrayexpress

Transcription profiling of brains, hindlimbs and tails of Xenopus laevis tadpoles after treatment with thyroid hormone

Project description:Premetamorphic Xenopus laevis tadpole tail respond to thyroid hormone by resorption. The goal of this experiment is to identify the genes involved in the TH-induced resorption tadpole tail and compare it to TH-induced proliferation and differentiation program in tadpole limb and brain. Xenopus tadpoles (NF54) were treated with 100 nM T3(triioodthyronine) in 0.1 x MMR for another 24h and 48h or without T3 for 48h (control group). NF 61 tadpoles were in 0.1 X MMR till they reached NF stage 62. The tails were dissected after the experiment.

2006-11-08 | E-MNIA-94 | biostudies-arrayexpress

A Hierarchy of H3K4me3 and H3K27me3 Acquisition in Spatial Gene Regulation in Xenopus Embryos

Project description:Epigenetic mechanisms set apart the active and inactive regions in the genome of multicellular organisms to produce distinct cell fates during embryogenesis. Here, we report on the epigenetic and transcriptome genome-wide maps of gastrula-stage Xenopus tropicalis embryos using massive parallel sequencing of cDNA (RNA-seq) and DNA obtained by chromatin immunoprecipitation (ChIP-seq) of histone H3 K4 and K27 trimethylation and RNA Polymerase II (RNAPII). These maps identify promoters and transcribed regions. Strikingly, genomic regions featuring opposing histone modifications are mostly transcribed, reflecting spatially regulated expression rather than bivalency as determined by expression profile analyses, sequential ChIP, and ChIP-seq on dissected embryos. Spatial differences in H3K27me3 deposition are predictive of localized gene expression. Moreover, the appearance of H3K4me3 coincides with zygotic gene activation, whereas H3K27me3 is predominantly deposited upon subsequent spatial restriction or repression of transcriptional regulators. These results reveal a hierarchy in the spatial control of zygotic gene activation. ChIP-seq profiles of two histone modifications (H3K4me3 and H3K27me3) and RNA Polymerase II, and a RNA-seq profile, of gastrula stage Xenopus tropicalis embryos

2009-09-15 | E-GEOD-14025 | biostudies-arrayexpress

ChIP-chip Designs to Interrogate the Xenopus Embryo Genome for Transcription Factor Binding and Epigenetic Regulation

Project description:Background: Chromatin immunoprecipitation combined with genome tile path microarrays or deep sequencing can be used to study genome-wide epigenetic profiles and the transcription factor binding repertoire. Although well studied in a variety of cell lines, these genome-wide profiles have so far been little explored in vertebrate embryos. Principal findings: Here we report on two genome tile path ChIP-chip designs for interrogating the Xenopus tropicalis genome. In particular, a whole-genome microarray design was used to identify active promoters by close proximity to histone H3 lysine 4 trimethylation. A second microarray design features these experimentally derived promoter regions in addition to currently annotated 5â ends of genes. Conclusions: A whole-genome and a dedicated promoter microarray design was developed which can be used to study epigenetic phenomena and transcription factor binding in developing Xenopus embryos. H3K4me3 and TBP ChIP-chip on Xenopus tropicalis tiling arrays

2010-05-17 | E-GEOD-19413 | biostudies-arrayexpress

Nucleotide composition-linked divergence of vertebrate core promoter architecture

Project description:Transcription initiation involves the recruitment of basal transcription factors to the core promoter. A variety of core promoter elements exists, however for most of these motifs the distribution across species is unknown. Here we report on the comparison of human and amphibian promoter sequences. We have used oligo-capping in combination with deep sequencing to determine transcription start sites in Xenopus tropicalis. To systematically predict regulatory elements we have developed a de novo motif finding pipeline using an ensemble of computational tools. A comprehensive comparison of human and amphibian promoter sequences revealed both similarities and differences in core promoter architecture. Some of the differences stem from a highly divergent nucleotide composition of Xenopus and human promoters. Whereas the distribution of some core promoter motifs is conserved independent of species-specific nucleotide bias, the frequency of another class of motifs correlates with the single nucleotide frequencies. This class includes the well-known TATA box and SP1 motifs, which are more abundant in Xenopus and human promoters, respectively. While these motifs are enriched above the local nucleotide background in both organisms, their frequency varies in step with this background. These differences are likely adaptive as these motifs can recruit TFIID to either CpG island or sharply initiating promoters. Our results highlight both conserved and diverged aspects of vertebrate transcription, most notably showing co-opted motif usage to recruit the transcriptional machinery to promoters with diverging nucleotide composition. This shows how sweeping changes in nucleotide composition are compatible with highly conserved mechanisms of transcription initiation. ChIP-seq profiles of TBP in Xenopus tropicalis stage 12 embryos and TSS-seq profiles of Xenopus oocytes and stage 12 embryos

2010-12-30 | E-GEOD-21482 | biostudies-arrayexpress

Dynamic liver transcriptome response of Xenopus tropicalis to benzo[a]pyrene

Project description:Chronological RNA-seq of comparison of liver from xenopus tropicalis exposed or not to benzo[a]pyrene (10ﾵg/L)

2014-08-18 | E-MTAB-2444 | biostudies-arrayexpress

Chromatin immunoprecipitation to identify CUG-BP1/EDEN-BP target mRNAs in Xenopus tropicalis eggs

Project description:Identification of RNA bound to the RNA-binding protein CUGBP1/EDENBP in Xenopus tropicalis eggs.

2008-02-21 | E-MEXP-1466 | biostudies-arrayexpress