Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Regional expression of X. tropicalis transcription factors in early gastrula embryos

ABSTRACT: Purpose: We wished to obtain spatial expression profiles of transcription factor gene expression and expression of other genes. Methods: Embryos were dissected and RNA-seq was performed to determine expression levels of genes. Comparisons between explanted regions permits determination of spatial enrichment of gene expression. mRNA-seq performed on 5 dissected regions of NF stage 10.5 X. tropicalis embryos and stage-matched sibling whole embryos. Experiment performed in duplicate.

ORGANISM(S): Xenopus tropicalis

SUBMITTER: Kitt Paraiso

PROVIDER: E-GEOD-81458 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Publications

A catalog of Xenopus tropicalis transcription factors and their regional expression in the early gastrula stage embryo.

Blitz Ira L IL Paraiso Kitt D KD Patrushev Ilya I Chiu William T Y WTY Cho Ken W Y KWY Gilchrist Michael J MJ

Developmental biology 20160728 2

Gene regulatory networks (GRNs) involve highly combinatorial interactions between transcription factors and short sequence motifs in cis-regulatory modules of target genes to control cellular phenotypes. The GRNs specifying most cell types are largely unknown and are the subject of wide interest. A catalog of transcription factors is a valuable tool toward obtaining a deeper understanding of the role of these critical effectors in any biological setting. Here we present a comprehensive catalog o ...[more]

PMID: 27475627

Similar Datasets

Project description:Successfully replacing damaged cartilage with tissue-engineered constructs requires integration with the host tissue and could benefit from leveraging the native tissue's intrinsic healing capacity; however, efforts are limited by a poor understanding of how cartilage repairs minor defects. Here, we investigated the conditions that foster natural cartilage tissue repair to identify strategies that might be exploited to enhance the integration of engineered/ grafted cartilage with host tissue. We damaged porcine articular cartilage explants and using a combination of pulsed SILAC-based proteomics, ultrastructural imaging, and catabolic enzyme blocking strategies reveal that integration of damaged cartilage surfaces is not driven by neo-matrix synthesis, but rather local depletion of proteoglycans. ADAMTS4 expression and activity are upregulated in injured cartilage explants, but integration could be reduced by inhibiting metalloproteinase activity with TIMP3. These observations suggest that catabolic enzyme-mediated proteoglycan depletion likely allows existing collagen fibrils to undergo cross-linking, fibrillogenesis, or entanglement, driving integration. Catabolic enzymes are often considered pathophysiological markers of osteoarthritis. Our findings suggest that damage-induced upregulation of metalloproteinase activity may be a part of a healing response that tips towards tissue destruction under pathological conditions and in osteoarthritis, but could also be harnessed in tissue engineering strategies to mediate repair. Statement of significance: Cartilage tissue engineering strategies require graft integration with the surrounding tissue; however, how the native tissue repairs minor injuries is poorly understood. We applied pulsed SILACbased proteomics, ultrastructural imaging, and catabolic enzyme blocking strategies to a porcine cartilage explant model and found that integration of damaged cartilage surfaces is driven by catabolic enzyme-mediated local depletion of proteoglycans. Although catabolic enzymes have been implicated in cartilage destruction in osteoarthritis, our findings suggest that damage-induced upregulation of metalloproteinase activity may be a part of a healing response that tips towards tissue destruction under pathological conditions. They also suggest that this natural cartilage tissue repair process could be harnessed in tissue engineering strategies to enhance the integration of engineered cartilage with host tissue.

Dataset Information

Regional expression of X. tropicalis transcription factors in early gastrula embryos

Publications

A catalog of Xenopus tropicalis transcription factors and their regional expression in the early gastrula stage embryo.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure