Mouse Digits Regeneration RNA-seq Data
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA540258 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Mice were subjected to hindlimb distal phalanx (P3) amputation to digit 3. For each amputation, mice were anesthetized, the hindlimb claw was extended, and the distal phalanx and footpad was sharply dissected. A regenerating distal phalanx was generated by amputating ≤33% of the P3. Skin wounds were allowed to heal without suturing. Mice were subjected to micro-computed tomography (microCT) one day prior to surgery and immediately after amputation to confirm ≤ 33% removal of the P3. Any digit that did not fall within the ≤ 33% amputation guideline was omitted from the study. Based on our criteria, 17 animals were removed from the study resulting in a final total of 30 mice. P3 mice were collected at hours (0h, 3h, 6h ,12h, and 24h), and days (3d, 7d, 14d, and 21d). Each time point contained 3 mice, except day 7 (6 mice). At the time of P3 collection, samples were immediately immersed in RNAlater for 24h at 4C. The digits were then removed from RNAlater and stored at -80C until performing RNA sequencing.
2020-02-19 | GSE130438 | GEO
Project description:Morphological characters are the result of developmental gene expression. Hence the identity of a character is ultimately grounded in the gene regulatory network directing development and thus whole genome gene expression data can provide evidence about character identity. Here we use transcriptomic data to address one of the most enduring paradoxes in evolutionary biology, the identity of the avian wing digits. Deep Sequencing of mRNA from embryonic chicken digits is performed and the gene expression profiles are analyzed. Analysis of mRNA-seq data from 16 samples of chicken digits covering two embryonic stages.
2011-09-07 | E-GEOD-28156 | biostudies-arrayexpress
Project description:Morphological characters are the result of developmental gene expression. Hence the identity of a character is ultimately grounded in the gene regulatory network directing development and thus whole genome gene expression data can provide evidence about character identity. Here we use transcriptomic data to address one of the most enduring paradoxes in evolutionary biology, the identity of the avian wing digits. Deep Sequencing of mRNA from embryonic chicken digits is performed and the gene expression profiles are analyzed.
2011-09-08 | GSE28156 | GEO
Project description:The distal mouse digit tip undergoes complex tissue regeneration following amputation, a process facilitated by the formation of a cellular structure called the blastema. Through single-cell RNA sequencing of the blastema, we identified the gene Mest (mesoderm specific transcript) highly expressed in a subset of blastemal fibroblasts. To determine if Mest expression is necessary for mouse digit tip regeneration, we analyzed Mest wildtype (WT) versus homozygous knockout (KO) post amputation digits. Through single-cell sequencing and FACS analysis of WT and KO regenerating tissues, we determined that this phenomenon was due to a prolonged immune response in the KO digits.
2024-07-03 | GSE267553 | GEO
Project description:MicroRNA-seq data of mouse during skeletal muscle regeneration after acute injury
| PRJNA595084 | ENA
Project description:RNA-seq data from adult zebrafish caudal fin regeneration
| PRJNA447984 | ENA
Project description:The liver is the only organ in mammals, which fully regenerates after injury. To identify novel regulators of liver regeneration, we performed quantitative large-scale proteomics analysis of subcellular fractions from normal versus regenerating mouse liver. Proteins of the ubiquitin-proteasome pathway were rapidly regulated by partial hepatectomy, with the ubiquitin ligase Nedd4-1 being among the top hits. Knock-down of Nedd4-1 in hepatocytes in vivo through nanoparticle-mediated delivery of siRNA caused severe liver damage after partial hepatectomy and impaired regeneration, resulting in liver failure. Mechanistically, we demonstrate that Nedd4-1 is required for efficient activation of Erk1/2 signaling by receptor tyrosine kinases involved in liver regeneration through inhibition of receptor internalization, thus controlling a major pro-mitogenic and cytoprotective signaling pathway in the regenerating liver. These results highlight the power of large-scale proteomics to identify key players in liver regeneration and the importance of posttranslational regulation of growth factor signaling in this process.
2017-09-13 | PXD004108 | Pride
Project description:Purpose: Investigate the transcriptomic landscape throughout the time course of murine digit regeneration after level-dependent amputation. Methods: The terminal phalanx bone of hind limb digits was subjected to either a distal amputation (25% bone length loss) or proximal amputation (65% bone length loss). Total RNA was isolated from bone and fibrous tissues distal to the distal interphalangeal joint at 12, 14, and 21 days post-amputation (DPA). mRNA library was sequenced using Illumina HiSeq 3000. Trimmed reads were aligned to the mouse genome mm10 and batch-corrected. Results: A limb-specific developmental signaling pathway is transiently upregulated at 14 DPA after distal amputation, corresponding with regeneration of digit tip tissues. Absence of a limb-specific pathway after proximal amputation corresponded with minimal regeneration and fibrotic scarring. Conclusions: Digit regeneration is a level-dependent and spatiotemporally controlled process, with distal and proximal amputations showing significant differences in gene expression and tissue regrowth over time.
2020-06-10 | GSE131078 | GEO
Project description:The evolution of tetrapod limbs from fish fins enabled the conquest of land by vertebrates and thus represents a key step in evolution. Despite the use of comparative gene expression analyses, critical aspects of this transformation remain controversial, in particularly the origin of digits. Hoxa and Hoxd genes are essential for the specification of the different limb segments and their functional abrogation leads to large truncations of the appendages. Here we show that the selective transcription of mouse Hoxa genes in proximal and distal limbs is related to a bimodal higher order chromatin structure, similar to that reported for Hoxd genes, thus revealing a generic regulatory strategy implemented by both gene clusters during limb development. We found the same bimodal chromatin architecture in fish embryos, indicating that the regulatory strategy used to pattern tetrapod limbs predates the divergence between fish and tetrapods. However, when assessed in mice, both fish regulatory domains triggered transcription in proximal, rather than distal limb territories, supporting an evolutionary scenario whereby digits arose as true tetrapod novelties through genetic retrofitting of a preexisting bimodal chromatin framework. We discuss the possibility to consider regulatory circuitries, rather than expression patterns, as essential parameters to define evolutionary synapomorphies. Circular Chromosome Conformation Capture (4C seq) at the mouse HoxA and HoxD loci in proximal and distal forelimbs and forebrain at E12.5 and at the zebrafish HoxAa, HoxAb and HoxDa loci in 5 dpf whole embryos.
2014-01-21 | E-GEOD-47644 | biostudies-arrayexpress
Project description:RNA-seq data from mouse articular chondrocytes
| PRJNA705224 | ENA