Effect of FGF singaling inhibition on gene expression on limb bud mesenchyme explants.
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA926330 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR23185574_1.fastq.gz | Fastqsanger.gz | |||
| SRR23185574_2.fastq.gz | Fastqsanger.gz | |||
| SRR23185575_1.fastq.gz | Fastqsanger.gz | |||
| SRR23185575_2.fastq.gz | Fastqsanger.gz | |||
| SRR23185576_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 12 |
Similar Datasets
Project description:To investigate the role FGF signaling in limb bud development we inhibited FGF signaling in limb bud explants by treatment with 5µM SU5402, an FGFR inhibitor, or DMSO as control. We then performed mRNA sequencing on RNA collected after 48h of treatment to analyse the effect on gene expression.
2023-08-24 | GSE223444 | GEO
Project description:Vertebrate limbs develop by integrating signals that control patterning along three main orthogonal axes. Flank-produced retinoic acid (RA) is initially required for limb induction and establishment of the apical ectodermal ridge (AER), a distal signaling center that produces fibroblast growth factors (FGFs), which are essential for limb growth and distalization. Once the AER is established, RA:FGF antagonism determines the restricted expression of a set of genes that control limb proximodistal patterning. Essential for this antagonism is the activation by FGF of the RA-degrading enzyme CYP26B1 in the distal limb bud. In addition, sonic hedgehog produced from the zone of polarizing activity (ZPA) is essential for distal limb anteroposterior patterning and contributes to RA reduction by cooperating in CYP26B1 activation. Meis transcription factors are expressed in the proximal limb bud, are activated by RA and can regulate proximodistal limb development; however, the mechanisms underlying their activity remain unknown. Here we studied Meis function in the mouse limb bud through Meis2 conditional overexpression and elimination of Meis1 and Meis2. We found that Meis activity is first required for limb bud initiation and the proper establishment of the AER and ZPA signaling centers, and subsequently for the development of proximal limb structures. Functional genomic analyses reveal that Meis is an important conveyor of the RA:FGF antagonism through the regulation of components of the RA and FGF signaling pathways, including CYP26B1. In addition, Meis regulates a set of proximal limb genes controlling proximodistal patterning and differentiation. Our work reveals a regulatory module essential for limb patterning and potentially co-opted in other patterning processes involving RA:FGF antagonism.
2018-09-25 | GSE51374 | GEO
Project description:During limb development, fibroblast growth factors (FGFs) govern proximal-distal outgrowth and patterning. FGFs also synchronize developmental patterning between the proximal-distal and anterior-posterior axes by maintaining sonic hedgehog (SHH) expression in cells of the zone of polarizing activity (ZPA) in the distal posterior mesoderm. SHH, in turn, maintains FGFs in the apical ectodermal ridge (AER) which caps the distal tip of the limb bud. Crosstalk between FGF and SHH signaling is critical for patterned limb development, but the mechanisms underlying this feedback loop are not well characterized. Implantation of FGF beads in the proximal posterior limb bud can maintain SHH expression in the former ZPA domain (evident 3hrs after application), while prolonged exposure (24hrs) can induce SHH outside of this domain. Although temporally and spatially disparate, comparative analysis of transcriptome data from these different populations enriched molecules required for FGF-mediated SHH regulation.
2018-12-18 | GSE114661 | GEO
Project description:Analysis of mouse limb bud (E10.5) lacking the Bhlha9 gene. Bhlha9 knockout mouse shows syndactyly and poliosis in the limb. This microarray results provides insight into the molecular mechanisms underlying Bhlha9 function in the limb development DNA microarray analysis was performed using Affymetrix mouse genome 430 2.0 array. RNA samples were obtained from the whole limb bud of the E10.5 wild-type and Bhlha9 knockout embryos described above. Total RNA (200 ng) was reverse-transcribed and biotinylated using the GeneChip 3â² IVT Express Kit (Affymetrix). The microarray data were summarized using the MAS 5.0 method.
2016-05-31 | E-GEOD-81223 | biostudies-arrayexpress
Project description:Comparing gene expression of cells from the E10.5 limb bud ZPA and the rest of the E10.5 limb bud from Shhgfpcre heterozygotes separated by FACS. Experiment Overall Design: 8 samples, 4 ZPA and 4 rest of the limb
2008-06-15 | E-GEOD-7598 | biostudies-arrayexpress
Project description:Analysis of mouse limb bud (E10.5) lacking the Bhlha9 gene. Bhlha9 knockout mouse shows syndactyly and poliosis in the limb. This microarray results provides insight into the molecular mechanisms underlying Bhlha9 function in the limb development
2016-05-31 | GSE81223 | GEO
Project description:During embryonic development, fields of progenitor cells form complex spatial structures through dynamic interactions with external signaling molecules. However, how complex signaling inputs are integrated to yield appropriate gene expression responses is poorly understood. For instance several critical signals have been well characterized in the early limb bud, including Sonic hedgehog (Shh) and Fibroblast growth Factor 8 (Fgf8). While the former is expressed in the distal posterior mesenchyme where it acts as the mediator of anterior to posterior (AP) patterning, the latter is produced by the apical ectodermal ridge (AER) at the distal tip of the limb bud and directs the outgrowth and the proximal to distal (PD) organization of the limb. Here we use cultured limb mesenchyme cells to try and assess the response of the target Hoxd genes to these two factors. We find that they act synergistically and that both factors are required to get activation of Hoxd13 in limb mesenchymal cells. However, the analysis of the enhancer landscapes flanking the HoxD cluster reveals that the bimodal regulatory switch observed in vivo is not fully achieved under these in vitro conditions, suggesting the requirement for other factors.
2017-03-06 | GSE92556 | GEO
Project description:During embryonic development, fields of progenitor cells form complex spatial structures through dynamic interactions with external signaling molecules. However, how complex signaling inputs are integrated to yield appropriate gene expression responses is poorly understood. For instance several critical signals have been well characterized in the early limb bud, including Sonic hedgehog (Shh) and Fibroblast growth Factor 8 (Fgf8). While the former is expressed in the distal posterior mesenchyme where it acts as the mediator of anterior to posterior (AP) patterning, the latter is produced by the apical ectodermal ridge (AER) at the distal tip of the limb bud and directs the outgrowth and the proximal to distal (PD) organization of the limb. Here we use cultured limb mesenchyme cells to try and assess the response of the target Hoxd genes to these two factors. We find that they act synergistically and that both factors are required to get activation of Hoxd13 in limb mesenchymal cells. However, the analysis of the enhancer landscapes flanking the HoxD cluster reveals that the bimodal regulatory switch observed in vivo is not fully achieved under these in vitro conditions, suggesting the requirement for other factors.
2017-03-06 | GSE92555 | GEO
Project description:Shh signal mediated by Gli family of transcription factors regulates digit growth and patterning in early limb development. Shh expression in the posterior margin of the limb bud defines the zone of polarizing activity. However, much less is know about downstream targets that mediate Shh signal functions. In this dataset, we include the expression data obtained from dissected anterior and posterior halves of mouse limb bud respectively. These data are used to obtain 889 transcripts that were upregulated 1.3 fold or more in the posterior limb bud, and 1189 transcripts that were enriched in the anterior limb bud at 1.3 fold or more.
2013-01-06 | GSE41691 | GEO
Project description:Shh signal mediated by Gli family of transcription factors regulates digit growth and patterning in early limb development. Shh expression in the posterior margin of the limb bud defines the zone of polarizing activity. However, much less is know about downstream targets that mediate Shh signal functions. In this dataset, we include the expression data obtained from dissected anterior and posterior halves of mouse limb bud respectively. These data are used to obtain 889 transcripts that were upregulated 1.3 fold or more in the posterior limb bud, and 1189 transcripts that were enriched in the anterior limb bud at 1.3 fold or more. Two samples were analyzed. We generate pairwise comparisons between anterior and posterior limb tissues. Genes with a fold-change ≥1.3 were selected.
2013-01-06 | E-GEOD-41691 | biostudies-arrayexpress