Digit patterning is controlled by a Bmp-Sox9-Wnt Turing network modulated by morphogen gradients
Ontology highlight
ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE58158 | GEO | 2014/06/15
SECONDARY ACCESSION(S): PRJNA251405
REPOSITORIES: GEO
Similar Datasets
Project description:The goal of this microarray analysis was to see which genes are differentially expressed between Sox9-EGFP positive cells and Sox9-EGFP negative cells in E11.5 mouse limb bud autopods of the reporter Sox9-EGFP knock-in mouse(Nakamura et al 2011). This was done in order to gain insight of the genes that could contribute to the specification of the digits (Sox9 positive cells). Mesenchymal cells were extracted from the mouse (Sox9EGFP knock-in, Nakamura et al . 2011) embryo forelimb autopod at stage E11.5. Sox9EGFP-positive cells were FACS-sorted from Sox9EGFP-negative cells . Each FACS-sorted sample was made from several forelimb autopods (approximately n=10). Three replicates were used for each group of Sox9EGFP-positive cells and Sox9EGFP-negative cells. Extraction of total RNA, labeling and hybridization to the microarray were performed using attached protocols. We identified the genes that were differentially expressed between the two groups.
2014-06-15 | E-GEOD-58158 | biostudies-arrayexpress
Project description:To define the repertoire of Sox9-dependent genes that contribute to the regulation of chondrogenesis, we generated Sox9-3'enhanced green fluorescent protein (EGFP) knock-in mice (Sox9-3'EGFP) and Sox9-EGFP/EGFP null chimeras. EGFP-positive cells of Sox9-3'EGFP knock-in and Sox9-EGFP/EGFP null chimeric embryos harvested from limb buds at embryonic day 12.5 were sorted using a FACSAria flow cytometer (Becton-Dickinson). Total RNA of sorted cells was extracted using the RNeasy Mini Kit (QIAGEN) and amplified according to the instructions provided by Affymetrix. Microarray analysis using the Affymetrix Mouse Genome 430 2.0 Array was performed according to the manufacturer's instructions.
2011-02-16 | E-MTAB-537 | biostudies-arrayexpress
Project description:As the only truly flying mammals, bats use their unique wing formed from elongated digits connected by membranes to power their flight. The forelimb of bats consists of four elongated digits (digits II-V) and one shorter digit (digit I) that is morphologically similar to the hindlimb digits. Elongation of bat forelimb digits is thought to results from changes in the temporal and spatial expression of a number of developmental genes. As a result, comparing gene expression profiles between short and elongated digit morphologies of the fore- and hindlimbs may elucidate the molecular mechanisms underlying digit elongation in bats. Here, we performed a large-scale analysis of gene expression of forelimb digit I, forelimb digits II-V, and all five hindlimb digits in Myotis ricketti using digital gene expression tag profiling approach. Results of this study not only implicate several developmental genes as robust candidates underlying digit elongation in bats, but also provide a better understanding of the genes involved in autopodial development in general. A large-scale analysis of gene expression of 3 different parts of autopods in Myotis ricketti using digital gene expression tag profiling approach.
2010-12-06 | E-GEOD-20038 | biostudies-arrayexpress
Project description:Genes specific to Sox9+ pancreatic progenitors were identified by comparing the gene expression in embryonic and adult Sox9+ cells. We used microarray analysis to detail the global changes in gene expression as Sox9 positive embryonic pancreatic progenitors differentiatiate into adult ductal cells or the endocrine lineage. GFP positive cells from Sox9-EGFP mouse pancreas were isolated by FACS at different stages of development (e10.5, e15.5, and p23) for RNA extraction and hybridization to Affymetrix microarrays. To obtain populations highly enriched in Sox9 expression, we collected only GFP Hi populations for analysis. To identify gene expression changes specific to the differentiation of progenitors to ductal cells or endocrine cells, we also isolated and analyzed the gene expression profile of GFP negative cells isolated at p23, as well as GFP positive cells isolated from Ngn3-EGFP mouse pancreas at e15.5. These two populations allow the identification of genes whose expression is associated with the newly differentiated endocrine progeny in the embryo (Ngn3-GFP positive) and adult acinar and endocrine cells at p23.
2012-08-01 | E-GEOD-34060 | biostudies-arrayexpress
Project description:Transcriptional profiling of intestinal epithelial cells expressing either Negative, Sublow, Low or High levels of the Sox9-EGFP reporter transgene FACS-isolated from jejunum of non-irradiated mice or at 5 days after 14Gy abdominal irradiation. 4 distinct cell populations, FACS-isolated based on expression levels of the Sox9-EGFP reporter transgene (Sox9-EGFP Negative, Sublow, Low and High cells); 2 conditions: Non-irradiated vs Irradiated; Biological replicates: 7 independent non-irradiated mice and 3 independent irradiated (studied at day 5 post-irradiation) mice
2012-06-17 | E-GEOD-32227 | biostudies-arrayexpress
Project description:Next Generation Sequencing Facilitates Quantitative Analysis of Sox9+/IRES-EGFP and Sox9+/Y440X-IRES-EGFP Limbs Transcriptomes
| PRJNA830521 | ENA
Project description:Vascular calcification and increased extracellular matrix (ECM) stiffness are hallmarks of vascular ageing. Sox9 (SRY-Box Transcription Factor 9) is a master regulator of chondrogenesis, also expressed in the vasculature, that has been implicated in vascular smooth muscle cell (VSMC) osteo-chondrogenic conversion. Here, we investigated the relationship between vascular ageing, calcification and Sox9-driven ECM regulation in VSMCs. Immunohistochemistry in human aortic samples showed that Sox9 was not spatially associated with vascular calcification but correlated with the senescence marker p16. Analysis of Sox9 expression in vitro showed it was mechanosensitive with increased expression and nuclear translocation in senescent cells and on stiff matrices. Manipulation of Sox9 via overexpression and depletion, combined with atomic force microscopy (AFM) and proteomics, revealed that Sox9 regulates ECM stiffness and organisation by orchestrating changes in collagen expression and reducing VSMC contractility, leading to the formation of an ECM that mirrored that of senescent cells. These ECM changes promoted phenotypic modulation of VSMCs whereby senescent cells plated onto ECM synthesized from cells depleted of Sox9 returned to a proliferative state, while proliferating cells on a matrix produced by Sox9 expressing cells showed reduced proliferation and increased DNA damage, reiterating features of senescent cells. Procollagen-lysine, 2-oxoglutarate 5-dioxygenase 3 (LH3) was identified as a Sox9 target, and key regulator of ECM stiffness. LH3 is packaged into extracellular vesicles (EVs) and Sox9 promoted EV secretion, leading to increased LH3 deposition within the ECM. These findings identify cellular senescence and Sox9 as a key regulators of ECM stiffness during VSMC ageing and highlight a crucial role for ECM structure and composition in regulating VSMC phenotype. We identify a positive feedback cycle whereby cellular senescence and increased ECM stiffening promote Sox9 expression which drives further ECM modifications that act to accelerate vascular stiffening and cellular senescence.
2024-06-16 | PXD046001 | Pride
Project description:Purpose: SOX9Y440X is the most commonly reported SOX9 mutation identified in human patients with Campomelic dysplasia, a dominant semi-lethal skeletal disease characterized by congenital shortening and angulation of long bones (campomelia). To understand how the SOX9Y440X mutant cause the abnormal limb development and compare with previously heterozygous Sox9 null mutant, a mouse model with Sox9Y440X mutation has been generated. The goal of this study is to carry out transcriptome analyses (RNA-seq) of E13.5 limbs collected from Sox9+/IRES-EGFP and Sox9+/Y440X-IRES-EGFP mice. GFP+ and GFP- cells were collected from each genotype by FACS. Comparing transcriptome profiles of cells from these two genotypes aims to reveal how the SOX9Y440X mutant causes abnormal limb development. Method: Forelimbs (FL) and hindlimbs (HL) mRNA profiles of E13.5 Sox9+/IRES-EGFP (WT) and Sox9+/Y440X-IRES-EGFP (CD) mice were generated by sequencing. 4-6 pairs of FL and HL buds were collected separately for each genotype. Limb tissues were then digested into single cells, then EGFP positive and negative cells were collected by FACS for each sample. Total RNA from each sample was prepared using Ambion RNA isolation kit (Cat. AM1580). 100ng of total RNA was used from each sample for RNA-sequencing. cDNA libraries were prepared by TruSeq Stranded mRNA Sample Prep Kit (Illumina). Pair-End sequencing of 101bp was done using HiSeq 1500 Sequencer Model. Data processing: Reads was pre-processed and aligned to the mouse GRCm38 (mm10) reference genome and expression levels were quantified using the nfcore/rnaseq workflow. The count matrix from featureCounts was used in the downstream analyses. The Nextflow pipeline for downstream analysis is available at https://github.com/fuxialexander/sox9. With R library edgeR 3.36.0, read counts were normalized using the ‘TMM’ method. We identified differentially expressed genes between the WT and CD groups in GFP+ or GFP- samples with the ‘glmQLFTest’ function and a Benjamini & Hochberg adjusted P-value cutoff of 0.05. Conclusions: Our study represents the first detailed analysis of mouse foetal limbs transcriptomes between Sox9Y440X mutant and wild type. Our work contributes to gain insight into the molecular signalling pathways affected by SOX9Y440X in vivo.
2022-12-31 | GSE201261 | GEO
Project description:The bat offers an alternative paradigm to the standard mouse and chick model of limb development as it has extremely divergent forelimbs (long digits supporting a wing) and hindlimbs (short digits and claws) due the distinct requirements of both aerial and terrestrial locomotion. We used a cross-species microarray approach to identify differentially expressed (DE) genes between the bat (Minniopterus natalensis) forelimb and hindlimb autopods at Carollia developmental stages (CS) 16 and CS17, and between the bat (CS17) and mouse (E13.5) forelimb autopods. Several DE genes were identified, including two homeobox genes, Meis2, a proximal limb-patterning gene, and Hoxd11, a gene involved in digit elongation. Both genes are significantly over-expressed in the developing bat forelimb as compared to the hindlimb and equivalently staged mouse forelimbs.
2014-02-15 | GSE51042 | GEO
Project description:As the only truly flying mammals, bats use their unique wing formed from elongated digits connected by membranes to power their flight. The forelimb of bats consists of four elongated digits (digits II-V) and one shorter digit (digit I) that is morphologically similar to the hindlimb digits. Elongation of bat forelimb digits is thought to results from changes in the temporal and spatial expression of a number of developmental genes. As a result, comparing gene expression profiles between short and elongated digit morphologies of the fore- and hindlimbs may elucidate the molecular mechanisms underlying digit elongation in bats. Here, we performed a large-scale analysis of gene expression of forelimb digit I, forelimb digits II-V, and all five hindlimb digits in Myotis ricketti using digital gene expression tag profiling approach. Results of this study not only implicate several developmental genes as robust candidates underlying digit elongation in bats, but also provide a better understanding of the genes involved in autopodial development in general.
2010-12-06 | GSE20038 | GEO