Transcriptomic landscape of developing PSM from Tailbud to somite in E8.5 mouse embryo and ES
Ontology highlight
ABSTRACT:
ORGANISM(S): Mus musculus
SUBMITTER: philippe moncuquet
PROVIDER: E-GEOD-39615 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Shared Molecules
Only show the datasets with similarity scores above: 0.5
Threshold
0.5
Similar Datasets
Project description:Stem cell-derived tissues have wide potential for modelling developmental and pathological processes as well as cell-based therapy. However, it has proven difficult to generate several key cell types in vitro, including skeletal muscle. In vertebrates, skeletal muscles derive during embryogenesis from the presomitic mesoderm (PSM). Treatment of mouse ES cells with a combination of the secreted Wnt activator R-Spondin3 and the BMP inhibitor Noggin generated cells expressing the early PSM marker Mesogenin1 (Msgn1) with high efficiency. To confirm their identity, we mapped gene expression profiles at successive stages of PSM differentiation in vivo and showed that the differentiated ES cells closely corresponded to the posterior PSM domain that expresses Msgn1 and then with time in culture matured to acquire the profile of the anterior Pax3 domain. When grafted into injured adult muscle in vivo these Pax3-expressing-cells generated large numbers of muscle fibers. Our system therefore efficiently produces myogenic precursors in vitro by recapitulating stepwise early myogenic differentiation in vivo. These findings should advance the development of cellular therapies for muscle degenerative diseases. Pre Somitic Mesoderm (PSM) were dissected into 7 pieces in Stage E8.5 Mouse embryo. The experiment was designed to have biological triplicate in each pieces. The PSM is a symmetric structure, left and right area were obtained from one embryo, another set of dissection was obtained from another embryo.
2015-01-01 | E-GEOD-39613 | biostudies-arrayexpress
Project description:Stem cell-derived tissues have wide potential for modelling developmental and pathological processes as well as cell-based therapy. However, it has proven difficult to generate several key cell types in vitro, including skeletal muscle. In vertebrates, skeletal muscles derive during embryogenesis from the presomitic mesoderm (PSM). Treatment of mouse ES cells with a combination of the secreted Wnt activator R-Spondin3 and the BMP inhibitor Noggin generated cells expressing the early PSM marker Mesogenin1 (Msgn1) with high efficiency. To confirm their identity, we mapped gene expression profiles at successive stages of PSM differentiation in vivo and showed that the differentiated ES cells closely corresponded to the posterior PSM domain that expresses Msgn1 and then with time in culture matured to acquire the profile of the anterior Pax3 domain. When grafted into injured adult muscle in vivo these Pax3-expressing-cells generated large numbers of muscle fibers. Our system therefore efficiently produces myogenic precursors in vitro by recapitulating stepwise early myogenic differentiation in vivo. These findings should advance the development of cellular therapies for muscle degenerative diseases. ES cellline E14 129P2/OlaHsd with DMSO, Rspo, and Noggin at Days 3 and 4
2015-01-01 | E-GEOD-39614 | biostudies-arrayexpress
Project description:4 microarray time series was generated to identify cyclic genes of the segmentation clock in the mouse (2 time series), the chicken and the zebrafish. The right posterior half presomitic mesoderms (PSM) from 20 mouse embryos, 18 chicken embryos and 21 zebrafish embryos were dissected while the contralateral side of the embryo containing the left PSM was immediately fixed to be analyzed by in situ hybridization using a Lfng (fot mosue and chicken) or hes7 (zebrafish) probe to order the samples along the segmentation clock oscillation cycle. Probes were produced from RNA extracted from each of the dissected posterior half PSMs using a two-step amplification protocol and were hybridized to Affymetrix GeneChip MOE430A, MOE430 2.0, Affymetrix GeneChip chicken genome array, or Affymetrix GeneChip zebrafish array.
2011-06-10 | E-MTAB-406 | biostudies-arrayexpress
Project description:A microarray time series was generated to identify cyclic genes of the segmentation clock in the mouse. The right posterior half presomitic mesoderms (PSM) from 17 mouse embryos were dissected while the contralateral side of the embryo containing the left PSM was immediately fixed to be analyzed by in situ hybridization using a Lfng probe to order the samples along the segmentation clock oscillation cycle. Probes were produced from RNA extracted from the 17 dissected posterior half PSMs using a two-step amplification protocol and were hybridized to Affymetrix GeneChip MOE430A. The reproducibility of the amplification procedure was initially assessed by comparing array data generated from the right and the left posterior PSM from the same embryo. Because of the symmetry of the paraxial mesoderm along the left-right axis, left and right samples are expected to show overtly similar gene expression. RNA was amplified from three such sample pairs (1, a and b; 2, a and b; 3, a and b) and hybridized on Murine Genome U74Av2 array (MG-U74Av2)
2006-11-06 | E-TABM-163 | biostudies-arrayexpress
Project description:During mammalian gastrulation, pluripotent epiblast stem cells migrate through the primitive streak to form the multipotent progenitors of the mesoderm and endoderm germ layers. Msgn1 is a bHLH transcription factor and is a direct target gene of the Wnt/bcatenin signaling pathway. Msgn1 is expressed in the mesodermal compartment of the primitive streak and is necessary for the proper development of the mesoderm. Msgn1 mutants show defects in somitogenesis leading to a lack of trunk skeletal muscles, vertebra and ribs. To study the molecular and cellular function of Msgn1 in Embryonic Stem Cells (ESC), we have generated doxycycline inducible gain-of-function ESC to overexpress Msgn1 in ESC. In order to identify Msgn1 targets, we performed transcriptional profiling of Msgn1 expressing ES cells and found that upon induction of Msgn1, multiple genes in the Notch pathway were differentially expressed compared to the uninduced cells. Moreover, Whole Mount Insitu Hybridization analysis in Msgn1 null mutants revealed that these Notch pathway genes required Msgn1 for their proper expression in vivo. Our studies demonstrate that Msgn1 is a critical effector of the Wnt pathway during mammalian somitogenesis, mediating crosstalk between the Wnt and Notch pathways. Inducible A2lox-Flag Msgn1 ES cells were differentiated to form Embryoid bodies (EBs) for 2 days. Flag-Msgn1 was induced on day 2 with doxycycline and samples were collected at three time points, 12h, 24h and 48h after addition of doxycycline. Uninduced cells were used as controls. Experiments were performed in triplicate
2011-07-01 | E-GEOD-29848 | biostudies-arrayexpress
Project description:This analysis aims at finding the microRNAs present in three chick embryo undifferentiated tissues (pools of tissues): Undetermined Presomitic Mesoderm (PSM-U), Determined Presomitic Mesoderm (PSM-D) and Distal limb bud (Limb).
2021-10-25 | E-MTAB-8176 | biostudies-arrayexpress
Project description:Dynamic gene expression in the PSM of vertebrates is critical for the spatial and temporal patterning of somites. Using microarray analysis, we explored in detail, genes that are differentially regulated upon removal of CREB family function from the mouse PSM. Mouse PSM from R26R^AC/AC (Control) and R26R^AC/AC;T-Cre (Mutant) were harvested for RNA extraction. Nine PSM's from control and mutant genotypes were combined to generate three biological replicates (three PSM's/replicate). Samples were then applied to microarray analysis to identify differentially expressed genes between controls and mutants.
2013-04-27 | E-GEOD-46426 | biostudies-arrayexpress
Project description:Within a given vertebrate species, the total number of vertebrae in each anatomical domain is precisely defined and shows little variation among individuals. In contrast, this number can vary tremendously between different species, ranging from as few as six vertebrae in frogs to as many as several hundred in some snakes and fish. Segmental precursors of the vertebrae, called somites are produced sequentially in the embryo from the presomitic mesoderm (PSM), until a final number characteristic of the species, is reached. Here, we show in the chicken embryo that, by controlling the rate of axis elongation, Hox genes control the total number of somites generated by the embryo. We observed that activation of the most posterior Hox genes in somite precursors of the tail bud correlates with an abrupt slowing-down of the speed of axis elongation. We show that progressively more posterior Hox genes, which are collinearly activated in somitic precursors of the epiblast, repress Wnt activity with increasing strength. This leads to a graded repression of the Brachyury/T transcription factor, reducing mesoderm ingression and slowing down the elongation process. Due to the continuation of somite formation, the PSM, which is not fed with sufficient supply of new cells posteriorly, becomes progressively exhausted, ultimately leading to an arrest of segment formation. Our data provide a conceptual framework to explain how the cross-talk between the segmentation clock and the Hox clock accounts for the diversity of vertebral formulae across animal species. Primitive streak aera corresponding to PSM precursors were dissected in Stage 9 somites chicken embryo overexpressing HoxA13 or a control H2B-Venus. The experiment was designed to have biological duplicate in each conditions. The gain-of-function was obtained by electroporating the embryo at Stage 5HH with a vector containing HoxA13 under the CAGGS promoter with an H2B venus reporter. In order to have enough material for the microarray, 7 embryos were pooled in each sample before the hybridization.
2012-05-22 | E-GEOD-38107 | biostudies-arrayexpress
Project description:In vertebrates, body axis elongation is fuelled by bipotent neuromesodermal progenitors (NMPs), which support the development of both spinal cord and paraxial mesoderm (PM). HOX transcription factors have been historically implicated in axial elongation, with their sequential activation playing a fundamental role in timing PM development. PBX1 and PBX2 are obligate anterior HOX cofactors, and therefore they represent prominent candidates for controlling the distinct response to individual HOX factors. In our work, we have demonstrated that PBX proteins play a fundamental role in promoting the expression of PM genes, including the master regulator Mesogenin1 (Msgn1). To address the role of PBX proteins in PM differentiation, RNA-seq was performed on wild-type (WT) and Pbx1/Pbx2 double-knockout (Pbx1/2-DKO) EpiSCs differentiated in vitro to pre-somitic mesoderm (PSM) at different time-points (12 hours and 24 hours). To establish the direct transcriptional regulation of Msgn1 by PBX/HOX, we employed the CRISPR/Cas9 technology to generate lines carrying base-pair substitutions on the Msgn1 promoter (pMsgn1-mut) that abrogate the recruitment of PBX/HOX complexes, and we performed RNA-seq of pMsgn1-mut EpiSCs differentiated in vitro to PSM at 24 hours. All differentiation experiments were performed in biological triplicates with WT and Pbx1/2-DKO lines, and in biological duplicates with pMsgn1-mut lines.
2021-07-21 | E-MTAB-9773 | biostudies-arrayexpress
Project description:In vertebrates, body axis elongation is fuelled by bipotent neuromesodermal progenitors (NMPs), which support the development of both spinal cord and paraxial mesoderm (PM). WNT signalling sustains both NMP expansion and PM differentiation, but the mechanism by which it distinguishes between these alternative fates is unknown. HOX transcription factors have been historically implicated in axial elongation, with their sequential activation playing a fundamental role in timing PM development. PBX1 and PBX2 are obligate anterior HOX cofactors, and therefore they represent prominent candidates for controlling the distinct response to individual HOX factors. In our work, we have demonstrated that PBX/HOX complexes establish a permissive chromatin landscape for de novo recruitment of the WNT-effector LEF1 on PM genes, including the master regulator Mesogenin1 (Msgn1). To assess the PBX-dependent changes in chromatin accessibility during PM differentiation, we performed ATAC-seq of wild-type (WT) and Pbx1/Pbx2 double-knockout (Pbx1/2-DKO) EpiSCs differentiated in vitro to pre-somitic mesoderm (PSM) at different time-points (EpiSCs, 6 hours, 12 hours, 24 hours, 36 hours, 48 hours). To assess the direct consequence of PBX/HOX binding on chromatin accessibility, we employed the CRISPR/Cas9 technology to generate lines carrying base-pair substitutions on the Msgn1 promoter (pMsgn1-mut) that abrogate the recruitment of PBX/HOX complexes, and we performed ATAC-seq of pMsgn1-mut EpiSCs differentiated in vitro to PSM at different time-points (12 hours, 24 hours, 36 hours, 48 hours).
2021-07-21 | E-MTAB-9776 | biostudies-arrayexpress