Similar Datasets
Project description:Capture-C from in situ HiC libraries in tailbud tissue containing pre-somitic mesoderm (PSM) dissected from Smchd1GFP/GFP, Smchd1MD43-GFP/MD43-GFP, Smchd1+/+ and Smchd1MD43/MD43 embryos E8.5 embryos at the 7-9 somite stage of development. Somite stage is a good indicator of the precise stage of embryonic development.
2023-04-04 | GSE228673 | GEO
Project description:RNAseq from 8 somite stage PSM
| PRJNA728097 | ENA
Project description:RNAseq from somite-matched tailbud tissue from E8-8.5 embryo tailbuds at the 6-11 somite developmental stages
2022-06-27 | GSE183733 | GEO
Project description:RNAseq from somite-matched frontonasal prominence (FNP) from E10.5 embryos at the 29-somite developmental stage
2021-05-08 | GSE174090 | GEO
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.
2012-05-23 | GSE38107 | GEO
Project description:To describe chromatin accessibility changes associated with differentiation of mouse presomitic mesoderm (PSM) cells into somites, ATAC sequencing (paired-end) was performed using non-cultured, wild-type PSM tissues that were microdissected into tailbud, posterior PSM, anterior PSM, and somite regions. Omni-ATAC protocol was used, and each condition includes six biological replicates.�
2025-08-06 | E-MTAB-13692 | biostudies-arrayexpress
Project description:To describe gene expression changes associated with differentiation of mouse presomitic mesoderm (PSM) cells into somites, RNA sequencing (paired-end) was performed using non-cultured, wild-type PSM tissues that were microdissected into tailbud, posterior PSM, anterior PSM, and somite regions. Smart-seq2 protocol was used, and each condition includes six biological replicates.
2025-08-06 | E-MTAB-13693 | 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:RNAseq from 29 somite stage FNP
| PRJNA728127 | ENA
Project description:Human stem cell-based embryo-like models have opened new avenues of research into the principles of embryonic development using experimentally amenable in vitro systems. One of the benefits of embryo-like models over organoids is their multilineage differentiation, which allows the co-development of different populations and interaction between tissues. Here, we develop a method of generating somite- and neural tube-containing models, called human Trunk-like Structures (hTLS). These hTLS contain SOX2+ TBXT+ neuromesodermal progenitors, presomitic mesoderm, and somitic epithelial tissues, alongside a neural tube structure. As well as the expression of Wnt/FGF ligands posteriorly and Retinoic Acid (RA) pathway components anteriorly, we observe oscillatory HES7 expression, and show that increasing exposure to a Sonic Hedgehog signalling agonist (SAG) increasingly ventralises tissue identity. Additionally, we show that RA and noncanonical Wnt interactions likely occur between the somites and neural tube. In particular, we observe medially-localised ALDH1A2 expression in the somites - at the interface with the neural tube – which we validated in mouse embryos, whereas in somite-only structures, ALDH1A2 is anteroposteriorly polarised. This suggests that interactions between the neural tube and the somites might be responsible for mediolateral somitic organisation, both in vitro and in vivo, and highlights the value of embryo models to reveal insights into mammalian tissue co-development.
2025-10-01 | GSE268451 | GEO