Homo sapiens
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA347518 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR4407924.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 1 of 1 |
Similar Datasets
Project description:VRTN Regulates the Number of Thoracic Vertebrae During Vertebrate Development
| PRJNA347516 | ENA
Project description:VRTN Regulates the Number of Thoracic Vertebrae During Vertebrate Development [RNA-seq]
| PRJNA347519 | ENA
Project description:The number of vertebrae is precisely defined in almost all vertebrate species, but varies considerably in pigs, making this animal an excellent model for studying the mechanisms that control vertebral number. Vertnin (VRTN) variants have been associated with thoracic vertebral number (TVN) in pigs. However, the causal relation between VRTN and TVN remains to be established, and the role of VRTN in modulating TVN is not yet known. Here, we demonstrate that VRTN is one of the genes responsible for determining TVN. We show that VRTN is a DNA-binding transcription factor, which is essential for the formation of thoracic vertebrae during early embryogenesis as VRTN-null mice showed embryonic lethality at the later thoracic somite stages and had fewer somites than their wild-type and heterozygous littermates. We also show that VRTN causative variants increase Notch signaling in pig embryos, suggesting that VRTN controls segment number by altering the pace of somatic segmentation. These findings advance our understanding of the role of VRTN in the formation of thoracic vertebrae and reveal new aspects of somite developmental biology.
2019-10-09 | GSE87774 | GEO
Project description:The number of vertebrae is precisely defined in almost all vertebrate species, but varies considerably in pigs, making this animal an excellent model for studying the mechanisms that control vertebral number. Vertnin (VRTN) variants have been associated with thoracic vertebral number (TVN) in pigs. However, the causal relation between VRTN and TVN remains to be established, and the role of VRTN in modulating TVN is not yet known. Here, we demonstrate that VRTN is one of the genes responsible for determining TVN. We show that VRTN is a DNA-binding transcription factor, which is essential for the formation of thoracic vertebrae during early embryogenesis as VRTN-null mice showed embryonic lethality at the later thoracic somite stages and had fewer somites than their wild-type and heterozygous littermates. We also show that VRTN causative variants increase Notch signaling in pig embryos, suggesting that VRTN controls segment number by altering the pace of somatic segmentation. These findings advance our understanding of the role of VRTN in the formation of thoracic vertebrae and reveal new aspects of somite developmental biology.
2019-10-09 | GSE87775 | GEO
Project description:We used single cell RNA sequencing (scRNA-seq) to decipher cell heterogeneity of human T-cell Acute Lymphoblastic Leukemia (M18) recovered from Bone Marrow Adipose Tissue (BMAT)-poor (Femur and Thoracic Vertebrae) and -rich (Tail Vertebrae) sites of xenografted immunodeficient mice (NSG,nonobese diabetic/severe combined immunodeficiency / interleukin-2Rγ null). We wanted to know whether some human T-ALL cells recovered in BMAT-poor sites resemble to those from BMAT-rich site.
2024-05-01 | GSE233600 | GEO
Project description:The vegetal pole cytoplasm represents a crucial source of maternal dorsal determinants for patterning the dorsoventral axis of the early embryo. Removal of the vegetal yolk in the zebrafish fertilised egg before the completion of the first cleavage results in embryonic ventralisation, but removal of this part at the two-cell stage leads to embryonic dorsalisation. How this is achieved remains unknown. Here, we report a novel mode of maternal regulation of BMP signaling during dorsoventral patterning in zebrafish. We identify Vrtn as a novel vegetally localised maternal factor with dorsalising activity and rapid transport towards the animal pole region after fertilisation. Co-injection of vrtn mRNA with vegetal RNAs from different cleavage stages suggests the presence of putative vegetally localised Vrtn antagonists with slower animal pole transport. Thus, vegetal ablation at the two-cell stage could remove most of the Vrtn antagonists, and allows Vrtn to produce the dorsalising effect. Mechanistically, Vrtn binds a bmp2b regulatory sequence and acts as a repressor to inhibit its zygotic transcription. Analysis of maternal-zygotic vrtn mutants further shows that Vrtn is required to constrain excessive bmp2b expression in the margin. Our work unveils a novel maternal mechanism regulating zygotic BMP gradient in dorsoventral patterning.
2017-08-26 | GSE103090 | GEO
Project description:Determining the genomic localization of chromatin features is an essential aspect of investigating gene expression control, and ChIP-Seq has long been the gold standard technique for interrogating chromatin landscapes. Recently, the development of alternative methods, such as CUT&Tag, have provided researchers with alternative strategies that eliminate the need for chromatin purification, and allow for in situ investigation of histone modifications and chromatin bound factors. Mindful of technical differences, we set out to investigate whether distinct chromatin modifications were equally compatible with these different chromatin interrogation techniques. We found that ChIP-Seq and CUT&Tag performed similarly for modifications known to reside at gene regulatory regions, such as promoters and enhancers, but major differences were observed when we assessed enrichment over heterochromatin-associated loci. Unlike ChIP-Seq, CUT&Tag detects robust levels of H3K9me3 at a substantial number of repetitive elements, with especially high sensitivity over evolutionarily young retrotransposons. IAPEz-int elements for example, exhibited underrepresentation in mouse ChIP-Seq datasets but strong enrichment using CUT&Tag. Additionally, we identified several euchromatin-associated proteins that co-purify with repetitive loci and are similarly depleted when applying ChIP-based methods. This study reveals that our current knowledge of chromatin states across the heterochromatin portions of the mammalian genome is extensively incomplete, largely due to36 limitations of ChIP-Seq. We also demonstrate that newer in situ chromatin fragmentation-based techniques, such as CUT&Tag and CUT&RUN, are more suitable for studying chromatin modifications over repetitive elements and retrotransposons.
2025-08-26 | PXD067760 | Pride
Project description:The PR domain containing 1a, with ZNF domain factor, gene prdm1a plays an integral role in the development of a number of different cell types during vertebrate embryogenesis, including neural crest cells, Rohon-Beard (RB) sensory neurons and the cranial neural crest-derived craniofacial skeletal elements. To better understand how Prdm1a regulates the development of various cell types in zebrafish, we performed a microarray analysis comparing wild type and prdm1a mutant embryos and identified a number of genes with altered expression in the absence of prdm1a. Rescue analysis determined that two of these, sox10 and islet1, lie downstream of Prdm1a in the development of neural crest cells and Rohon-Beard neurons, respectively. In addition, we identified a number of other novel downstream targets of Prdm1a that may be important for the development of diverse tissues during zebrafish embryogenesis. RNA was isolated from whole zebrafish embryos at 25hpf, three replicates each for wildtype and prdm1a mutant embryos.
2011-03-29 | E-GEOD-28199 | biostudies-arrayexpress
Project description:Stepwise Neofunctionalization of c-Rel during Vertebrate Evolution (ChIP-Seq)
| PRJNA1015721 | ENA
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