A shared temporal chromatin program for ventral spinal cord progenitors [CaTS-ATAC]
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1103700 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR28779800_1.fastq.gz | Fastqsanger.gz | |||
| SRR28779800_2.fastq.gz | Fastqsanger.gz | |||
| SRR28779801_1.fastq.gz | Fastqsanger.gz | |||
| SRR28779801_2.fastq.gz | Fastqsanger.gz | |||
| SRR28779802_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 332 |
Similar Datasets
Project description:A shared temporal program for ventral spinal cord progenitors [CaTS-RNA]
| PRJNA1101107 | ENA
Project description:The vertebrate neural tube generates a large diversity of molecularly and functionally distinct neurons and glia from a small progenitor pool. While the role of spatial patterning in organising cell fate specification has been extensively studied, temporal patterning, which controls the timing of cell type generation, is equally important. Here we define a global temporal programme in the spinal cord. This governs cell fate choices by regulating chromatin accessibility in neural progenitors. Perturbation of this cis-regulatory programme affects sequential transitions in spinal cord progenitors and the identity of progeny. The temporal programme operates in parallel to spatial patterning, ensuring the timely availability of regulatory elements for spatial determinants to direct cell-type specific gene expression. These findings identify a chronotopic spatiotemporal integration strategy in which a global temporal chromatin programme determines the output of a spatial gene regulatory network resulting in the temporally and spatially ordered allocation of cell type identity.
2024-04-22 | GSE264170 | GEO
Project description:The vertebrate neural tube generates a large diversity of molecularly and functionally distinct neurons and glia from a small progenitor pool. While the role of spatial patterning in organising cell fate specification has been extensively studied, temporal patterning, which controls the timing of cell type generation, is equally important. Here we define a global temporal programme in the spinal cord. This governs cell fate choices by regulating chromatin accessibility in neural progenitors. Perturbation of this cis-regulatory programme affects sequential transitions in spinal cord progenitors and the identity of progeny. The temporal programme operates in parallel to spatial patterning, ensuring the timely availability of regulatory elements for spatial determinants to direct cell-type specific gene expression. These findings identify a chronotopic spatiotemporal integration strategy in which a global temporal chromatin programme determines the output of a spatial gene regulatory network resulting in the temporally and spatially ordered allocation of cell type identity.
2024-04-23 | GSE264637 | GEO
Project description:Gene expression profiling in rat lumbar spinal cord following ventral root avulsion in the two inbred rat strains.
2006-08-15 | E-MEXP-671 | biostudies-arrayexpress
Project description:We generated single RNA-seq data to measure transcriptional profiles of six hESC-derived ventral populations, representing distinct regions of the developing human spinal cord. These cells are differentiated using a protocol that induces collinear activation of region-specific HOX genes during exposure to FGF8 and Wnt signaling (Lippmann et al, 2015 PMID:25843047). By transitioning to media containing retinoic acid, smoothened agonist (SAG), Purmorphamine (Pur), and DAPT after varying durations of Wnt signaling, ventral neuronal cultures are generated with unique rostrocaudal identities. In total we recovered the transcriptomes of 12,540 cells. Analysis verified expression of increasingly caudal HOX paralogs that could be correlated to cervical (HOX1-8; H24-vN, H48-vN, and H72-vN), thoracic (HOX1-9; H120-vN), lumbar (HOX1-11; H168-vN), and lumbosacral (HOX1-13; H216-vN) spinal regions. However, inconsistent differentiation between samples resulted in a mix of neural progenitor, neuron, mesodermal, and neural crest derivatives.
2022-07-28 | GSE186696 | GEO
Project description:Circulating sex steroids are critical for the development of neuroplasticity in the respiratory motor system. A primary locus of inducible respiratory neuroplasticity is the phrenic motor nucleus, a column of motor neurons in the ventral cervical spinal cord (C3-C5). In specific, exposure to acute intermittent hypoxia (AIH) induces strengthened synaptic connections to phrenic motor neurons and increased motor output; a form of neuroplasticity called phrenic long-term facilitation (pLTF). Gonadectomy (surgical removal of the testes in males and ovaries in females) reduces circulating sex steroids and eliminates AIH-induced phrenic pLTF in both females and males, implicating sex steroids as critical mediators for the development of neuroplasticity. To begin interrogating mechanisms of sex steroid influence on phrenic motor neurons and to determine the effect of gonadectomy on local gene expression, we performed RNA sequencing on ventral cervical spinal cord samples containing the phrenic motor nucleus. Our findings identified sex-specific gene expression in gonadally-intact rats and suggested that gonadectomy caused greater changes to the transcriptomes of male rats compared to females.
2022-05-13 | GSE202381 | GEO
Project description:The current experiment is a continuation of a previous study (E-MTAB-303) where spinal cords from a F2 (DAxPVG) intercross exposed to ventral root avulsion was studied. The F2 experiment revealed specific genetic regions of interest. Now, congenic lines, i.e. DA rats containing small inserts of PVG DNA fragments, have been developed, clinically evaluated and selected to study further with transcriptional profiling in order to understand the genetic pathways underlying the observed differential clinical phenotypes, determined by the small DNA inserts.
2013-05-31 | E-MTAB-920 | biostudies-arrayexpress
Project description:MicroRNAs negatively regulate gene expression and may serve as biomarkers for human cardiomyopathy. In the domestic cat, hypertrophic cardiomyopathy (HCM) represents the most common primary cardiomyopathy. In humans, the etiology of HCM is linked to mutations in genes of contractile muscle proteins, while in cats a clear proof for causal mutations is missing. The etiology of feline HCM is uncertain. Diagnosis is made by heart ultrasound examination and measuring the serum level of N-terminal pro B-type natriuretic peptide. The purpose of this study was to investigate whether microRNA profiles in the serum of cats with HCM are different from the profiles of healthy cats and whether specific miRNAs can be detected to serve as potential biomarkers for feline HCM or may help in understanding the etiology of this disease Blood was drawn from two groups of cats: 12 healthy cats and 11 cats suffering from hypertrophic cardiomyopathy. After clotting, samples were centrifuged and total mRNA was extracted from serum. These 23 serum samples were analyzed and the groups were compared
2015-07-22 | E-GEOD-49427 | biostudies-arrayexpress
Project description:BACKGROUND: MicroRNAs negatively regulate gene expression and play a pivotal role in the pathogenesis of human type 2 diabetes mellitus (T2DM). As the domestic cat presents a spontaneous animal model for human T2DM, the purpose of this study was to investigate whether microRNAs are detectable in feline serum and whether microRNA expression profiles differ between healthy and diabetic cats. METHODS: Total RNA was extracted from 400 M-BM-5l serum of healthy lean (HL) and newly diagnosed diabetic (D) cats. MicroRNA microarrays representing 1079 distinct mouse miRNA targets were used to measure miRNA expression in samples from eight HL and eight D cats. RESULTS: By microarray, 227 distinct microRNAs were identified. Nineteen miRNAs were differentially expressed in diabetic cats, but only two reached statistical significance after correction for multiple comparisons. In qRT-PCR, miR-122* was found to be upregulated in diabetic cats more than 40-fold compared to HL cats, while miR-193b was upregulated about 10-fold. MiR-483* showed a 6- fold increase in diabetic cats compared to HL cats. CONCLUSIONS: Small volumes of serum samples yield sufficient material to detect altered microRNA expression profiles in diabetic cats. The domestic cat may be considered a useful animal model for studying miRNAs involved in human T2DM. Blood was drawn from two groups of cats: 8 healthy cats and 8 cats suffering from diabetes. After clotting, samples were centrifuged and total mRNA was extracted from serum. These 16 serum samples were analyzed and the groups were compared. Due to technical problems during hybridization (leaking chamber), sample 1_4_B (Serum_diabetic_8) was not included into analysis.
2013-04-11 | E-GEOD-37177 | biostudies-arrayexpress
Project description:Stem cells have received substantial interest both for their potential as in vitro tools to study development and as potential therapeutic agents in a range of degenerative diseases of the nervous system. We have generated clonal neural stem cell lines from human foetal spinal cord conditionally immortalised with 4-hydroxy tamoxifen inducible cMyc (cMycERTAM), and performed a detailed assessment of their identity in terms of their expression of homeodomain transcription factors and their capacity to generate particular neuronal subtypes of the spinal cord. These lines retain a ventral spinal cord progenitor phenotype and give rise to electrically active neuronal subtypes characteristic of specific ventral progenitor subdomains. Upon grafting into lesioned rat spinal cord these cells differentiate into ChAT+ve motorneurons and show robust survival after 4 months. Total RNA was obtained from three proliferative undifferentiated neural stem cell lines at 75% confluence in culture. Two replicates of each clonal line were generated for microarray analysis.
2012-06-15 | E-GEOD-37282 | biostudies-arrayexpress