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ChIP-seq of Drosophila embryos to investigate chromatin state during dorsal-ventral patterning

ABSTRACT: ChIP-seq of Drosophila embryos to investigate chromatin state during dorsal-ventral patterning

PROVIDER: PRJEB39232 | ENA |

REPOSITORIES: ENA

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ChIP-seq of Drosophila embryos to investigate chromatin state during dorsal-ventral patterning

Project description:We carried out ChIP-seq for H3K27ac and H3K27me3 in embryos from Tollrm9/rm10 mutant mothers. The embryos from mutant mothers produce only a single tissue type (neuroectoderm) along the dorsal-ventral axis. We used these embryos to compare chromatin state across tissues.

2021-01-08 | E-MTAB-9303 | biostudies-arrayexpress

Hi-C of Drosophila embryos to investigate chromatin conformation during dorsal-ventral patterning

Project description:Hi-C of Drosophila embryos to investigate chromatin conformation during dorsal-ventral patterning

| PRJEB39238 | ENA

Micro-C of Drosophila embryos to investigate chromatin conformation during dorsal-ventral patterning

Project description:Micro-C of Drosophila embryos to investigate chromatin conformation during dorsal-ventral patterning

| PRJEB41445 | ENA

Micro-C of Drosophila embryos to investigate chromatin conformation during dorsal-ventral patterning

Project description:Micro-C was carried out for control embryos and embryos produced from gd7 mutant mothers. The embryos from mutant mothers produce only a single type along the dorsal-ventral axis (dorsal ectoderm). We used these embryos to compare chromatin conformation across tissues.

2021-01-08 | E-MTAB-9784 | biostudies-arrayexpress

Single-cell RNA-seq of Drosophila embryos to investigate gene expression during dorsal-ventral patterning

Project description:Single-cell RNA-seq of Drosophila embryos to investigate gene expression during dorsal-ventral patterning

| PRJEB39233 | ENA

Hi-C of Drosophila embryos to investigate chromatin conformation during dorsal-ventral patterning

Project description:Hi-C was carried out for control embryos and embryos produced from gd7, Tollrm9/rm10, and Toll10B mutant mothers. The embryos from mutant mothers produce only a single type along the dorsal-ventral axis. We used these embryos to compare chromatin conformation across tissues.

2021-01-08 | E-MTAB-9306 | biostudies-arrayexpress

A Non-Canonical Raf Function Is Required for Dorsal-Ventral Patterning in Drosophila Embryogenesis

Project description:Embryonic development requires the establishment of directional axes. In Drosophila, spatially discrete expression of transcription factors determines the anterior to posterior organization of the early embryo, while the Toll and TGF-beta signalling pathways determine the early dorsal to ventral pattern. Embryonic MAPK/ERK signaling contributes to both anterior to posterior patterning in the terminal regions and to dorsal to ventral patterning during oogenesis and embryonic stages. Here we describe a novel loss of function mutation in the Raf kinase gene, which leads to loss of ventral cell fates as seen through the loss of the ventral furrow, the absence of Dorsal/NF-kB nuclear localization, the absence of mesoderm determinants Twist and Snail, and the expansion of TGF-beta. Gene expression analysis showed cells adopting ectodermal fates similar to loss of Toll signaling. Our results combine novel mutants, live imaging, optogenetics and transcriptomics to establish a novel role for Raf, that appears to be independent of the MAPK cascade, in embryonic patterning.

2021-08-03 | GSE178187 | GEO

Single-cell RNA-seq of Drosophila embryos to investigate gene expression during dorsal-ventral patterning

Project description:Single-cell RNA-seq was carried out for control embryos and embryos produced from gd7, Tollrm9/rm10, and Toll10B mutant mothers. The embryos from mutant mothers produce only a single type along the dorsal-ventral axis. We used these embryos to compare single-cell gene expression patterns across tissues.

2021-01-08 | E-MTAB-9304 | biostudies-arrayexpress

Comprehensive identification of Drosophila dorsal-ventral patterning genes using a whole-genome tiling array

Project description:Dorsal-ventral (DV) patterning of the Drosophila embryo is initiated by Dorsal, a sequence specific transcription factor distributed in a broad nuclear gradient in the precellular embryo.Previous studies have identified as many as 70 protein-coding genes and one microRNA gene that are directly or indirectly regulated by this gradient. A gene regulation network, or circuit diagram, including the functional interconnections among 40 Dorsal target genes and 20 associated tissue-specific enhancers, has been determined for the initial stages of gastrulation. Here, we attempt to extend this analysis by identifying additional DV patterning genes using a recently developed whole-genome tiling array. This analysis led to the identification of another 30 protein-coding genes, including the Drosophila homolog of Idax, an inhibitor of Wnt signaling. In addition, remote 5' exons were identified for at least 10 of the ~100 protein-coding genes that were missed in earlier annotations. As many as 9 intergenic, uncharacterized transcription units were identified, including two that contain known microRNAs, miR-1 and miR-9a. We discuss the potential functions of these newly identified genes, and suggest that intronic enhancers are a common feature of the DV gene network. Keywords: gene expression, dorsal-ventral pattern genes, tiling array

2006-08-04 | GSE5434 | GEO

Distinct transcriptomic, proteomic and epigenetic stress-responses in dorsal and ventral hippocampus

Project description:The hippocampus - one of the most studied brain regions – is a key target of the stress response and vulnerable to the detrimental effects of stress. Although its intrinsic organization is highly conserved throughout its long dorsal-ventral axis, the dorsal hippocampus is linked to spatial navigation and memory formation, whereas the ventral hippocampus is linked to emotional regulation. Here, we provide the first combined transcriptomic and proteomic profiling that reveals striking differences between dorsal and ventral hippocampus. Using various acute stress challenges we demonstrate that both regions display very distinct molecular responses, and that the ventral hippocampus is particularly responsive to the effects of stress. We demonstrate that separately analyzing dorsal and ventral hippocampus greatly increases the ability to detect region-specific stress effects, and we identify an epigenetic network, which is specifically sensitive to acute stress in the ventral hippocampus.

2019-10-03 | PXD006781 | Pride

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