Similar Datasets
Project description:Chromosome conformation capture (4C-Seq) in Drosophila embryos from a wild-type line and from transgenic fly lines carrying the E3 enhancer of twist at ectopic locations. Two time points (2-5 hrs and 5-8 hrs after egg lay) and two viewpoints located near the twist promoter were assayed. Two independent collections were performed at each timepoint and each viewpoint.
2023-12-08 | E-MTAB-12153 | biostudies-arrayexpress
Project description:To test if there is a physical interaction between the IRF8 promoter and the rs2280381-containing region, we conducted circular chromatin conformation capture assay in the U937 cell. For the IRF8 viewpoint group, we used CSP6I as the first digested enzyme and NlaIII as the second enzyme. For the rs2280381-containing region, we used MboI as the first digested enzyme and NlaIII as the second enzyme. We use 4C-PCR primer to construct IRF8 point view and rs2280381-containing region 4C library.
2021-07-01 | E-MTAB-10120 | biostudies-arrayexpress
Project description:Here, we present Methyltransferase Targeting-based chromosome Architecture Capture (MTAC), a method that maps the contacts between a target site (viewpoint) and the rest of the genome with high resolution and sensitivity. By targeting M.CviPI DNA methyltransferase to the viewpoint and by detecting differentially methylated regions, MTAC detects hundreds of intra- and inter-chromosomal interactions in the budding yeast genome that cannot be captured by 4C, Hi-C, or Micro-C.
2023-09-05 | GSE242394 | GEO
Project description:Chromosome Conformation Capture (4C seq) at the rs9929218 locus in colorectal cancinogensis
2020-10-01 | GSE121623 | GEO
Project description:High-throughput sequencing of Drosophila melanogaster small RNAs. total RNA, ~18-26nt RNAs isolated using PAGE, ligation to adapters requires 5' monophosphate and 3' OH Keywords: High-throughput solexa sequencing
2008-05-01 | GSE10794 | GEO
Project description:Live imaging has revolutionized the analysis of developmental biology over the last few years. The ability to track in real time the dynamic processes that occur at tissue and cellular levels gives a much clearer view of development, and allows greater temporal resolution, than is possible with fixed tissue. Drosophila imaginal discs are a particularly important model of many aspects of development, but their small size and location inside the larva and pupa has prevented live imaging techniques from extensively being used in their study. Here, we introduce the use of viscous culture medium to enable high resolution imaging of imaginal disc development. As a proof of principle, we have analyzed the transformation that occurs during metamorphosis of the wing imaginal disc into the mature wing and report several previously unobserved stages of this model of organogenesis. These imaging methods are especially useful to study the complex and dynamic changes that occur during morphogenesis, but we show that they can also be used to analyze other developmental and cellular events. Moreover, our viscous medium creates a platform for future adaptation of other tissue culture conditions to allow imaging of a wide range of developmental events and systems.
| S-EPMC2922528 | biostudies-literature
Project description:High-throughput sequencing of Drosophila melanogaster small RNAs. total RNA, ~18-26nt RNAs isolated using PAGE, ligation to adapters requires 5' monophosphate and 3' OH Keywords: High-throughput solexa sequencing Small RNAs were sequenced from D. melanogaster S2 and KC cells. Raw sequences were clipped by 3' linker sequences recognition, and select clipped sequences longer than 18 nt
2008-04-30 | E-GEOD-10794 | biostudies-arrayexpress
Project description:In Drosophila melanogaster, Hox genes are organized in an anterior and a posterior cluster, called Antennapedia complex and bithorax complex, located on the same chromosome arm and separated by 10 Mb of DNA. Both clusters are repressed by Polycomb group (PcG) proteins. Here, we show that genes of the two Hox complexes can interact within PcG bodies in the cell nucleus in tissues where they are corepressed. This colocalization increases during development and depends on PcG proteins. Hox gene contacts are part of a large gene interaction network that includes other PcG target genes. Moreover, they are conserved in the distantly related Drosophila virilis species, and mutations on one of the loci weaken silencing of genes in the other locus, resulting in the exacerbation of homeotic phenotypes in a sensitized genetic background. Thus, the three-dimensional organization of Polycomb target genes in the cell nucleus is an evolutionarily conserved phenomenon that stabilizes the maintenance of epigenetic gene silencing. Chromosome Conformation Capture on Chip (4C) was used to establish chromosomal interactions involving the Fab7 polycomb response element from the bithorax complex of Drosophila melanogaster. Larval brain and anterior discs from 3rd instar larvae were dissected to produce 2 replicate experiments with wild-type (WT-r1, WT-r2) and Fab-712 (F12-r1, F12-r2) fly lines. The 3C was performed as previously described (Hagege et al., 2007; Miele and Dekker, 2009) with the main differences being the use of DpnII (New England Biolabs), a 4 bp cutter restriction enzyme, and a fixation in 3% para-formaldehyde for 30 min, maximizing sensitivity and resolution of contact detection. The 4C DNA and DpnII digested genomic DNA (Control) samples were hybridized using a tiling array mapping the whole chromosome 3R which includes the antenapedia and bithorax hox clusters.
2010-12-31 | E-GEOD-23887 | biostudies-arrayexpress
Project description:Organ growth and size are finely tuned by intrinsic and extrinsic signaling molecules. In Drosophila, the BMP family member Dpp is produced in a limited set of imaginal disc cells and functions as a classic morphogen to regulate pattern and growth by diffusing throughout imaginal discs. However, the role of TGF?/Activin-like ligands in disc growth control remains ill-defined. Here, we demonstrate that Myoglianin (Myo), an Activin family member, and a close homolog of mammalian Myostatin (Mstn), is a muscle-derived extrinsic factor that uses canonical dSmad2-mediated signaling to regulate wing size. We propose that Myo is a myokine that helps mediate an allometric relationship between muscles and their associated appendages.
| S-EPMC7371420 | biostudies-literature
Project description:High-resolution chromosome conformation capture-sequencing of RE6-9 heterozygous mutants. We investigated the three-dimensional organization of the Scn5a-Scn10a locus in whole hearts of RE6-9 heterozyous mutants and wildtype littermates. Viewpoint were set on enhancer 1 (enh1, located in the intronic region of Scn10a) and the Scn5a promoter (P1_2). The liver of FVB mice was used as controle tissue to determine the specificity of the Scn5a-Scn10a interaction domain in the heart.
2019-10-04 | GSE129062 | GEO