Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

16 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Drosophila melanogaster 4C-Seq experiments in wild-type and ectopic E3 enhancer-inserted embryos

ABSTRACT: 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.

INSTRUMENT(S): NextSeq 500

ORGANISM(S): Drosophila melanogaster

SUBMITTER: Yad Ghavi-Helm

PROVIDER: E-MTAB-12153 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Three-dimensional folding and functional organization principles of the Drosophila genome

Project description:Chromosomes are the physical realization of genetic information and thus form the basis for its reading, hindering and propagation. Here we present a high-resolution chromosomal contact map derived from a new genome-wide chromosome conformation capture approach (a simplified version of the Hi-C method) applied to Drosophila embryonic nuclei. The data show that the entire genome is linearly partitioned into well-demarcated physical domains that overlap extensively with active and repressive epigenetic marks. Chromosomal contacts are hierarchically organized between domains. Global modeling of compaction and clustering of domains show that inactive domains are condensed and confined to their chromosomal territories, while active domains reach out of the territory to form remote intra- and inter-chromosomal contacts. One pilot sample, comprising seven paired-end Illumina GA-II lanes; one deep-sequenced sample, comprising seven paired-end Illumina HiSeq lanes

2012-01-20 | E-GEOD-34453 | biostudies-arrayexpress

Transient Pairing of Homologous Oct4 Alleles Accompanies the Onset of Embryonic Stem Cell Differentiation

Project description:The relationship between chromatin organization and transcriptional regulation is an area of intense investigation. We have characterized the spatial relationships between alleles of the Oct4, Sox2, and Nanog genes in single cells during the earliest stages of mouse embryonic stem cell (ESC) differentiation and during embryonic development. We describe homologous pairing of the Oct4 alleles during ESC differentiation and embryogenesis, and present evidence that pairing is correlated with the kinetics of ESC differentiation. Importantly, we identify critical DNA elements within the Oct4 promoter/enhancer region that mediate pairing of Oct4 alleles. Finally, we show that mutation of OCT4/SOX2 binding sites within this region abolishes inter-chromosomal interactions and affects accumulation of the repressive H3K9me2 modification at the Oct4 enhancer. Our findings demonstrate that chromatin organization and transcriptional programs are intimately connected in ESCs, and that the dynamic positioning of the Oct4 alleles is associated with the transition from pluripotency to lineage specification. Examination of chromatin contacts between Oct4 alleles using PE-4Cseq

2015-02-03 | E-GEOD-65510 | biostudies-arrayexpress

Six in situ Hi-C libraries of control and mESC auxin-inducible degrons for Scc1 and Ring1b.

Project description:In this experiment, we've examined chromatin conformation differences of E14 mESC against cohesin and Ring1b degrons. We performed a modified in situ Hi-C protocol from (Rao et al., 2014) that can be found in detail at (Díaz et al., 2018). Samples were digested with MboI restriction enzyme. The aim of the experiment was to characterize the role of cohesin and polycomb on the 3D structure of mouse chromatin.

2020-01-23 | E-MTAB-7816 | biostudies-arrayexpress

Four Hi-C datasets from mESCs and 2C-like cells generated by knocking down the histone chaperone CAF-1 in mESCs

Project description:In this experiment, we've examined chromatin conformation of mESCs and 2C-like cells generated from a CAF-1 knockdown. The method to generate the knockdown was described in (). We performed a modified in situ Hi-C protocol from (Rao et al., 2014) and that can be found in detail at (Díaz et al., 2017, under revision). Samples were digested with MboI restriction enzyme having as starting material 100k cells with two biological replicates per sampling point. The aim of the experiment was to analyze the potential chromatin conformational changes that accompany the mESC to 2C-like transition.

2023-11-16 | E-MTAB-6330 | biostudies-arrayexpress

Control of VEGF-A trancriptional programs by pausing and genomic compartmentalization

Project description:Vascular endothelial growth factor A (VEGF-A) is a master regulator of vascular development and function. Consequently, VEGF-A regulated gene expression programs have been under heavy research. In this study we study the transcriptional regulation of VEGF-A-responsive genes in primary aortic endothelial cells (HAEC) and vein endothelial cells (HUVEC) using genome wide global run-on sequencing (GRO-Seq). We show that half of VEGF-A induced genes display a paused phenotype under basal conditions and are thus poised for rapid gene activation. Promoters of paused genes are distinguished from those of non-paused by higher basal enrichment for active histone marks H3K4me3, H3K9ac and H3K27ac. We also show that nearly 100% of the VEGF-upregulated genes are induced at the level of elongation, whereas 38-53% are also induced at the level of initiation. We also report a comprehensive chromatin interaction map generated in HUVECs using tethered conformation capture (TCC) and characterize chromatin interactions in relation to transcriptional activity. We demonstrate that sites of active transcription are more likely to engage in chromatin looping and identify chromatin compartments enriched for VEGF-regulated genes. Cell-type specific transcriptional activity was also shown to reflect boundaries of chromatin interactions within the HOXA cluster. Collectively, these findings provide new insight into mechanisms behind VEGF-A-regulated transcriptional programs in endothelial cells. ChIP-Seq (H3K4me2), GRO-Seq and HiC profiling was performed in HUVECs and HAECs.

2014-10-27 | E-GEOD-52642 | biostudies-arrayexpress

Chromatin contact maps of 24 and 48 hours post-fertilisation zebrafish (Danio rerio) embryos and 48 hours post-fertilisation fibroblasts

Project description:In this experiment, we've examined chromatin conformation of zebrafish embryos at 24 and 48 hours post-fertilization (hpf), as well as 48 hpf fibroblasts. The aim of this study was to characterise the 3D chromatin structure of zebrafish and perform an evolutionary comparison with mammalian genomes (Homo sapiens and Mus musculus) focusing on syntenic regions and zebrafish ohnologs (duplicated genes that were kept in the genome after the third round of whole-genome duplication).

2023-11-17 | E-MTAB-6313 | biostudies-arrayexpress

Low input Hi-C datasets for a diffuse large B-cell lymphoma sample, healthy control human B-cells and mouse embryonic stem cells

Project description:In this experiment, we've examined chromatin conformation of OG2 (B6; CBA-Tg(Pou5f1-EGFP)2Mnn/J; stock number 004654) mouse stem cells cultured as described in (Shi et al., 2008), using different amounts of starting cells. We performed a modified in situ Hi-C protocol for 6 samples digested with MboI restriction enzyme having as starting material 1 million (M), 100 thousand (k), 50k, 25k, 10k or 1k cells. As well as, to 2 samples digested with HindIII restriction enzyme that had as starting material 5M or 100k cells. Traditional in situ Hi-C protocols recommend 5-10 million starting cells. The aim of the experiment was to assess the impact of decreasing the cell number on reproducibility, library complexity, chromatin structure visualization in order to adapt the method to the study of rare cell populations. Furthermore, we have characterised the 3D structure of peripheral blood mononuclear cells (PBMCs) obtained from a blood extraction from a healthy donor and from a lymph node biopsy from a DLBCL patient as a proof of concept for the suitability of Low-C for rare cell population analysis.

2018-11-30 | E-MTAB-5875 | biostudies-arrayexpress

Genotyping-by-sequencing (GBS) of wild and cultivated Lens accessions and the domestication history of lentils

Project description:To use NGS data to investigate the history of lentil domestication.

2020-09-30 | E-MTAB-9222 | biostudies-arrayexpress

MNase and HpaII sensitivity assays in MCF7 breast cancer cells

Project description:DNA are packaged into nucleosomes and chromatin. We performed incomplete MNase digestion of chromatin to identify nucleosome-free regions that may indicate active promoters and regulatory regions. Additionally, HpaII digestion was performed which cleaves CCGG sites when the internal C remains unmodified. The hypomethylation state and nuclease sensitivity of the chromatin are indicators of transcription regulatory regions.

2015-02-25 | E-MTAB-1958 | biostudies-arrayexpress

4C Sequencing using the Fos gene promoter and enhancers as viewpoints in mouse hindbrain cells at different time points during development

Project description:Measuring contacts between the Fos gene promoter and enhancers in developing mouse hindbrain cells

2021-01-09 | E-MTAB-8295 | biostudies-arrayexpress