01621de5-0afb-4ff4-8f73-8c249cf7e2df - samples
Ontology highlight
ABSTRACT:
PROVIDER: EGAD00001005210 | EGA |
REPOSITORIES: EGA
Similar Datasets
Project description:Allele-specific circular chromosome conformation capture sequencing (4C-seq) using the single nucleotide polymorphism rs2836411 as a bait was performed in two cell types: human umibilical vein endothelial cells (HUVECs) and human aortic smooth muscle cells (HASMCs).
2019-10-11 | GSE137288 | GEO
Project description:We have performed circular chromosome conformation capture sequencing (4C-seq) with six baits located at the Runx1 locus in the mouse hematopoietic progenitor cell line HPC-7. 4C baits were designed to the P1 and P2 promoters and to the previously characterised +24 hematopoietic enhancer (P1, P2 and 24), with secondary baits located at nearby cohesin/CTCF (cc) binding sites (P1cc, 24cc, P2cc).
2017-10-22 | GSE86994 | GEO
Project description:The ability to correlate chromosome conformation and gene expression gives a great deal of information regarding the strategies used by a cell to properly regulate gene activity. 4C-seq is a relatively new and increasingly popular technology where the set of genomic interactions generated by a single point in the genome can be determined. 4C-seq experiments generate large, complicated datasets and it is imperative that signal is properly distinguished from noise. Currently there are a limited number of methods for analyzing 4C-seq data. Here, we present a new method, fourSig, which, in addition to being simple to use and as precise as current methods, also includes a new feature to prioritize significantly enriched interactions and predict their reproducibility among experimental replicates. Here, we demonstrate the efficacy of fourSig with previously published and novel 4C-seq datasets and show that our significance prioritization correlates with the ability to reproducibly detect interactions amongst replicates. The datasets provided include those generated from allele-specific 4C-Seq with a viewpoint of the TSS for the gene Ibtk on mouse Chromosome 9. FASTQ files, text files containing genomic coordiantes and read counts, and bedGraph formats for UCSC Genome Browser tracks are provided. All sequences were mapped relative to mouse genome build mm9. Sequencing of circular chromosome conformation capture (4C-Seq) was performed at the transcription start site (TSS) for the gene Ibtk for three replicates in F1 hybrid mouse trophoblast stem (TS) cells. Experiment was designed to detect allele specific patterns using SNP differences between the inbred lines mated to produce the TS cells (C57Bl/6 and CAST/EiJ)
2014-02-22 | E-GEOD-50907 | biostudies-arrayexpress
Project description:To study GJB2 gene regulation, we used Circular Chromosome Conformation Capture technique (4C) to analyse chromatin interactions inside DFNB1 locus.
2022-07-13 | GSE201205 | GEO
Project description:To understand regulatory function in human neural differentiation, we performed ATAC-seq in human induced pluripotent stem cells (iPSC), in vitro-differentiated neural progenitor cells (NPC) and ganglionic eminence-like (GE) cells, as well as commercially available neural stem cells, GABAergic neurons, and glutamatergic neurons. We also performed circular chromosome conformation capture (4C)-seq on these cells.
2021-05-20 | GSE174727 | GEO
Project description:We identified a novel super-enhance-driven oncogene PPP1R15B overexpressed in multiple myeloma as compared to normal plasma cells and B lymphoma cells. Circular chromosome conformation capture sequencing (4C-seq) was used to confirm the interactions between PPP1R15B enhancer and promoter.
2024-09-30 | GSE212986 | GEO
Project description:Here we report that the spatial organization of yeast tRNA genes depends upon both locus position and tRNA identity; supporting the idea that the genomic organization of tRNA loci utilizes tRNA dependent signals within the nucleoprotein-tRNA complexes that form into clusters. We use high-throughput sequencing coupled to Circular Chromosome Conformation Capture to detect interactions with two wild type tRNAs and these same positions replaced with suppressor tRNAs (SUP4-1). Detect DNA-DNA interactions (Circular chromosome conformation capture; 4C) with two wild type tRNAs and these same positions replaced with suppressor tRNAs (SUP4-1) Supplementary files: Alignment files generated by Topography v1.19 software.
2012-06-13 | E-GEOD-30103 | biostudies-arrayexpress
Project description:Background: The packaging of long chromatin fibres in the nucleus poses a major challenge, as it must fulfil both physical and functional requirements. Until recently, insight into the chromosomal architecture of plants was mainly provided by cytogenetic studies. Complementary to these analyses, chromosome conformation technologies promise to refine and improve our view on chromosomal architecture and to provide a more generalised description of nuclear organization. Results: Employing circular chromosome conformation capture (4C), this study describes chromosomal architecture in Arabidopsis nuclei from a genome-wide perspective. Surprisingly, the linear organisation of chromosomes is reflected in the genome-wide interactome. In addition, we studied the interplay of the interactome and epigenetic marks and report that the heterochromatic knob on the short arm of chromosome 4 (hk4s) maintained a pericentromere-like interaction profile and interactome despite its euchromatic surrounding. Conclusion: Despite the extreme condensation that is necessary to pack the chromosomes into the nucleus, the Arabidopsis genome appears to be packed in a predictive manner, according to the following criteria: (i) heterochromatin and euchromatin represent two distinct interactomes, (ii) interactions between chromosomes correlates with the linear position on the chromosome arm, and (iii) distal chromosome regions have a higher potential to interact with other chromosomes. This study includes circular chromosome conformation capture (4C) sequencing information of 13 samples, present in two batches, each present in duplicates (A and B). The individual 4C sequencing information can be retrieved by the 4C primer sequence, given in the 4C primer information file.
2013-11-01 | E-GEOD-50181 | biostudies-arrayexpress
Project description:The spatial proximity between regulatory elements and their target genes has a profound affect on gene expression. X Chromosome Inactivation (XCI) is an epigenetic process by which an entire chromosome is rendered, for the most part, transcriptionally silent. A few genes are known to escape XCI and the mechanism for this escape remains unclear. Here, using mouse trophectodermal stem cells, we address whether specific chromosomal interactions facilitate escape from XCI by bringing escape-specific regulatory elements in close proximity to gene promoters. Our results suggest a model where escape from XCI occurs within topologically associated domains. As such, escaping genes and the regulatory sequences required for their escape are likely located within close linear proximity to each other. The datasets provided include those generated from allele-specific 4C-Seq of genes escaping XCI, genes subject to XCI, and non-genic regions of the X chromosome. FASTQ files, text files containing genomic coordiantes, and BED aligmnets are provided. All sequences were mapped relative to mouse genome build mm9. Deep sequencing of circular chromosome conformation capture (4C-Seq) of genes escaping X inactivation in mouse trophoblast stem cells
2014-03-26 | E-GEOD-49111 | biostudies-arrayexpress
Project description:We have identified putative repressor region (PRR) to exon-1 of β-globin (βE1) in the β-globin cluster as a core region in alll the HPFH deletions that activates fetal hemoglobin and silences adult hemoglobin. To test the impact of PRR-βE1 gene editing in β-globin cluster configuration, we employed Circular chromosome conformation capture (4C) analysis to assess the LCR interaction to the gamma-globin promoter. Using HBG2 promoter as viewpoint,4C analysis showed an increased interaction of HBG promoter to the hypersensitive (HS) sites of the LCR in HUDEP-2 clones harbouring PRR-βE1 biallelic deletions compared to control HUDEP-2 cells. Link for 4C output files Mendeley - Venkatesan, Vigneshwaran (2022), “4C data set ”, Mendeley Data, V1, doi: 10.17632/cz3thnr9kf.1
2022-04-26 | GSE201388 | GEO