MND_Exome Capture
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ABSTRACT:
REPOSITORIES: ENA
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Project description:Genome organization influences transcriptional regulation by facilitating interactions between gene promoters and distal regulatory elements. To analyse distal promoter contacts we used Capture Hi-C (CHi-C) to enrich for promoter-interactions in a HiC lib
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Project description:Multiplexed Chromatin Conformation Capture in Mouse Erythroid cells , from hundreds of targeted loci, using agilent oligo capture technology and high throughput sequencing.
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Project description:Multiplexed Chromatin Conformation Capture in Mouse Erythroid cells , from hundreds of targeted loci, using agilent oligo capture technology and high throughput sequencing. Two erythroid Ter119+ cell replicates and a mouse ES cell control
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Project description:One of the strongest associated type 2 diabetes (T2D) loci reported to date resides within the TCF7L2 gene. Previous studies point to the T allele of rs7903146 in intron 3 as the causal variant at this locus. To aid in the identification of the actual gene(s) under the influence of this variant, we first generated a CRISPR/Cas9 mediated 1.4kb deletion of the genomic region harboring rs7903146 in the HCT116 cell line followed by global gene expression analysis (see experiment E-MTAB-4839). We then carried out high-throughput chromosome conformation capture assays in the HCT116 and NCM460 cell lines and in colon tissue in order to ascertain which of these perturbed genes promoters made consistent physical contact with the genomic region harboring the variant. To assess consistency and reproducibility we utilized two different techniques: Circularized Chromosome Conformation Capture (4C) and Capture C. In both types of assays, after preparing 3C libraries, our bait of interest was the region harboring rs7903146. Loci interacting with such bait are enriched for by inverse PCR in 4C and by oligonucleotide capture in capture C. 4C assays were carried out in the following samples: two on NCM460 cells (using different primer sets), one on HCT116 cells, one on HCT116 cells with a CRISPR/Cas9 mediated 1.4kb deletion of the genomic region harboring the SNP rs7903146, and one on colon tissue. Capture C assays were carried out in one sample each of the cell lines NCM 460 and HCT116. This experiment, coupled with the associated E-MTAB-4839, revealed just one gene, ACSL5, which resides in the same topologically associating domain as TCF7L2.
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Project description:Capture-C interaction profiles from the viewpoints of the promoters of Chac2, Cpeb4 and Fbxw11 in mouse erythroid and ES cells.
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Project description:Identification of Nanog promoter binding protein by CAPTURE
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