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Circularized chromosome conformation capture followed by sequencing (4C-seq) in A549 cell line

ABSTRACT: Circularized chromosome conformation capture followed by sequencing (4C-seq) in A549 cell line

PROVIDER: PRJNA936096 | ENA |

REPOSITORIES: ENA

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circularized chromosome conformation capture followed by sequencing (4C-seq) in the heterozygous (T/C) A549 cell line

Project description:circularized chromosome conformation capture followed by sequencing (4C-seq) in the heterozygous (T/C) A549 cell line

| PRJNA879734 | ENA

Circularized chromosome conformation capture (4C-seq) in A549 cells after glucocorticoid re-induction

Project description:Circularized chromosome conformation capture (4C-seq) in A549 cells after glucocorticoid re-induction

| PRJEB42000 | ENA

Circularized chromosome conformation capture (4C-seq) in A549 and U2OS cells stably expressing rat GRα

Project description:Circularized chromosome conformation capture (4C-seq) in A549 and U2OS cells stably expressing rat GRα

| PRJEB18677 | ENA

Circularized chromosome conformation capture (4C-seq) in A549 cells after glucocorticoid re-induction

Project description:We performed 4C-seq in the A549 cell line to investigate changes in chromatin interactions at the ZBTB16 locus. Cells were treated with either 100 nM dexamethasone or 0.1% ethanol. After 4 hours, cells were washed 2x with PBS and cultured in hormone-free medium for 24 hours, after which cells were treated again for 4 hours with either 100 nM dexamethasone or 0.1% ethanol. Experiments were performed in two biological replicates. For each treatment, 4C-seq data were generated for the following two viewpoints: ZBTB16 promoter-proximal viewpoint coordinates: chr11:113929670-113930464 (hg19) ZBTB16 intronic viewpoint coordinates: chr11:114051224-114051804 (hg19)

2021-05-03 | E-MTAB-9915 | biostudies-arrayexpress

Circularized chromosome conformation capture followed by sequencing (4C-seq) in A549 cell line

Project description:To examine target genes that interact with different alleles of rs1663689 in a heterozygous cell line A549(T/T),A549(C/C).

2023-05-10 | GSE225518 | GEO

Circularized chromosome conformation capture (4C-seq) in A549 and U2OS cells stably expressing rat GR

Project description:To investigate the interaction landscape at the GILZ locus we performed 4C-seq in A549 (ATCC CCL-185) and U2OS cells stably expressing rat GR (Rogatsky et al. , Mol Cell Biol, 1997. 17(6): p. 3181-93.) upon hormone treatment (1.5 h, 1 M dexamethasone). Experiments were performed in two biological replicates using hg19 chrX:106,960,488-106,960,865 as a viewpoint.

2018-04-12 | E-MTAB-5350 | biostudies-arrayexpress

4C-seq of insulin promoter

Project description:We report the 4C (Circularized Chromosome Conformation Capture)-seq data of insulin promoter in EndoC βH1 and HeLa cells.

2018-04-06 | GSE111863 | GEO

Chromosome Conformation Capture (4C seq) at the rs9929218 locus in colorectal cancinogensis

Project description:Chromosome Conformation Capture (4C seq) at the rs9929218 locus in colorectal cancinogensis

2020-10-01 | GSE121623 | GEO

circularized chromosome conformation capture followed by sequencing (4C-seq) in the heterozygous (T/C) A549 cell line

Project description:To examine target genes that interact with different alleles of rs1663689 in a heterozygous cell line A549(A/C).

2023-05-10 | GSE213196 | GEO

4C and Capture-C in HCT116, NCM460 cells and colon tissue

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.

2016-08-15 | E-MTAB-4845 | biostudies-arrayexpress

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