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Studying changes in chromatin accessibility in U2OS-GR cells by ATAC-seq directly after 4-hour glucocorticoid treatment and following a 24-hour hormone washout

ABSTRACT: Studying changes in chromatin accessibility in U2OS-GR cells by ATAC-seq directly after 4-hour glucocorticoid treatment and following a 24-hour hormone washout

PROVIDER: PRJEB41974 | ENA |

REPOSITORIES: ENA

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Dataset's files

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			Action	DRS
	ERR4982320_1.fastq.gz	Fastqsanger.gz
	ERR4982320_2.fastq.gz	Fastqsanger.gz
	ERR4982321_1.fastq.gz	Fastqsanger.gz
	ERR4982321_2.fastq.gz	Fastqsanger.gz
	ERR4982322_1.fastq.gz	Fastqsanger.gz

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Studying changes in chromatin accessibility in U2OS-GR cells by ATAC-seq directly after 4-hour glucocorticoid treatment and following a 24-hour hormone washout

Project description:We performed ATAC-seq in the U2OS-GR cell line. The cell line is derived from U2OS ATTC:HTB-96 and stably transfected with an expression construct for rat GR. Cells were treated with dexamethasone (100 nM) or vehicle (ethanol) for 4 hours and either harvested immediately or washed 2x with PBS and subsequently cultured in hormone-free medium for 24 hours before harvest.

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Project description:We performed ChIP-seq targeting the glucocorticoid receptor (GR) in the U2OS-GR cell line. The cell line is derived from U2OS ATTC:HTB-96 and stably transfected with an expression construct for rat GR. The cells were treated with 100 nM dexamethasone for 4 hours, washed 2x with PBS and cultured in hormone-free medium for 24 hours before harvest.

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Studying enhancer activity by FAIRE-STARR-seq in the U2OS-GR and the U2OS-AR cells upon hormone treatment

Project description:To quantify functional enhancers, we performed STARR-seq (Self-Transcribing Active Regulatory Region sequencing) in the U2OS-GR and the U2OS-AR cell lines (derived from U2OS ATTC:HTB-96, stably transfected with an expression construct for rat GR or human AR, respectively). U2OS-GR cells were treated with dexamethasone (1 µM) or vehicle (ethanol) for 14 hours. U2OS-AR cells were treated with R1881 (5 nM) or vehicle (DMSO) for 14 hours. To limit the number of putative enhancers, the STARR library contained genomic regions isolated by FAIRE (Formaldehyde Assisted Isolation of Regulatory Elements) from dexamethasone-treated U2OS-GR cells to include regions that gain accessibility upon GR activation. We added unique molecular identifiers (UMIs) during the reverse transcription stage to facilitate quantitative measurements of enhancer activity for each fragment. The UMI for each read is present within the sequence identifier line (directly following the y coordinate and separated by a ':') of the fastq files.

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Glucocorticoid and androgen receptor profiling (ChIP-seq) in U2OS-GR and U2OS-AR cells upon hormone treatment

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