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Homo sapiens

ABSTRACT: The functional enhancer repertoire of human embryonic stem cells [plasmid DNA-seq]

PROVIDER: PRJNA389114 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR5642860_1.fastq.gz	Fastqsanger.gz
	SRR5642860_2.fastq.gz	Fastqsanger.gz
	SRR5642861_1.fastq.gz	Fastqsanger.gz
	SRR5642861_2.fastq.gz	Fastqsanger.gz
	SRR5642862_1.fastq.gz	Fastqsanger.gz

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Project description:We provide a novel functional genomics atlas of non-coding regulatory elements derived from human neural stem cells (NSCs), using the massively parallel reporter assay ChIP-STARR-seq. ChIP-STARR-seq was performed in NSCs using chromatin immunoprecipitation for H3K27ac, H3K4me1, YY1 and SOX2, and the generated STARR-seq plasmid reporter libraries were profiled for their enhancer activity in H9 derived NSCs and human embryonic stem cells. Subsequently a multi-omics data integration was performed, including the development of a convolutional neural network called BRAIN-MAGNET that allows to predict the effect of single nucleotide variants in non-coding regulatory elements on the enhancer activity. The various data sets generated in this study include ChIP-seq experiments in NSCs, DNA sequencing of the generated plasmid libraries, RNA-seq of transfected cells from the ChIP-STARR-seq experiments, generated ATAC-seq data sets used for data integration and the contribution scores from BRAIN-MAGNET for each nucleotide assessed in this ChIP-STARR-seq study.

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The functional enhancer repertoire of human embryonic stem cells [plasmid DNA-seq]

Project description:We combined Self-Transcribing Active Regulatory Region Sequencing (STARR-seq) with an enrichment step using chromatin immunoprecipitation in a massively parallel reporter assay. We applied this assay, termed ChIP-STARR-seq, to normal (primed) and naive human embryonic stem cells, building up a comprehensive catalogue of functional enhancers. This database record describes the DNA-seq component from plasmid libraries prior to transfection.

2017-07-05 | GSE99629 | GEO

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