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Systematic mapping of 3D enhancer interactions reveals lineage specific regulatory networks during early mouse developmental decisions [ChIP-Exo]

ABSTRACT: Systematic mapping of 3D enhancer interactions reveals lineage specific regulatory networks during early mouse developmental decisions [ChIP-Exo]

PROVIDER: PRJNA985766 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR24971816_1.fastq.gz	Fastqsanger.gz
	SRR24971816_2.fastq.gz	Fastqsanger.gz
	SRR24971817_1.fastq.gz	Fastqsanger.gz
	SRR24971817_2.fastq.gz	Fastqsanger.gz
	SRR24971818_1.fastq.gz	Fastqsanger.gz

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Systematic mapping of 3D enhancer interactions reveals lineage specific regulatory networks during early mouse developmental decisions [ChIP-Exo]

Project description:To model and characterize the chromatin regulatory landscape of the very first developmental cell fates, we made use of three previously derived and well-characterized Trophoblast Stem Cell (TSCs), Embryonic Stem Cell (ESC) and Extra Embryonic Stem Cell lines (XENs) We performed ChIP-Exo for CTCF to map the insulator regions in ESC, TSC and XEN

2023-08-21 | GSE235386 | GEO

Systematic mapping of 3D enhancer interactions reveals lineage specific regulatory networks during early mouse developmental decisions

Project description:Systematic mapping of 3D enhancer interactions reveals lineage specific regulatory networks during early mouse developmental decisions

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Systematic mapping of 3D enhancer interactions reveals lineage specific regulatory networks during early mouse developmental decisions [HiChIP]

Project description:Systematic mapping of 3D enhancer interactions reveals lineage specific regulatory networks during early mouse developmental decisions [HiChIP]

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Systematic mapping of 3D enhancer interactions reveals lineage specific regulatory networks during early mouse developmental decisions [4C-Seq]

Project description:Systematic mapping of 3D enhancer interactions reveals lineage specific regulatory networks during early mouse developmental decisions [4C-Seq]

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Systematic mapping of 3D enhancer interactions reveals lineage specific regulatory networks during early mouse developmental decisions [ATAC-Seq]

Project description:Systematic mapping of 3D enhancer interactions reveals lineage specific regulatory networks during early mouse developmental decisions [ATAC-Seq]

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Systematic mapping of 3D enhancer interactions reveals lineage specific regulatory networks during early mouse developmental decisions [Hi-C]

Project description:Systematic mapping of 3D enhancer interactions reveals lineage specific regulatory networks during early mouse developmental decisions [Hi-C]

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Systematic mapping of 3D enhancer interactions reveals lineage specific regulatory networks during early mouse developmental decisions [ChIP-Seq]

Project description:Systematic mapping of 3D enhancer interactions reveals lineage specific regulatory networks during early mouse developmental decisions [ChIP-Seq]

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Systematic mapping of 3D enhancer interactions reveals lineage specific regulatory networks during early mouse developmental decisions [RNA-Seq]

Project description:Systematic mapping of 3D enhancer interactions reveals lineage specific regulatory networks during early mouse developmental decisions [RNA-Seq]

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Systematic mapping of 3D enhancer interactions reveals lineage specific regulatory networks during early mouse developmental decisions

Project description:This SuperSeries is composed of the SubSeries listed below.

2023-08-21 | GSE213645 | GEO

Optimized ChIP-exo for mammalian cells and patterned sequencing flow cells

Project description:By combining chromatin immunoprecipitation (ChIP) with an exonuclease that digests the ends of protein-bound DNA fragments, ChIP-exo characterizes genome-wide protein-DNA interactions at near base-pair resolution. However, the widespread adoption of ChIP-exo has been hindered by several technical challenges, including lengthy protocols, the need for multiple custom reactions, and incompatibilities with recent Illumina sequencing platforms. To address these barriers, we systematically optimized and adapted the ChIP-exo library construction protocol for the unique requirements of mammalian cells and current sequencing technologies. We introduce a Mammalian-Optimized ChIP-exo (MO-ChIP-exo) protocol that builds upon previous ChIP-exo protocols with systematic optimization of crosslinking, harvesting, and library construction. We validate MO-ChIP-exo by comparing it to previously published ChIP-exo protocols and demonstrate its adaptability to both suspension (K562) and adherent (HepG2, mESC) cell lines. This improved protocol provides a more robust and efficient method for generating high-quality ChIP-exo libraries from mammalian cells.

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