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PRO-seq, ATAC-seq, and Pol II ChIP-seq in 20 hour sea urchin embryos (ATAC-Seq)

ABSTRACT: PRO-seq, ATAC-seq, and Pol II ChIP-seq in 20 hour sea urchin embryos (ATAC-Seq)

PROVIDER: PRJNA673239 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR12939162_1.fastq.gz	Fastqsanger.gz
	SRR12939162_2.fastq.gz	Fastqsanger.gz
	SRR12939164.fastq.gz	Fastqsanger.gz
	SRR12939165.fastq.gz	Fastqsanger.gz
	SRR13302653_1.fastq.gz	Fastqsanger.gz

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PRO-seq, ATAC-seq, and Pol II ChIP-seq in 20 hour sea urchin embryos

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PRO-seq, ATAC-seq, and Pol II ChIP-seq in 20 hour sea urchin embryos (PRO-Seq)

Project description:PRO-seq, ATAC-seq, and Pol II ChIP-seq in 20 hour sea urchin embryos (PRO-Seq)

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PRO-seq, ATAC-seq, and Pol II ChIP-seq in 20 hour sea urchin embryos (ChIP-seq)

Project description:PRO-seq, ATAC-seq, and Pol II ChIP-seq in 20 hour sea urchin embryos (ChIP-seq)

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PRO-seq, ATAC-seq, and Pol II ChIP-seq in 20 hour sea urchin embryos (ATAC-Seq)

Project description:PRO-seq, ATAC-seq, and Pol II ChIP-seq signals are used to predict active developmental enhancers.

2021-06-03 | GSE160461 | GEO

PRO-seq, ATAC-seq, and Pol II ChIP-seq in 20 hour sea urchin embryos (ChIP-seq)

Project description:PRO-seq, ATAC-seq, and Pol II ChIP-seq signals are used to predict active developmental enhancers.

2021-06-03 | GSE160462 | GEO

PRO-seq, ATAC-seq, and Pol II ChIP-seq in 20 hour sea urchin embryos (PRO-Seq)

Project description:PRO-seq, ATAC-seq, and Pol II ChIP-seq signals are used to predict active developmental enhancers.

2021-06-03 | GSE160460 | GEO

Accessibility and activity of transcriptional regulatory elements during sea urchin embryogenesis and differentiation [ATAC-seq]

Project description:Transcriptional regulatory elements (TREs) are the primary nodes of the gene regulatory networks that control development. TREs are identified by PRO-seq and their accessibility by ATAC-seq during sea urchin embryonic development and differentiation. Our analysis identifies surprisingly early accessibility in 4-cell cleavage embryo TREs that is not necessarily followed by subsequent transcription, and an excess of ATAC-seq peaks transcriptionally disengaged during the stages analyzed. Embryonic accessibility shifts are driven by transcriptionally engaged TREs, and PRO-seq transcriptional differences at TREs provide more contrast among embryonic stages than ATAC-seq accessibility differences. TRE accessibility reaches a maximum around the 20-hour late blastula, which coincides with major embryo regionalizations. At the same time, a large number of distal TREs become transcriptionally disengaged, in support of an early Pol II primed model for developmental gene regulation that eventually resolves in transcriptional activation or silencing. A transcriptional potency model based on labile nucleosome TRE occupancy driven by DNA sequences and the prevalence of histone variants is proposed in order to explain the basal accessibility of transcriptionally inactive TREs during early embryogenesis.

2023-07-27 | GSE234139 | GEO

Accessibility and activity of transcriptional regulatory elements during sea urchin embryogenesis and differentiation [PRO-seq]

2023-07-27 | GSE234140 | GEO

Genome-wide analyses of chromatin interactions after the loss of Pol I, Pol II and Pol III [ATAC-seq]

Project description:Genome binding/occupancy profiling by high throughput sequencing ｜ Expression profiling by high throughput sequencing | Other We analyzed Hi-C, HiChIP, Ocean-C, RNA-seq, ATAC-seq, ChIP-seq and 4C-seq data to provide the most comprehensive evidence to date to demonstrate that transcription plays a marginal role in organizing the 3D genome in mammalian cells: 1) degraded Pol I, Pol II and Pol III proteins in mESCs, and showed their loss results in little or no changes of global 3D chromatin structures for the first time; 2) selected RNA polymerases high abundance binding sites-associated interactions and found they still persist after the degradation; 3) generated higher resolution chromatin interaction maps and revealed that transcription inhibition mildly alters small loop domains; 4) identified Pol II bound but CTCF and Cohesin unbound loops and disclosed that they are largely resistant to transcription inhibition Interestingly, we found that Pol II depletion for a longer time significantly affects the chromatin accessibility and Cohesin occupancy, suggesting RNA polymerases are capable of affecting the 3D genome indirectly. So, the direct and indirect effects of transcription inhibition explain the previous confusing effects on the 3D genome. We conclude that Pol I, Pol II, and Pol III loss only mildly alter chromatin interactions in mammalian cells, suggesting the 3D chromatin structures are preestablished and relatively stable.

2020-06-02 | GSE145785 | GEO

Integrative multi-omics increase resolution of the sea urchin posterior gut gene regulatory network at the single-cell level

Project description:We use multi-omics (ATAC-seq, single cell RNA-seq and differential bulk RNA-seq) to increase resolution of the sea urchin posterior gut GRN for the cells expressing the ParaHox gene Sp-Pdx1.

2024-08-06 | GSE262916 | GEO

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