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Unique regulation of cis-regulatory elements facilitates reacquisition of pluripotency [ATAC-seq]

ABSTRACT: Unique regulation of cis-regulatory elements facilitates reacquisition of pluripotency [ATAC-seq]

PROVIDER: PRJNA481459 | ENA |

REPOSITORIES: ENA

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Unique regulation of cis-regulatory elements facilitates reacquisition of pluripotency

Project description:Unique regulation of cis-regulatory elements facilitates reacquisition of pluripotency

| PRJNA481462 | ENA

Unique regulation of cis-regulatory elements facilitates reacquisition of pluripotency [RNA-seq]

Project description:Unique regulation of cis-regulatory elements facilitates reacquisition of pluripotency [RNA-seq]

| PRJNA481460 | ENA

Unique regulation of cis-regulatory elements facilitates reacquisition of pluripotency [ChIP-seq]

Project description:Unique regulation of cis-regulatory elements facilitates reacquisition of pluripotency [ChIP-seq]

| PRJNA481461 | ENA

Unique regulation of cis-regulatory elements facilitates reacquisition of pluripotency [RNA-seq]

Project description:Ectopic expression of selected transcription factors enables reprogramming of somatic cells to pluripotency. Despite steady progress in the field the exact molecular mechanisms that coordinate this remarkable transition remain still largely elusive. To better understand the final steps during the acquisition of pluripotency, we optimized an experimental system where cells exit pluripotency and then are systematically challenged to reacquire pluripotency. Using this approach we identify a transient period of deterministic reprogramming during which cells exposed to ectopic transcription factors, but not serum/LIF alone, revert to pluripotency with near 100% efficiency before approaching somatic kinetics (1-2 weeks) and efficiencies (1-2%). Investigation of the transient phase reveals unique molecular dynamics that point to a set of cis-regulatory elements that appear central to facilitating reprogramming. Interestingly, these regions retain an epigenetic signature during in vitro and in vivo differentiation and may act as primary targets of ectopically induced factors during somatic cell reprogramming.

2019-09-19 | GSE117204 | GEO

Unique regulation of cis-regulatory elements facilitates reacquisition of pluripotency [ChIP-seq]

2019-09-19 | GSE117203 | GEO

Unique regulation of cis-regulatory elements facilitates reacquisition of pluripotency [ATAC-seq]

2019-09-19 | GSE117202 | GEO

Unique regulation of cis-regulatory elements facilitates reacquisition of pluripotency

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

2019-09-19 | GSE117205 | GEO

The H3K27 demethylase Utx facilitates somatic and germ cell epigenetic reprogramming to pluripotency

Project description:This SuperSeries is composed of the following subset Series: GSE35775: The H3K27 demethylase Utx facilitates somatic and germ cell epigenetic reprogramming to pluripotency [Affymetrix gene expression] GSE37821: The H3K27 demethylase Utx facilitates somatic and germ cell epigenetic reprogramming to pluripotency [ChIP-Seq] Refer to individual Series

2012-05-29 | E-GEOD-37822 | biostudies-arrayexpress

CRISPR-mediated mutagenesis of RNA editing cis-regulatory elements

Project description:We used CRISPR KI technology to mutagenize the cis-regulatory elements including the editing stem and the editing complementary sequence of three RNA editing substrates-NEIL1, TTYH2, AJUBA. We designed single nucleotide variants, double-nucleotide variants and other mutant isoforms to interrogate the primary sequence and the secondary structures around the endogenous RNA editing sites. Gene specific primers were used to make the NGS library for each locus. The unique mutation of each tested isoform can be used as barcode and RNA editing level can be measured for each isoform from the pooled library. We found that RNA sequence and structure features synergistically determine the editing levels. Several features, such as mutation number, free energy, and probability of active conformation, play an important role in determining editing efficiency. This study systematically investigated the contribution of cis-regulatory elements to ADAR1 RNA editing by combining CRISPR-based saturation mutagenesis and deep sequencing technology.

2020-06-01 | GSE138860 | GEO

Characterizing cis-regulatory elements associated with mammary gland function

Project description:The goal of this study is to improve the quality, efficiency, and sustainability of milk production by improving the understanding of the function of cis-regulatory elements in regulating the bovine mammary gland. To this end, we have characterized the non-lactating and lactating mammary gland transcriptomes by whole transcriptome shotgun sequencing (RNA-seq). We will identify cis-regulatory elements in the non-lactating and lactating bovine mammary gland genome-wide. Finally, we will annotate and characterize mammary gland cis-regulatory elements by computational analysis and identify high-resolution genome-wide in vivo footprints of diverse trans-acting-factors (TF), over-represented TF bindings sites and overlapping SNPs.

2021-04-06 | GSE116079 | GEO

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