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Trans-differentiation takes place without reprogramming of developmental-specific DNA methylation, a key determinant of stable cell identity [RRBS]

ABSTRACT: Trans-differentiation takes place without reprogramming of developmental-specific DNA methylation, a key determinant of stable cell identity [RRBS]

PROVIDER: PRJNA1060277 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR27403116_1.fastq.gz	Fastqsanger.gz
	SRR27403116_2.fastq.gz	Fastqsanger.gz
	SRR27403117_1.fastq.gz	Fastqsanger.gz
	SRR27403117_2.fastq.gz	Fastqsanger.gz
	SRR27403118_1.fastq.gz	Fastqsanger.gz

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Trans-differentiation takes place without reprogramming of developmental-specific DNA methylation, a key determinant of stable cell identity

Project description:Trans-differentiation takes place without reprogramming of developmental-specific DNA methylation, a key determinant of stable cell identity

| PRJNA1060271 | ENA

Trans-differentiation takes place without reprogramming of developmental-specific DNA methylation, a key determinant of stable cell identity [RRBS]

Project description:A number of studies have demonstrated that it is possible to directly convert one cell type to another by factor-mediated trans-differentiation, but in the vast majority of cases, the resulting reprogrammed cells are unstable in the sense that they are unable to maintain their new cell identity. To better understand this phenomenon, we have developed a new analytical approach for better characterizing trans-differentiation-associated changes in DNA methylation, a major determinant of long-term cell identity. By examining various models of trans-differentiation both in vitro and in vivo, our studies indicate that despite convincing expression changes, trans-differentiated cells seem unable to alter their original developmentally-mandated methylation patterns. We propose that this blockage is due to basic developmental limitations built into the regulatory-sequence that govern epigenetic programming of cell identity. These results shed new light on the molecular rules of stable somatic cell reprogramming.

2024-09-12 | GSE252354 | GEO

Trans-differentiation takes place without reprogramming of developmental-specific DNA methylation, a key determinant of stable cell identity [RNA-seq]

Project description:Trans-differentiation takes place without reprogramming of developmental-specific DNA methylation, a key determinant of stable cell identity [RNA-seq]

| PRJNA1060275 | ENA

Trans-differentiation takes place without reprogramming of developmental-specific DNA methylation, a key determinant of stable cell identity [RNA-seq]

2024-09-12 | GSE252353 | GEO

place holder

Project description:place holder

| PRJEB44523 | ENA

Trans-differentiation takes place without reprogramming of developmental-specific DNA methylation, a key determinant of stable cell identity

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

2024-09-12 | GSE252355 | GEO

Cis-trans

Project description:Cis-trans

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Smart-RRBS for single cell methylome and transcriptome analysis [scRRBS]

Project description:The integration of DNA methylation and transcriptional state within single cells is of broad interest. Several single-cell dual- and multi-omics approaches have been reported recently that will enable further investigation into cellular heterogeneity including the discovery and in depth study of rare cell populations. Such analyses will continue to provide important mechanistic insights into the regulatory consequences of epigenetic modifications. Last year we reported a new method for profiling the DNA methylome and transcriptome from the same single cell. Here we present details of the protocol and provide guidance on its utility. Our Smart-RRBS protocol entails physically separating mRNA and genomic DNA and combines Smart-Seq2 and Reduced Representation Bisulfite Sequencing (RRBS). It generates paired epigenetic promoter and RNA-expression measurements for a substantial fraction (approximately one-fourth) of protein-coding genes in a typical single cell. It also works for micro-dissected tissue samples comprising hundreds of cells. The protocol, excluding sequencing, takes ~3 days to process up to 192 samples manually

2021-04-15 | GSE157114 | GEO

Smart-RRBS for single cell methylome and transcriptome analysis [scRNAseq]

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Trans-Seq for mammalian retinotectal circuit mapping

Project description:The mouse visual system serves as an accessible model to understand mammalian circuit wiring. Despite rich knowledge in retinal circuits, the long-range connectivity map from distinct retinal ganglion cell (RGC) types to diverse brain neuron types remains unknown. Here we developed an integrated approach, named Trans-Seq, to map RGC to superior collicular (SC) circuits. Trans-Seq combines a fluorescent anterograde transsynaptic tracer, consisting of codon-optimized wheat germ agglutinin fused to mCherry, with single-cell RNA Sequencing. We used Trans-Seq to classify SC neuron types innervated by genetically-defined RGC types and predicted a neuronal pair from αRGCs to Nephronectin-positive wide-field neurons (NPWFs). We validated this connection using genetic labeling, electrophysiology, and retrograde tracing. We then utilized transcriptomic data from Trans-Seq to identify Nephronectin as a determinant for selective synaptic choice from αRGC to NPWFs via binding to Integrin-α8β1. The Trans-Seq approach can be broadly applied for postsynaptic circuit discovery from genetically-defined presynaptic neurons.

2022-05-07 | GSE202257 | GEO

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