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Probing cell identity hierarchies by fate titration and collision during direct reprogramming [scRNA-seq & scATAC-seq]

ABSTRACT: Probing cell identity hierarchies by fate titration and collision during direct reprogramming [scRNA-seq & scATAC-seq]

PROVIDER: PRJNA872404 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR21171455_1.fastq.gz	Fastqsanger.gz
	SRR21171455_2.fastq.gz	Fastqsanger.gz
	SRR21171456_1.fastq.gz	Fastqsanger.gz
	SRR21171456_2.fastq.gz	Fastqsanger.gz
	SRR21171457_1.fastq.gz	Fastqsanger.gz

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Probing cell identity hierarchies by fate titration and collision during direct reprogramming

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Probing cell identity hierarchies by fate titration and collision during direct reprogramming [scRNA-Seq]

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Probing cell identity hierarchies by fate titration and collision during direct reprogramming [Cut & Tag]

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Probing cell identity hierarchies by fate titration and collision during direct reprogramming [scRNA-seq & scATAC-seq]

Project description:Collide-seq: A systematic comparison of how different reprogramming transcription factors achieve conversion as well as an in-depth analysis of how cells resolve the conflict when more than one fate is instructed.

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Probing cell identity hierarchies by fate titration and collision during direct reprogramming.

Project description:Despite the therapeutic promise of direct reprogramming, basic principles concerning fate erasure and the mechanisms to resolve cell identity conflicts remain unclear. To tackle these fundamental questions, we established a single-cell protocol for the simultaneous analysis of multiple cell fate conversion events based on combinatorial and traceable reprogramming factor expression: Collide-seq. Collide-seq revealed the lack of a common mechanism through which fibroblast-specific gene expression loss is initiated. Moreover, we found that the transcriptome of converting cells abruptly changes when a critical level of each reprogramming factor is attained, with higher or lower levels not contributing to major changes. By simultaneously inducing multiple competing reprogramming factors, we also found a deterministic system, in which titration of fates against each other yields dominant or colliding fates. By investigating one collision in detail, we show that reprogramming factors can disturb cell identity programs independent of their ability to bind their target genes. Taken together, Collide-seq has shed light on several fundamental principles of fate conversion that may aid in improving current reprogramming paradigms.

| S-EPMC9476893 | biostudies-literature

Probing cell identity hierarchies by fate titration and collision during direct reprogramming

Project description:Despite the therapeutic promise of direct reprogramming, basic principles concerning fate erasure and the mechanisms to resolve cell identity conflicts remain unclear. To tackle these fundamental questions, we established a single-cell protocol for the simultaneous analysis of multiple cell fate conversion events based on combinatorial and traceable reprogramming factor expression: Collide-seq. Collide-seq revealed the lack of a common mechanism through which fibroblast specific gene expression loss is initiated. Moreover, we found that the transcriptome of converting cells abruptly changes when a critical level of each reprogramming factor is attained, with higher or lower levels not contributing to major changes. By simultaneously inducing multiple competing reprogramming factors, we also found a deterministic system in which titration of fates against each other yields dominant or colliding fates. By investigating one collision in detail, we show that reprogramming factors can disturb cell identity programs independent of their ability to bind their target genes. Taken together, Collide-seq has shed light on several fundamental principles of fate conversion that may aid improving current reprogramming paradigms.

| S-SCDT-MSB-2022-11129 | biostudies-other

Probing cell identity hierarchies by fate titration and collision during direct reprogramming

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

2022-09-16 | GSE211864 | GEO

Probing cell identity hierarchies by fate titration and collision during direct reprogramming [scRNA-Seq]

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Probing cell identity hierarchies by fate titration and collision during direct reprogramming [Cut & Tag]

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In-culture titration experiment for sRSE

Project description:In order to test the transcriptome-wide functionality of the identified sRSE instances, we performed an in vivo titration experiment in which synthetic RNA oligonucleotides harboring tandem sRSE1 repeats were used as intracellular decoys that would bind the putative trans factor, preventing it from targeting endogenous transcripts. Capped and poly-adenylated RNAs carrying tandem sRSE elements were transfected along with scrambled RNA molecules as control. 48 hours post-transfection, samples were subjected to transcriptome profiling to measure the regulatory consequences of the in-vivo titration of the sRSE-binding trans factor.

2014-07-24 | E-GEOD-49609 | biostudies-arrayexpress

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