Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Induction of Pluripotent Stem Cells from Mouse Embryonic Fibroblasts by Jdp2, Glis1, Essrb and Sall4 [RNA-seq]

ABSTRACT: Reprogramming somatic cells to pluripotency represents a paradigm for cell fate determination. A binary logic of closing and opening chromatin provides a simple way to understand iPSC reprogramming driven by both Yamanaka factors or chemicals. Here we apply this logic to the design a four factor combination, Jdp2, Glis1, Essrb and Sall4 (4F), that reprogram MEFs to chimera competent iPSCs efficiently. RNA- and ATAC-seq reveal differences between JGES and 7F induced pluripotency, 7IP and JGES IP, in transcriptomic and chromatin accessibility dynamics(CAD). Sall4 emerges as a dominant force that can close and open chromatin with the help of Jdp2 and Glis1 in resetting somatic chromatin to a pluripotent state. These results reveal a previously unknown path between somatic and pluripotent states, open a door for cell fate control.

ORGANISM(S): Mus musculus

PROVIDER: GSE140006 | GEO | 2022/11/05

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Induction of Pluripotent Stem Cells from Mouse Embryonic Fibroblasts by Jdp2, Glis1, Essrb and Sall4 (dataset II)

Project description:Reprogramming somatic cells to pluripotency represents a paradigm for cell fate determination. A binary logic of closing and opening chromatin provides a simple way to understand iPSC reprogramming driven by both Yamanaka factors or chemicals. Here we apply this logic to the design a four factor combination, Jdp2, Glis1, Essrb and Sall4 (4F), that reprogram MEFs to chimera competent iPSCs efficiently. RNA- and ATAC-seq reveal differences between JGES and 7F induced pluripotency, 7IP and JGES IP, in transcriptomic and chromatin accessibility dynamics(CAD). Sall4 emerges as a dominant force that can close and open chromatin with the help of Jdp2 and Glis1 in resetting somatic chromatin to a pluripotent state. These results reveal a previously unknown path between somatic and pluripotent states, open a door for cell fate control.

2022-02-08 | GSE145478 | GEO

Induction of Pluripotent Stem Cells from Mouse Embryonic Fibroblasts by Jdp2, Glis1, Essrb and Sall4 [ATAC-seq]

2022-11-05 | GSE140007 | GEO

Induction of Pluripotency by Alternative Factors (RNA-Seq)

Project description:Reprogramming somatic cells to pluripotency represents a paradigm for cell fate determination. A binary logic of closing and opening chromatin provides a simple way to understand iPSC reprogramming driven by both Yamanaka factors or chemicals. Here we apply this logic to the design a seven factor combination, Jdp2, Jhdm1b, Mkk6, Glis1, Nanog, Essrb and Sall4 (7F), that reprogram MEFs to chimera competent iPSCs efficiently. RNA- and ATAC-seq reveal differences between 7F and Yamanaka induced pluripotency, 7IP and YIP, in transcriptomic and chromatin accessibility dynamics(CAD). Sall4 emerges as a dominant force that can close and open chromatin with the help of Jdp2 and Glis1 in resetting somatic chromatin to a pluripotent state. These results reveal a previously unknown path between somatic and pluripotent states, open a door for cell fate control.

2019-06-18 | GSE127927 | GEO

Induction of Pluripotency by Alternative Factors (ATAC-Seq)

Project description:Reprogramming somatic cells to pluripotency represents a paradigm for cell fate determination. A binary logic of closing and opening chromatin provides a simple way to understand iPSC reprogramming driven by both Yamanaka factors or chemicals. Here we apply this logic to the design a seven factor combination, Jdp2, Jhdm1b, Mkk6, Glis1, Nanog, Essrb and Sall4 (7F), that reprogram MEFs to chimera competent iPSCs efficiently. RNA- and ATAC-seq reveal differences between 7F and Yamanaka induced pluripotency, 7IP and YIP, in transcriptomic and chromatin accessibility dynamics(CAD). Sall4 emerges as a dominant force that can close and open chromatin with the help of Jdp2 and Glis1 in resetting somatic chromatin to a pluripotent state. These results reveal a previously unknown path between somatic and pluripotent states, open a door for cell fate control.

2019-06-18 | GSE127926 | GEO

Induction of Pluripotent Stem Cells from Mouse Embryonic Fibroblasts by Jdp2, Glis1, Essrb and Sall4 [scRNA-seq]

Project description:Reprogramming somatic cells to pluripotency has revolutionized our understanding of cell fate control. Yet, most of that knowledge has been predicated on a single system powered by Oct4, Sox2, Klf4 and Myc. Here we describe two four factor sets capable of reprogramming mouse embryonic fibroblasts (MEFs) to pluripoten-cy. We first developed Jdp2, Glis1, Essrb and Sall4 or JGES that can mediate ro-bust reprogramming by orchestrating a unique chromatin accessibility dynamics involving loci encoding genes for mitochondrial respiration and meiosis/germ cell development. Single cell sequencing further reveals early Sox2+ intermediates as well as late neuron-, hematoendothelial-, mesoderm-, visceral endoderm- and plu-ripotent-like fates. Along a fate continuum, we show distinct transitions of differen-tially expressed genes marked by a critical crossover point. Among genes sus-tained after the point, we identify Zfp296, Etv5, Sall1 and Tfap2c or ZEST that can reprogram MEFs to pluripotency. Our study suggests that the JGES and ZEST sys-tem may allow deeper understanding of cell fate control.

2022-11-05 | GSE145388 | GEO

NURD dependent Reprogramming by Sall4-Jdp2-Esrrb-Glis1 (ChIP-seq)

Project description:Cell fate decision involves rewiring of the genome, but remains poorly understood at the chromatin level. We report a system to reprogramming somatic cells to pluripotency by four factor combination (Sall4, Esrrb, Jdp2, Glis1). Mechanism study demonstrate that the Sall4-NuRD axis plays a critical role in the early phase of reprogramming. These results identify a previously unrecognized role of NuRD in reprogramming, may help establish early chromatin closing as a pre-requisite step in cell fate control.

2022-10-12 | GSE199612 | GEO

NURD dependent Reprogramming by Sall4-Jdp2-Esrrb-Glis1 (ATAC-seq)

2022-10-12 | GSE199609 | GEO

NURD dependent Reprogramming by Sall4-Jdp2-Esrrb-Glis1 (RNA-seq)

2022-10-12 | GSE199613 | GEO

Cell fate decision by a morphogen-transcription factor-chromatin modifier axis

Project description:Bulk RNA-sequences show the differences upon primitive endoderm cell related gene expression between JGES induced somatic cell reprogramming with or without BMP4 treatment, and between WT-SALL4 or delN12-SALL4 induced transdifferentiation from E13.5 mouse embryonic fibroblasts, primitive endoderm cell related gene are from our single cell RNA sequence data So as to estimate the chromatin remodeling differences between SALL4-WT and SALL4-delN12 during single factor induced PrE formation, we performed Tn5 dependent ATAC-sequence to compare the open and close chromatin of the two group. In order to identify the bingding differences of SALL4 and H3K27ac level diversity between SALL4-WT and SALL4-delN12 on PrE related genes, wo performed CUTandTAG experiments. Single cell analysis provides clarity unattainable with bulk approaches. Here we apply single cell RNA-seq to a newly established mouse somatic cell reprogramming system with or without BMP4 treatment at Day 7, this reprogramming system are induced by four transcriptional factors Jdp2-Glis1-Esrrb-Sall4 or JGES and cultured in iCD3. We first show that cells could be clustered into four group, primitive endoderm cell like cells, pluripotent cells, endothelial cells, and intermediate state cells which are hard to be clarified, after BMP4 treatment, a placenta-like state arise, the percentage of endothelial cells and primitive endoderm cell like cells increase and pluripotent cells decrease sharply. Our results not only show the ability of JGES and BMP4 in different cell lineage induction but also provide a model to explore mechanisms of first and second cell lineage decision during early embryogenesis.

2024-06-06 | GSE242851 | GEO

NURD dependent Reprogramming by Sall4-Jdp2-Esrrb-Glis1

Project description:NURD dependent Reprogramming by Sall4-Jdp2-Esrrb-Glis1

| PRJNA820848 | ENA