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Dynamics of transcriptomes of hPSCs treated by CHIR99021 for 21 hours

ABSTRACT: Dynamics of transcriptomes of hPSCs treated by CHIR99021 for 21 hours

PROVIDER: PRJNA597479 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR10763865.fastq.gz	Fastqsanger.gz
	SRR10763866.fastq.gz	Fastqsanger.gz
	SRR10763867.fastq.gz	Fastqsanger.gz
	SRR10763868.fastq.gz	Fastqsanger.gz
	SRR10763869.fastq.gz	Fastqsanger.gz

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Dynamics of transcriptomes of hPSCs treated by CHIR99021 for 21 hours

Project description:We have evidence to demonstrate that hPSCs enter mesoderm or endoderm lineages dependent on the dose of WNT signaling activation. To understand the underlying mechanism of CHIR99021-induced definitive endoderm (DE) differentiation, we collected hPSCs treated by CHIR99021 for 21 hours and performed RNA sequencing, to investigate the dynamics of transcriptomes in every three hours post CH treatment.

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Identifying CHIR99021 and AICAR-regulated genes in the J1 mESCs

Project description:It has been demonstrated that CHIR99021 promotes self-renewal of mouse embryonic stem cells, however, the target genes of CHIR99021 is not fully understood. AICAR is the activator of AMP-activated protein kinase. It is reported that AICAR plays important role in mouse embryonic stem cells, however the moleculor mechanism of this phenomenon is unknown. To better understand the downstream target genes of CHIR99021 and AICAR, we performed Microarray analyses to identify their downstream targets. The data show the genes regulated by CHIR99021 or AICAR. J1 mESCs maintained in medium containing 1000 U/mL LIF and supplemented without or with CHIR99021 or AICAR for 24 hours, then total RNA was extracted for analysis.

2013-01-01 | E-GEOD-40959 | biostudies-arrayexpress

Gene expression profiling of mouse embryonic kidney (E12.5) treated with CHIR99021 or DMSO

Project description:Purpose: To investigate GSK3 inhibitor effect on gene expression during renal development. Methods: mRNA profiles of in-vitro organ culture of mouse embryonic kidney (E12.5) treated with 5 µM CHIR99021 or 0.1% DMSO for 72 hours were generated by deep sequencing in quadruplicate. Results: When comparing CHIR99021 group to DMSO group, in 30890 genes tested, 950 genes were upregulated, and 1,879 genes were downregulated, with a fold change ≥2 and p (padj value) <0.05.

2021-05-01 | GSE131240 | GEO

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Project description:Our studies showed that Wnt activation influenced patterning of the mouse cochlea across the radial axis. To identify genes responding to Wnt activation, mouse embryonic cochleas were treated in the presence and absence of the GSK 3beta inhibitor, CHIR99021. Cochleas were harvested on E12.5 and cultured in vitro for 24 hours. On the next day (day 1), cochleas were treated with either DMSO vehicle control or CHIR99021. The 6-hour treatment helped to identify the immediate genes transcribed following Wnt activation.

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Identifying CHIR99021 and AICAR-regulated genes in the J1 mESCs

2013-01-01 | GSE40959 | GEO

Genome-wide analysis of gene expression in LIF and LIF plus CHIR99021 in C57BL/6 mouse embryonic stem cells(B6 mESCs)

Project description:Analysis of genes induced by CHIR99021 CHIR99021 is a inhibitor of glycogen synthase kinase 3 (GSK3) and can promote B6 mESC sef-renewal when combined with LIF in serum condition. Total RNA obtained from B6 mESCs treated with LIF or LIF/CHIR99021 for 12 hours.

2013-08-29 | E-GEOD-50393 | biostudies-arrayexpress

Expression data of hPSCs differentiated into Paraxial mesoderm

Project description:Stem cell-derived tissues have wide potential for modelling developmental and pathological processes as well as cell-based therapy. However, it has proven difficult to generate several key cell types in vitro, including skeletal muscle. In vertebrates, skeletal muscles derive during embryogenesis from the presomitic mesoderm (PSM). Using PSM development as a guide, we establish conditions for the differentiation of monolayer cultures of human pluripotent stem (hPSC) cells into PSM-like cells without the introduction of transgenes or cell sorting. We differentiated human PSCs in serum-free medium supplemented with Chir99021 only (C medium) or with also the Bmp inhibitor LDN193189 (CL medium). In vivo, the PSM cells are first expressing MSGN1 (posterior PSM marker) and then mature to express Pax3 (anterior PSM marker). After 4-5 days of differentiation of hPSCs, MSGN1-positive cells were FACS-sorted and their transcriptome analyzed.

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MEIS1 regulates hematopoiesis in hPSCs

Project description:MEIS1 regulates hematopoiesis in hPSCs

| PRJNA357013 | ENA

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Project description:Human pluripotent stem cell- (hPSC)-derived skeletal muscle progenitors (SMP)—defined as PAX7-expressing cells with myogenic potential—can provide an abundant source of donor material for muscle stem cell therapy owing to the near-infinite replication potential of PSCs. As in vitro myogenesis is decoupled from in vivo timing and the 3D-embryo structure, it remains difficult to definitively characterize what stage or type of muscle is modeled in culture. Here, gene expression profiling is analyzed in hPSCs over a 50 day skeletal myogenesis protocol and compared to gene expression datasets of other hPSC-derived skeletal muscle and adult murine satellite cells. Furthermore, day 2 cultures differentiated with high or lower concentrations of CHIR99021 were contrasted. Expression profiling of the 50 day time course identified successively expressed gene subsets involved in mesoderm/paraxial mesoderm induction, somitogenesis, and skeletal muscle commitment/formation which could be regulative by a putative cascade of transcription factors. Initiating differentiation with higher CHIR99021 concentrations resulted in significantly higher expression of MSGN1 and TGFB-superfamily genes, notably NODAL, resulting in enhanced paraxial mesoderm and reduced ectoderm/neuronal gene expression. Comparison to adult satellite cells revealed that genes expressed in day 50 cultures correlated better with those expressed by quiescent or early activated satellite cells, which have a greater therapeutic potential than late activated satellite cells. Day 50 cultures were similar to other hPSC-derived skeletal muscle and both expressed known and novel SMP surface proteins.

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Comparison of hPSCs-derived cholangiocyte-like cells with primary biliary tissue.

Project description:We established a step-wise protocol for the generation of human induced pluripotent stem cells (hPSCs) derived cholangiocyte-like cells (CLCs). The aim of this experiment was to provide in depth characterisation of the transcriptome of CLCs. These cells were compared with two of their in vitro progenitors, hPSCs and hepatoblasts (HBs), and to freshly isolated primary biliary tissue.

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