Genes regulated by pharmacological Wnt activation by CHIR99021 in the embryonic mouse cochlea
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ABSTRACT:
PROVIDER: PRJNA1077987 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR28006918_1.fastq.gz | Fastqsanger.gz | |||
| SRR28006918_2.fastq.gz | Fastqsanger.gz | |||
| SRR28006919_1.fastq.gz | Fastqsanger.gz | |||
| SRR28006919_2.fastq.gz | Fastqsanger.gz | |||
| SRR28006920_1.fastq.gz | Fastqsanger.gz |
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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.
2024-03-01 | GSE256069 | GEO
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.
2013-01-01 | GSE40959 | GEO
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
Project description:Purpose: Wnt activation can induce regeneration in the early postnatal cochlea, but the regenerative capacity of the postnatal cochlea diminishes between P0 to P5. The goal of this study was to utilize RNA-Seq for the overall evaluation of expression patterns, comparing P1 and P4 newborn cochlea with and without Wnt activation. Methods: Sox2-CreER; β-cateninflox(Exon3)/+ mice were used to stabilize β-catenin in Sox2+ cochlear supporting cells. Tamoxifen was injected to the mother at either P1 or P4 to induce Cre activation in the pups. mRNA libraries were generated from treated and untreated pups 3 days after injection in triplicates (overall 12 samples) using ThruPLEX DNA-seq kit (Rubicon Genomics) and then sequenced using Illumina NextSeq500 Single-End 75bp. Reads were aligned to mm10 and quality control was assessed using FastQC and Qualimap followed by FeatureCounts, Sailfish v0.10.1 and tximport. Differential expression was evaluated using DESeq2 and subsequent pathway analysis was performed using Ingenuity Pathway Analysis Software (Qiagen). Results: 40-50 million reads were detected per sample. PCA and Pearson correlation demonstrated a clear segragation of the samples by age that was supported by the identification of 2914 differentially expressed genes between P1 and P4 samples. Additional affect of treatment resulted is 530 differentially expressed genes between treated and untreated samples at P1 and 304 genes were differentially expressed between treated and untreated samples at P4. Clear activation of the Wnt pathway was apparent at both time-points after treatment. However, activation of downstream pathways that may be involved in regeneration was detected at P1 but not at P4, mainly the involvement of cell-cycle and proliferation as well as Erbb2 associated genes. Conclusions: Our results suggest that the Wnt pathway is still active and can be further induced at early and late postnatal stages in a similar manner. However, at early stages, exogenous Wnt activation potentially promotes an arrest of maturation progression or even partial dedifferentiation of supporting cells into a less mature state that enables regeneration, while the downstream affect is not as prominenet later on. Proliferative capacity in the early postnatal cochlea is correlated with a unique transcriptional response that diminishes in the older cochlea, including a robust increase in the expression of cell cycle genes and cellular growth and development genes. Our results suggest that the downstream transcriptional response to Wnt activation is the key factor mediating a regenerative response, or a lack-thereof, in the mammalian cochlea and that efforts to stimulate regeneration in the adult auditory organ may require recapitulating the transcriptional response of the early neonatal cochlea to exogenous Wnt activation and subsequent alterations of silenced state of Wnt target genes. .
2018-12-01 | GSE113719 | GEO
Project description:NOTUM-MEDIATED WNT SILENCING DRIVES EXTRAVILLOUS TROPHOBLAST CELL LINEAGE DEVELOPMENT [CHIR99021]
| PRJNA848827 | ENA
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.
2019-12-25 | GSE142572 | GEO
Project description:Our work describes the application of mass spectrometry-based label-free quantitative proteomics for the identification of differentially expressed proteins between different-aged cochlea. We report proteins exclusively present as well as up- and downregulated in the cochlear sensory epithelium at significant developmental stages. Additionally, we report proteins exclusively present on P3 that were recently identified in the cochlea for the first time. We use bioinformatics to provide insight on biological functions and potential primary and secondary partners of the differentially expressed proteins. This study provides the first differentially expressed proteome in the mammalian cochlea at significant developmental stages; before hearing, during the onset of hearing, and when hearing is fully developed. We believe that these results will provide insights into the function of proteins that change during development and identify potential protein biomarkers related to hearing impairments.
2018-08-29 | PXD001973 | Pride
Project description:The aim of this study was to unravel the effects of an initial WNT/β-catenin pulse on the in vitro differentiation of human iPSCs towards mesodermal progenitors and subsequent specification of chondrocytes. Therefore, mesodermal progenitors were generated from hiPSCs according to standard protocol (ctrl) or treated with 5 µM WNT/β-catenin agoinst CHIR99021 for 24h. To understand the long-term effects of short-initial WNT pulse on mesodermal differentiation, the global gene expression profile of day 14 mesodermal progenitors was compared.
2020-12-31 | E-MTAB-9226 | biostudies-arrayexpress
Project description:Presomitic mesoderm (PSM) cells are the precursors of the somites, which flank both sides of the neural tube and give rise to the musculo-skeletal system shaping the vertebrate body. WNT and FGF signalling control the formation of both the PSM and the somites, and show a graded distribution with highest levels in the posterior PSM. We have employed reporter for the PSM control gene Tbx6 to investigate the differentiation of mouse ESCs from the naĂŻve state to PSM state. Feeder-free ESCs were seeded and grown on fibronectin (3-5 ng/ml)-coated plates in ESC medium containing LIF, PD0325901 and CHIR99021 (2i medium) to bring them to a naive state of pluripotency. Following this, the cells were brought to an EpiSC state by treating them with Activin A and FGF2. The EpiSC-like cells were then differentiated to PSM using CHIR99021 either alone or along with FGF ligands, FGF2 or FGF8 (Low concentration: 10 ng/ml or High concentration: 250ng/ml).
2016-06-01 | E-MTAB-3784 | biostudies-arrayexpress
Project description:WNT activated signal transduction is a conserved regulator of morphogenesis of many organ systems, including the placenta. In human trophoblast stem (TS) cells, activation of canonical WNT signaling is a key to maintenance of the TS cell stem state. NOTUM, a negative regulator of canonical WNT signaling, was prominently expressed in first trimester EVT cells developing in situ and upregulated in EVT cells derived from human TS cells. Furthermore, NOTUM was required for human TS cell differentiation to EVT cells. Canonical WNT signaling is essential for maintaining human trophoblast cell stemness and prevention of human TS cell differentiation. Downregulation of canonical WNT signaling via the actions of NOTUM is required for EVT cell differentiation.
2024-03-06 | GSE206034 | GEO