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Bulk RNA-seq of mouse cells from the dorsal cerebral cortex during its formation, with knocked-out Ski gene

ABSTRACT: From mice treated with knocked-out Ski gene. Dorsal cortices from embryonic day E11.5 to E18.5 were micro-dissected and dissociated into single cell suspensions using Papain and Ovo-mucoid mix. Cells were washed with L15 medium and FAC-sorted for GFP positive NSCs using FACSariaIII (BD Biosciences) derived from Hes5::GFP transgenic embryos for NSCs and Tbr2::GFP transgenic embryos for BPs and NBNs.

ORGANISM(S): Mus musculus

PROVIDER: GSE134690 | GEO | 2020/12/31

REPOSITORIES: GEO

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Bulk RNA-seq of mouse cells from the dorsal cerebral cortex during its formation

Project description:Dorsal cortices from embryonic day (E10.5) to postnatal day 1 (PN) were micro-dissected and dissociated into single cell suspensions using Papain and Ovo-mucoid mix. Cells were washed with L15 medium and FAC-sorted for GFP positive NSCs using FACSariaIII (BD Biosciences) derived from Hes5::GFP transgenic embryos for NSCs and Tbr2::GFP transgenic embryos for BPs and NBNs.

2020-12-31 | GSE134688 | GEO

Single-cell RNA-seq of mouse cells from the dorsal cerebral cortex during its formation

Project description:Dorsal cortices from embryonic day (E10.5) to postnatal day 3 (P3) were micro-dissected and dissociated into single cell suspensions using Papain and Ovo-mucoid mix. Cells were washed with L15 medium and FAC-sorted for GFP positive NSCs using FACSariaIII (BD Biosciences) derived from Hes5::GFP transgenic embryos for NSCs and Tbr2::GFP transgenic embryos for BPs and NBNs.

2020-12-31 | GSE134738 | GEO

Cistrome analysis of SKI and RUNX1 in HL60

Project description:SKI is a transcriptional co-regulator and overexpressed in various human tumors, for example in acute myeloid leukemia (AML). SKI contributes to the origin and maintenance of the leukemic phenotype. Here we use ChIP-seq and RNA-seq to identify the epigenetic alterations induced by SKI overexpression in AML cells. We show that approximately two thirds of differentially expressed genes are up-regulated upon SKI deletion, of which nearly 50% harbour SKI binding sites in their proximity, primarily in enhancer regions. Gene ontology analysis reveals that many of the differentially expressed genes are annotated to hematopoietic cell differentiation and inflammatory response, corroborating our finding that SKI deletion causes a release of the myeloid differentiation block in HL60 cells. We find that SKI peaks are enriched for RUNX1 consensus motifs, particularly in up-regulated SKI targets. RUNX1 ChIP-seq demonstrates that nearly 70% of RUNX1 binding sites overlap with SKI peaks, mainly at enhancer regions. SKI and RUNX1 co-occupy the same genomic sites and cooperate in gene silencing. Our work demonstrates for the first time on a genome-wide scale the predominant co-repressive function of SKI in AML cells and uncovers the transcription factor RUNX1 as an important mediator of SKI-dependent transcriptional repression.

2018-02-07 | GSE107553 | GEO

SK-NEP-1 treated with SKI-5C

Project description:Wilm’s tumor(WT) is the most common malignant renal tumor in children, representing approximately 6-14% of all childhood cancers and about 95% of all pediatric renal malignancies. SKI-5C is a newly developed Sphk1 inhibitor. This small molecular inhibitor was firstly reported at 2009 by Wang et al. This study investigated the antitumor activity of SKI-5C in SK-NEP-1 cells. SKI-5C inhibited cell proliferation of SK-NEP-1 cells in a dose-dependent manner. Annexin V, Tunel and Hochest 33342 staining analysis showed that SKI-5C-treated cells showed more apoptotic features compared with the control.

2016-12-31 | GSE72980 | GEO

Transcriptome analysis of SKI knock-out in HL60 cells

Project description:Whole transcriptome for SKI knock-out and control HL60 cells was sequenced. SKI control and knockout samples were compared to find differentially expressed genes. Differentially expressed genes were further analysed to find the significance of SKI in HL60 cells.

2018-02-07 | GSE107555 | GEO

Reversing SKI–SMAD4-mediated suppression is essential for TH17 cell differentiation

Project description:Disruption of Ski/Smad4 license Th17 differentiation. TGF-b-Ski-Smad4-RORgt-Th17 axis

2017-10-25 | GSE101527 | GEO

Differentiation of Mammary Tumors by SKI-606 (bostutinib) (illumina)

Project description:While c-Src is infrequently mutated in human cancers, it mediates oncogenic signals of many activated growth factor receptors and thus remains a key potential target of cancer therapy. However, the widespread function of Src in many cell types and processes requires evaluation of Src-targeted therapeutics within a normal developmental and immune competent environment. In an effort to direct clinical use of Src inhibitors, we tested the effectiveness of one of the four Src inhibitors in clinical testing, SKI-606 (bosutinib), in the MMTV-PyVmT transgenic mouse model of breast cancer. Tumor formation in this model is dependent on the presence of Src, but the necessity of Src kinase activity for tumor formation has not been determined. Furthermore, Src inhibitors have not been examined in an autochthonous tumor model. Here we show that oral administration of the Src inhibitor SKI-606 inhibited the phosphorylation of Src in mammary tumors, and caused a rapid decrease in the Ezh2 Polycomb group histone H3K27 methyltransferase and an increase in epithelial organization. SKI-606 prevented the appearance of palpable tumors in more than half of the animals treated from puberty and stopped tumor growth in older animals with preexisting tumors. These antitumor effects were accompanied by decreased cellular proliferation, altered tumor blood vessel organization and dramatically increased differentiation to lactational and epidermal cell fates. SKI-606 controls the development of mammary tumors in this model by inducing differentiation. Differentiation of Mammary Tumors by SKI-606 (bostutinib)

2010-09-15 | E-GEOD-20921 | biostudies-arrayexpress

Differentiation of Mammary Tumors by SKI-606 (bostutinib) (gene expression)

2011-01-01 | E-GEOD-22150 | biostudies-arrayexpress

Reversing SKI–SMAD4-mediated suppression is essential for TH17 cell differentiation [ChIP-seq]

Project description:Disruption of Ski/Smad4 license Th17 differentiation. TGF-b-Ski-Smad4-RORgt-Th17 axis

2017-10-25 | GSE101593 | GEO

The Ski complex binds 80S ribosomes for 3’ to 5’ decay of mRNA

Project description:Cytoplasmic degradation of eukaryotic mRNAs in 3’ to 5’ direction is catalyzed by the exosome complex together with the Ski complex and, in the yeast Saccharomyces cerevisiae, the Ski7 protein. This exosome-Ski-system also degrades ribosome-associated aberrant mRNAs lacking a stop codon, a pathway called non-stop-mRNA decay (NSD). However, the interplay between the Ski components and the ribosome is unknown. Here, we report that the Ski complex can associate with ribosomes in vitro and in vivo independently of Ski7. Ribosome profiling suggests that this association is important for NSD but also for general mRNA turnover. A cryo-electron microscopy structure reveals that the Ski complex binds near the mRNA entry site of the 40S subunit, facilitating the threading of the mRNA into the Ski2 helicase. Collectively, these results demonstrate an unanticipated role for the Ski complex in mRNA decay of ribosome-associated mRNAs, mediated by a direct interaction with the translation machinery.

2017-02-10 | GSE70259 | GEO

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