Whole transcriptome analysis of Sox17.Epi and Endo cells in mouse embryos
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Project description:This experiment has been done to understand the dynamics of gene expression in Sox17.Epi and Endo cells using multiplex RNA-Seq technology. Sox17.Epi (Sox17^GFP+EpCAM+) and Sox17.Endo (Sox17^GFP+EpCAM-) cells were isolated by FACS from E9.5 mouse embryos. The spatial comparison between Sox17.Epi versus Sox17.Endo provides insight into which genes are differentially of specifically expressed in two populations.
2012-07-20 | E-MTAB-970 | biostudies-arrayexpress
Project description:SOX17 activity in the uterine epithelium is essential for the implantation of mouse embryos. Previously, we demonstrated that female Sox17-heterozygous mutant mice are subfertile, and two active copies of Sox17 are required for the proper implantation of mouse embryos. To understand which implantation step is most sensitive to the Sox17 gene dosage, we comprehensively investigated the RNA transcriptomes of Sox17-heterozygous mutant mice.
2020-03-10 | GSE146630 | GEO
Project description:Transcription profiling by high throughput sequencing of Sox17.Epi and Endo cells from mouse embryos
2019-05-15 | E-MTAB-970 | ExpressionAtlas
Project description:The onset of the liver inflamentation in the Sox17+/- embryos. The expression of Cxcl10, Cxcl2, Cxcl1 and stress-induced heat shock protein Hspa1a and Hspa1b were elevated in Sox17+/- livers at 17dpc, as compared with the wildtype livers. Total RNAs from liver tissues of wildtype and Sox17+/- mice at 17dpc were subjected to microarray analyses. Two biological replicates of each genotype were analyzed.
2013-01-09 | E-GEOD-33106 | biostudies-arrayexpress
Project description:The onset of the liver inflamentation in the Sox17+/- embryos. The expression of Cxcl10, Cxcl2, Cxcl1 and stress-induced heat shock protein Hspa1a and Hspa1b were elevated in Sox17+/- livers at 17dpc, as compared with the wildtype livers.
2013-01-09 | GSE33106 | GEO
Project description:We identified and characterized a rice epigenetic mutant Epi-df which exhibits a dwarf stature and various floral defects that are inherited in a dominant fashion. We demonstrated that Epi-df participates in Polycomb repressive complex 2 (PRC2) mediated gene silencing. Epigenetic mutations results in ectopic expression of Epi-df and pleiotropic developmental defects in mutant plants. Moreover, ectopic expression of Epi-df leads to mis-regulated H3K27me3 and changed expression of hundreds of genes involved in a wide range of biological processes. We used microarrays to identify differentially expressed genes in Epi-df. For genome-wide expression analysis of Epi-df, three replicates of WT and Epi-df samples (RNA from 3-week-old seedlings) were analyzed on Affymetrix Genechip® Rice Genome arrays by an Affymetrix service facility (CapitalBio Corporation) according to the manufacturer’s protocols. Genes showing a 2-fold change with a q-value ≤ 0.05 were considered to be differentially expressed.
2012-07-12 | E-GEOD-39298 | biostudies-arrayexpress
Project description:To determine the effect of Sox17 overexpression in mouse embryonic stem (ES) cells, we performed gain-of-function analysis by generating ES cell lines carrying a doxycycline inducible FLAG-tagged Sox17 transgene. We treated Sox17-inducible ES cells with doxycycline, collected RNA and performed genome-wide transcriptional analysis. We found that genes invovled in adhesion function and basement membrane establishment were transcriptionally upregulated in ES cells upon induction of Sox17. We also observed downregulation in the transcription of genes involved in pathways known to be functionally important for ES cell pluripotency and self-renewal. However, Sox17 expression was not sufficient to rapidly down-regulate Sox2, Nanog, and Oct4. Two independent doxycycline inducible Sox17-overexpressing mouse embryonic stem cells were derived. The genes expression changes in the Sox17-induced cells were compared to untreated (no doxycycline) controls and to control cells treated with or without doxycycline. The total RNA from these samples were amplified using Ambion Illumina TotalPrep RNA Amplification kit and arrayed on Illumina MouseRef8 v2 chips.
2010-03-31 | E-GEOD-19028 | biostudies-arrayexpress
Project description:To determine the effect of Sox17 overexpression in mouse embryonic stem (ES) cells, we performed gain-of-function analysis by generating ES cell lines carrying a doxycycline inducible FLAG-tagged Sox17 transgene. We treated Sox17-inducible ES cells with doxycycline, collected RNA and performed genome-wide transcriptional analysis. We found that genes invovled in adhesion function and basement membrane establishment were transcriptionally upregulated in ES cells upon induction of Sox17. We also observed downregulation in the transcription of genes involved in pathways known to be functionally important for ES cell pluripotency and self-renewal. However, Sox17 expression was not sufficient to rapidly down-regulate Sox2, Nanog, and Oct4.
2010-03-31 | GSE19028 | GEO
Project description:As Sox17 plays a critical role in the development of multiple cell types during early embryogenesis, we utilized a dual-color lineage-tracing strategy in combination with single-cell RNA sequencing (scRNAseq) to capture and analyze Sox17-expressing lineages. GFP production from Sox17GFPCre allele marks cells that currently express Sox17 or short-term progeny of Sox17 expressing progenitors. TdTomato production from R26LSL.TdTomato reporter allele in the presence of Sox17GFPCre marks long-term progeny of Sox17-expressing progenitors. In brief, GFP and Tdtomato positive cells were isolated from E9.5 embryos of specific genotypes to generate two separate scRNAseq datasets, referred to in the manuscript as the GFP and TdTomato datasets, respectively.
2023-07-20 | E-MTAB-12719 | biostudies-arrayexpress
Project description:We identified and characterized a rice epigenetic mutant Epi-df which exhibits a dwarf stature and various floral defects that are inherited in a dominant fashion. We demonstrated that Epi-df participates in Polycomb repressive complex 2 (PRC2) mediated gene silencing. Epigenetic mutations results in ectopic expression of Epi-df and pleiotropic developmental defects in mutant plants. Moreover, ectopic expression of Epi-df leads to mis-regulated H3K27me3 and changed expression of hundreds of genes involved in a wide range of biological processes. We used microarrays to identify differentially expressed genes in Epi-df.
2012-07-13 | GSE39298 | GEO