Single cell seq of E13.5 and E15.5 pancreas of Setd2 WT and KO mice [scRNA-seq]
Ontology highlight
ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE218739 | GEO | 2023/12/22
REPOSITORIES: GEO
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Project description:Jarid2, a member of the Jumanji family of proteins, is a developmental regulator that is necessary for proper mouse development and stem cell differentiation. To investigate the specific functions of Jarid2 during pancreas development, we generated pancreas-specific Jarid2 mutants. We used microarrays to determine gene expression changes resulting from deletion of the Jarid2 gene in the pancreas.
2017-09-26 | GSE77238 | GEO
Project description:Purpose: This study aimed at exploring the deregulated genes in setd2 knockout mESCs compared with wt, more particularly to find the mechanism controlled by setd2,which was required for endoderm differentiation. Methods: Setd2 wt and ko mESCs were generated by deep sequencing, using Illumina GAIIx. Using Avadis NGS (version:1.3) software to analyze the sequence reads that passed quality filter to acquire the expression level of all genes. qRT–PCR validation was performed usingSYBR Green assays. Results: Using an optimized data analysis workflow, we mapped about 80 million sequence reads per sample to the mouse genome (build mm9) and identified 17,827 transcripts in the sted2 wt and ko mESCs. About 2,516 genes were deregulated in setd2 ko mESCs, more than 10 genes were validated using qRT-PCR. Conclusions: Through RNA-seq,we noticed that a subset of genes that related to MAPK signaling pathways were down-regulated in ko mESCs. This provided a bridge to connect setd2 and mESCs endoderm differentiation. One wt and one ko mESCs were generated by deep sequencing, using Illumina GAIIx.
2014-10-14 | E-GEOD-54932 | biostudies-arrayexpress
Project description:Patients with polycystic kidney disease (PKD) encounter a high risk of clear cell renal cell carcinoma (ccRCC), a malignant tumor with dysregulated lipid metabolism. SET domain–containing 2 (SETD2) has been identified as an important tumor suppressor gene in ccRCC. However, the role of SETD2 in tumorigenesis during the transition from PKD to ccRCC remains largely unexplored. Herein, we performed metabolomics, lipidomics, transcriptomics and proteomics with SETD2 loss induced PKD-ccRCC transition mouse model. To characterize biological responses triggered by SETD2 deletion during PKD-ccRCC transition at the protein level, we conducted global proteomics studies.
2023-10-31 | PXD038966 | Pride
Project description:RNA sequencing of SETD2 isogenic renal cell carcinoma cell lines. Examination of RNA expression in SETD2 isogenic cell lines
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Project description:To gain mechanistic insight into how Setd2 loss promotes activation of AKT signaling, we performed CUT&Tag sequencing in PDAC cells (KPC1199) with Setd2-KO and Setd2-WT). Setd2-WT and -KO murine PDAC cells were cultured and freshly collected as soon as possible. Hyperactive pA-Tn5 Transposase for CUT&Tag kit from Vazyme (TD901), and antibodies against H3K36me3 and H3K27me3 were employed. Trueprep index kit v2 and v3 for illumina were used to establish DNA library.
2023-02-06 | GSE176013 | GEO
Project description:Purpose: This study aimed at exploring the deregulated genes in setd2 knockout mESCs compared with wt, more particularly to find the mechanism controlled by setd2,which was required for endoderm differentiation. Methods: Setd2 wt and ko mESCs were generated by deep sequencing, using Illumina GAIIx. Using Avadis NGS (version:1.3) software to analyze the sequence reads that passed quality filter to acquire the expression level of all genes. qRT–PCR validation was performed usingSYBR Green assays. Results: Using an optimized data analysis workflow, we mapped about 80 million sequence reads per sample to the mouse genome (build mm9) and identified 17,827 transcripts in the sted2 wt and ko mESCs. About 2,516 genes were deregulated in setd2 ko mESCs, more than 10 genes were validated using qRT-PCR. Conclusions: Through RNA-seq,we noticed that a subset of genes that related to MAPK signaling pathways were down-regulated in ko mESCs. This provided a bridge to connect setd2 and mESCs endoderm differentiation.
2014-10-14 | GSE54932 | GEO
Project description:RNA sequencing was used to identify gene expression changes in the pancreas of E13.5 Prox1-nullyzygous mouse embryos.
2022-06-01 | GSE178173 | GEO
Project description:Purpose: To investigate whether pancreas progenitor specification may be altered, we performed single-cell RNA-sequencing (scRNA-seq) using E13.5 control and Dpy30∆P pancreas. To determine whether Dpy30∆P cells have a different developmental trajectory than control cells, we performed pseudo-temporal analysis (Trapnell et al., 2014). Methods: Floxed Dpy30 mice were crossed to Pdx1-Cre driver mice to obtain conditional deletion of Dpy30 exon 4 in the pancreas. In all studies, knockout mice (Dpy30∆P, Pdx1-Cre; Dpy30flox/flox) were compared to littermate controls (Dpy30flox/flox or Dpy30flox/wt). Results: In total, we sequenced 3,900 control and 3,044 Dpy30∆P cells from which 786 control and 477 Dpy30∆P epithelial cells were identified for further analysis. As expected, control progenitor cells gave rise to cells in two distinct branches corresponding to the acinar and endocrine lineages, with terminal markers upregulated in cells at the ends of these branches. Dpy30∆P progenitors differentiated along these same trajectories; however, relatively few Dpy30∆P cells were found at the ends of these branches, and acinar and endocrine terminal marker expression was reduced in Dpy30∆P cells. Interestingly, a higher fraction of Dpy30∆P cells were found within the MPC/BPC and acinar clusters, predominantly at the expense of endocrine cells. Analyzing the fraction of cells in G1 phase across pseudo-time showed that a higher fraction of Dpy30∆P acinar lineage cells were in G1 phase. Conclusions: Overall, this suggests that MPC/BPCs and acinar cells may have a prolonged G1 phase due to a failure to appropriately induce genes essential for progression through G2M or S phase.
2019-07-12 | GSE134179 | GEO
Project description:SETD2/HYPB has been known as a histone H3K36 specific methyltransferase. However, its roles in physiology such as development and cellular function remain unclear. In this study, using mESCs as cellular model, we show that Setd2 mainly regulates differentiation of murine embryonic stem cells (mESCs) towards primitive endoderm. This study aimed at exploring how did Setd2 regulate primitive endoderm. differentiation. We used microarrays to detail the global programme of gene expression controled by setd2, which is required for endoderm differentiation. Wild type and Setd2 knockout mESCs were selected for RNA extraction and hybridization on Affymetrix GeneChip® mouse genome 430 2.0 arrays. We sought to obtain some deregulated genes, which were required for primitive endoderm differentiation. For comparison, three biological repeats of each were performed.
2014-10-14 | E-GEOD-54931 | biostudies-arrayexpress