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TrxG complex catalytic and non-catalytic activity play distinct roles in pancreas progenitor specification and differentiation (E13.5 Dpy30∆P pancreas scRNA-Seq)

ABSTRACT: TrxG complex catalytic and non-catalytic activity play distinct roles in pancreas progenitor specification and differentiation (E13.5 Dpy30∆P pancreas scRNA-Seq)

PROVIDER: PRJNA554148 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR9672880.fastq.gz	Fastqsanger.gz
	SRR9672881.fastq.gz	Fastqsanger.gz

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TrxG complex catalytic and non-catalytic activity play distinct roles in pancreas progenitor specification and differentiation (E13.5 Dpy30∆P pancreas scRNA-Seq)

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

TrxG complex catalytic and non-catalytic activity play distinct roles in pancreas progenitor specification and differentiation (E18.5 Dpy30∆P pancreas scRNA-seq)

Project description:Purpose: To gain insight into why Dpy30∆P acinar cells fail to express terminal makers, we performed scRNA-seq using E18.5 control and Dpy30∆P pancreata. 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 8,050 control and 7,858 Dpy30∆P cells that with the E13.5 scRNA-seq data allowed us to identify 2,207 control and 2,354 Dpy30∆P epithelial cells. We found a cluster that contained almost entirely Dpy30∆P cells, where the expression of acinar cell digestive enzymes was consistently low. The distribution of gene expression values for terminal acinar markers suggested an increased distribution in gene expression levels in the Dpy30∆P cells relative to control cells; however, this was not the case for terminal endocrine markers. Comparing the variance-to-mean ratios in the Dpy30∆P and control cells showed an increase in variance in the Dpy30∆P acinar cells but not in endocrine cells. Conclusions: Overall, these data suggest increased variation in acinar cell transcript expression in the Dpy30∆P pancreas.

2019-07-12 | GSE134181 | GEO

TrxG complex catalytic and non-catalytic activity play distinct roles in pancreas progenitor specification and differentiation (E18.5 Dpy30∆P pancreas)

Project description:Purpose: To gain insight into why Dpy30∆P acinar cells fail to express terminal makers, we performed RNA-seq using E18.5 control and Dpy30∆P pancreata. 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: Differential gene expression analysis demonstrated that endocrine cell hormones such as Ins2 and acinar cell digestive enzymes were downregulated in the E18.5 Dpy30∆P pancreas compared to controls. GO term analysis indicated that genes involved in pancreatic secretion, digestion and proteolysis were reduced in Dpy30∆P cells. Notably, transcripts with very high expression levels (above 9000 FPKM) were more downregulated in the E18.5 Dpy30∆P pancreas compared to transcripts with lower expression levels. Conclusions: Overall, these data suggest increased variation in acinar cell transcript expression in the Dpy30∆P pancreas.

2019-07-12 | GSE134180 | GEO

TrxG complex catalytic and non-catalytic activity play distinct roles in pancreas progenitor specification and differentiation (E18.5 Dpy30∆P pancreas)

Project description:TrxG complex catalytic and non-catalytic activity play distinct roles in pancreas progenitor specification and differentiation (E18.5 Dpy30∆P pancreas)

| PRJNA554149 | ENA

TrxG complex catalytic and non-catalytic activity play distinct roles in pancreas progenitor specification and differentiation (shWdr5 lentivirus treated spheres )

Project description:Purpose: To determine the genome-wide effect of Wdr5 and Dpy30 suppression on acinar, duct and endocrine gene activation during pancreas spheroid differentiation Methods: We adapted an ex vivo mouse E13.5 pancreas spheroid model of growth and differentiation (Sugiyama et al., 2013) and generated RNA-sequencing data from pooled shScramble, shWdr5 and shDpy30 spheroids. Results: We identified 1,744 genes whose expression was substantially impaired and 693 genes with increased expression in shWdr5-treated spheres compared to shScramble controls. In shDpy30-treated spheres, we identified no genes with impaired expression and only 2 genes with increased expression compared to shScramble controls. Genes expressed in pancreas progenitors were largely not altered by either Wdr5 or Dpy30 suppression. However, genes expressed in the endocrine (Gcg, Ins1, Ins2 and Neurog3) and acinar (Cpa1, Cpa2 and Amy2) lineages had dramatically reduced expression in shWdr5-treated spheres, but were unaffected by Dpy30 suppression. Conclusions: These data suggest that the co-activator activity of the TrxG complexes and not their methyltransferase activity, is required for acinar and endocrine cell gene activation in an ex vivo model of pancreas development.

2019-07-12 | GSE134183 | GEO

TrxG complex catalytic and non-catalytic activity play distinct roles in pancreas progenitor specification and differentiation (shDpy30 lentivirus treated spheres)

2019-07-12 | GSE134182 | GEO

TrxG complex catalytic and non-catalytic activity play distinct roles in pancreas progenitor specification and differentiation (E18.5 Dpy30∆P pancreas scRNA-seq)

Project description:TrxG complex catalytic and non-catalytic activity play distinct roles in pancreas progenitor specification and differentiation (E18.5 Dpy30∆P pancreas scRNA-seq)

| PRJNA554150 | ENA

TrxG complex catalytic and non-catalytic activity play distinct roles in pancreas progenitor specification and differentiation

Project description:TrxG complex catalytic and non-catalytic activity play distinct roles in pancreas progenitor specification and differentiation

| PRJNA554147 | ENA

TrxG complex catalytic and non-catalytic activity play distinct roles in pancreas progenitor specification and differentiation (shDpy30 lentivirus treated spheres)

Project description:TrxG complex catalytic and non-catalytic activity play distinct roles in pancreas progenitor specification and differentiation (shDpy30 lentivirus treated spheres)

| PRJNA554151 | ENA

TrxG complex catalytic and non-catalytic activity play distinct roles in pancreas progenitor specification and differentiation (shWdr5 lentivirus treated spheres )

Project description:TrxG complex catalytic and non-catalytic activity play distinct roles in pancreas progenitor specification and differentiation (shWdr5 lentivirus treated spheres )

| PRJNA554152 | ENA

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