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Single cell RNA sequencing of mouse embryonic fibroblasts in autophagy processes

ABSTRACT: Single cell RNA sequencing of mouse embryonic fibroblasts in autophagy processes

PROVIDER: PRJNA784263 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR17055656.fastq.gz	Fastqsanger.gz
	SRR17055657.fastq.gz	Fastqsanger.gz
	SRR17055658.fastq.gz	Fastqsanger.gz
	SRR17055659.fastq.gz	Fastqsanger.gz
	SRR17055660.fastq.gz	Fastqsanger.gz

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Mouse embryonic fibroblasts in autophagy processes

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Project description:Autophagy, a catabolic process to remove unnecessary or dysfunctional cells, is triggered by various signals including nutrient starvation. Depending on the type of the nutrient deficiency, diverse sensing mechanisms and pathways are used for autophagy, suggesting subsequent nutrient dependent transcriptional regulation. Still, however, our knowledge about nutrient specific transcriptional regulation during autophagy is limited. To understand nutrient type dependent transcriptional mechanisms during autophagy, we performed single cell RNA sequencing (scRNAseq) for the mouse embryonic fibroblasts (MEFs) before and after applying glucose- (GS) as well as amino acid starvation (AAS). Trajectory analysis using scRNAseq identified sequential induction of potential transcriptional regulators for each deficiency condition. Gene regulatory rules inferred using TENET newly identified CCAAT/enhancer binding protein γ (C/EBPγ) regulates autophagy processes specifically to AAS condition. Strikingly, knockdown of C/EBPγ attenuated the autophagic process only in the AAS condition. Cell biological and biochemical studies validated that C/EBPγ plays a switching role for ATF4 to activate autophagy genes under AAS, but not under GS. Together, our data identified C/EBPγ as a previously unidentified key regulator under amino acid starvation-induced autophagy.

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Metabolomics Workbench ST000003 - GNPS - Metabolomic analysis of mouse embryonic fibroblasts, embryonic stem cells, and induced pluripotent stem cells

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Mouse embryonic fibroblasts in autophagy processes

Project description:This SuperSeries is composed of the SubSeries listed below.

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Efficacy of Single Incision (Embryonic NOTES) Laparoscopic Colorectal Surgery

Project description:Laparoscopic colon surgery has been performed widely. As a minimal invasive approach, single incision (Embryonic NOTES) colon surgery has been attempted. However, there are not sufficient evidences for single incision colon surgery in colon cancer. The investigators are researching the efficacy and safety of single incision laparoscopic sigmoidectomy in sigmoid colon cancer.

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T-cell intracellular antigen (TIA) proteins deficiency in murine embryonic fibroblasts alters cell cycle progression and induces autophagy

Project description:Background: Mice lacking either T-cell intracellular antigen 1 (TIA1) or TIA1-related/like protein (TIAR/TIAL1) show high rates of embryonic lethality, suggesting a relevant role for these proteins during embryonic development. However, intrinsic molecular and cellular consequences of either TIA1 or TIAR deficiency remain poorly defined. Results: By using genome-wide expression profiling approach, we demonstrate that either TIA1 or TIAR inactivation broadly alter normal development-associated signaling pathways in murine embryonic fibroblasts (MEF). Indeed, these analyses highlighted alterations of cytokine-cytokine and ECM-receptor interactions and Wnt, MAPK, TGF-beta dependent signaling pathways. Consistent with these results, TIA1 and TIAR knockout (KO) MEF show reduced rates of cell proliferation, cell cycle progression delay and increased cell size. Furthermore, TIA-proteins deficiency also caused metabolic deficiencies, increased ROS levels and DNA damage, promoting a gentle rise of cell death. Concomitantly, high rates of autophagy were detected in both TIA1 and TIAR KO MEF with induction of the formation of autophagosomes, as evidenced by the up-regulation of the LC3B protein, and autolysosomes, measured by colocalization of LC3B and LAMP1, as a survival mechanism attempt. Conclusions: Taken together, these observations support that TIA proteins orchestrate a transcriptome programme to activate specific developmental decisions. This program is likely to contribute to mouse physiology starting at early stages of the embryonic development. TIA1/TIAR might function as cell sensors to maintain homeostasis and promote adaptation/survival responses to developmental stress. Two independent replicates were performed for each experimental condition and hybridized to Agilent SurePrint G3 Mouse 8x60 microarrays.

2014-11-05 | E-GEOD-43077 | biostudies-arrayexpress

Expression data from mouse embryonic fibroblasts

Project description:Expression data from mouse embryonic fibroblasts

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Gene expression from Mouse Embryonic Fibroblasts

Project description:Gene expression from Wild-type and NFAT5 knock-out Mouse Embryonic Fibroblasts keywords: Mouse Embryonic Fibroblasts

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