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Bulk RNA sequencing of mouse embryonic fibroblasts in autophagy processes

ABSTRACT: Bulk RNA sequencing of mouse embryonic fibroblasts in autophagy processes

PROVIDER: PRJNA822101 | ENA |

REPOSITORIES: ENA

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Mouse embryonic fibroblasts in autophagy processes

Project description:Mouse embryonic fibroblasts in autophagy processes

| PRJNA822093 | ENA

Bulk RNA sequencing of mouse embryonic fibroblasts in autophagy processes

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.

2022-04-04 | GSE199923 | GEO

Single cell RNA sequencing of mouse embryonic fibroblasts in autophagy processes

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

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Single cell RNA sequencing of mouse embryonic fibroblasts in autophagy processes

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

Project description:mouse embryonic fibroblasts, embryonic stem cells, and induced pluripotent stem cells were compared via metabolomic analysis

2018-08-02 | MSV000082680 | GNPS

Metabolomic analysis of mouse embryonic fibroblasts, embryonic stem cells, and induced pluripotent stem cells

Project description:mouse embryonic fibroblasts, embryonic stem cells, and induced pluripotent stem cells were compared via metabolomic analysis

2013-01-16 | ST000003 | MetabolomicsWorkbench

Mouse embryonic fibroblasts in autophagy processes

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

2022-04-01 | GSE199924 | GEO

Bulk mRNA sequencing of wildtype (WT) and mutator mouse embryonic fibroblasts (MEFs)

Project description:Bulk mRNA sequencing of wildtype (WT) and mutator mouse embryonic fibroblasts (MEFs)

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Bulk ATAC-seq data of fibroblasts from healthy mouse tissues

Project description:Bulk ATAC-seq was performed on fibroblasts from 8 different healthy mouse tissues such as bone, epididymal and inguinal fat pads, omentum, liver, lung and lymph node. This data was used to examine tissue specific chromatin landscapes in fibroblasts.

2021-05-04 | E-MTAB-10316 | biostudies-arrayexpress

Quantification of PIPs species in LPIAT1 KO mouse embryonic fibroblasts (MEFs).

Project description:Using a supercritical fluid chromatography-mass spectrometry (SFC-MS)-based methodology, we quantified phosphoinositides (PIPs) species in LPIAT1 KO mouse embryonic fibroblasts (MEFs).

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