Whole transcriptomes analyses of organoids derived from Mist1Cre/ERT2 and Gpx4F/F Mist1Cre/ERT2 mice corpus
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ABSTRACT:
PROVIDER: PRJNA1162416 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
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| SRR30709217_1.fastq.gz | Fastqsanger.gz | |||
| SRR30709217_2.fastq.gz | Fastqsanger.gz |
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Project description:Whole transcriptomes analyses of organoids derived from Mist1Cre/ERT2 mice corpus with oxidative stress
| PRJNA1241869 | ENA
Project description:Purpose: To explore the molecular mechanisms of Mist1+ cells that are specifically resistance to oxidative stress, and the mechanism that oxidative stress in regulating the stemness of Mist1+ cells, RNA sequencing was performed to analyze the geome-wide change of Mist1+ cells under oxidative stress (high fat diet or Gpx4 knockout) compared with control mice, and further the difference between these two Mist1+ cells. Methods: Total mRNA was extracted from Mist1+ cells which were isolated from corpus of Mist1Cre/ERT2;RFPLSL mice (8 weeks) fed with normal diet and high fat diet. Besides, we formed Mist1+ organoids from Mist1Cre/ERT2;RFPLSL mice and Gpx4F/F;Mist1Cre/ERT2;RFPLSL mice respectively, organoids were passaged, and total mRNA was extracted from organoids in passage 5, 10 and 15. Then RNA quality was assessed using an Agilent Bioanalyzer 2100 and the sample reads were sequenced using Illumina NovaSeq 6000 platform. Results: Our results revealed differentially expressed genes in Mist1+ cells from high fat diet-fed mice compared with normal diet-fed mice. Further KEGG analysis enriched multiple pathways/biological processes including ROS, endocytosis, oxidative phosphorylation, Ras signaling, and ferroptosis. Further GSEA analysis showed that genes associated with stem cell maintenance and differentiation were significantly enriched in the high fat diet group, suggesting that Mist1+ cells enhance their stemness and transcriptional activity in response to oxidative stress induced by a high-fat diet. As for Gpx4 knockout-induced oxidative stress, we found that Gpx4 knockout in Mist1+ cells rewired multiple signaling pathways that drive cell growth, especially Hippo signaling pathway that is closely related with gastric cancer initiation and progression. Conclusion: Our study present the detailed transcripts analysis of Mist1+ cells under oxidative stress (high fat diet or Gpx4 knockout). Based on RNA-seq transcriptome characterization, we conclude a mechanism for Mist1+ cells that are resistance to oxidative stress and act as tumor initiation cells under oxidative stress.
2025-06-24 | GSE292919 | GEO
Project description:Purpose: To explore the molecular mechanisms of Mist1+ cells that are specifically resistance to oxidative stress, and the mechanism that Gpx4 knockout (oxidative stress) in regulating the stemness of Mist1+ cells, RNA sequencing was performed to analyze the geome-wide change of Mist1+ cells compared with Mist1- cells, and further the difference between Mist1+ cells and Gpx4 KO-Mist1+ cells. Methods: Total mRNA was extracted from organoids which were isolated from corpus of Mist1Cre/ERT2;RFPLSL and Gpx4F/F;Mist1Cre/ERT2;RFPLSL mice (8 weeks). Then RNA quality was assessed using an Agilent Bioanalyzer 2100 and the sample reads were sequenced using Illumina NovaSeq 6000 platform. Results: Our results revealed differentially expressed genes in Mist1+ cells when compared with Mist1- cells. Further KEGG analysis enriched multiple pathways/biological processes including ROS, endocytosis, oxidative phosphorylation, transcriptional misregulation in cancer, phagosome, cellular senescence, cell cycle and p53 signaling pathway. Further GSEA analysis showed that Mist1 signature genes were highly enriched in the Mist1+ group when compared to the Mist1- group, and Gpx4 knockout further enriched Mist1 signature genes, suggesting a role for Mist1 as a transcriptional factor in determining cellular resistance towards oxidative stress. At the same time, we found that Gpx4 knockout in Mist1+ cells rewired multiple signaling pathways that drive cell growth, especially Hippo signaling pathway that is closely related with gastric cancer initiation and progression Conclusion: Our study present the detailed transcripts analysis of Mist1-, Mist1+ and Gpx4 KO-Mist1+ cells. Based on RNA-seq transcriptome characterization, we conclude a mechanism for Mist1+ cells that are resistance to oxidative stress and act as tumor initiation cells under oxidative stress.
2025-06-24 | GSE277436 | GEO
Project description:To evaluate the potential role of Hes1 in regulation of type I IFNs and the downstream ISGs expression, we generated the bone marrow-derived macrophages (BMDMs) from Hes1+/+ Cre-ERT2 and Hes1fl/fl Cre-ERT2 mice. RNA-sequencing analysis of Poly(I:C) [(polyinosinic: polycytidylic acid), a mimic of viral double-stranded RNA]-treated BMDMs revealed that 49 genes were induced more than two-fold by Poly(I:C) for 3 hrs in Hes1-deficient BMDMs relative to their expression in Hes1+/+Cre-ERT2 cells. Notably, 67.3% of these upregulated genes were ISGs by screening the Interferome database, suggesting that Hes1 inhibits expression of TLR-mediated ISGs,these results indicated that Hes1 negatively regulates TLR3-mediated induction of ISGs in macrophages.
2019-04-16 | GSE111169 | GEO
Project description:Human brain organoids are three-dimensional cultures that recapitulate in vivo cell diversity and organization, which provide a novel source for transplantation therapies of neurological disorders. However, some remaining technical problems including surgical lesions which still limit the application of brain organoid transplantation. Here instead of transplanting mature organoids, we performed development of organoids in vivo (IVD-organoids) by injecting small early organoids into the adult mice corpus striatum. Single-cell transcriptome analysis suggested that IVD-organoids contain pericyte-like and hippocampal cells. Similar to previous studies in cerebral organoid transplantation, IVD-organoids also showed reduced cellular stress and death. We further demonstrated that more choroid plexus (ChP) cells were generated in IVD-organoids, which were important for maintaining brain homeostasis. Together, our study provides a novel method that allows in vivo generation of human brain organoids, which may serve as a potential cell therapy for neurological disease involving different brain regions.
2022-03-15 | GSE165975 | GEO
Project description:Purpose: The goal of this study is to detect differentially expressed genes, among Wild type caput, corpus, and cauda epididymis by RNA sequencing Methods: Caput, corpus, and cauda epidiymal mRNA profiles of 9-month-old wild-type mice were generated by deep sequencing, in triplicate, using Illumina GAIIx. Results: RNA-seq data identified transcripts differentially expressed in caput, corpus, and cauda epididymis. Conclusions: Our results show that the expression of many genes were differentially regulated in caput, corpus, and cauda epididymis.
2020-06-05 | GSE138517 | GEO
Project description:RNA-seq of and Ethonal and Tamoxifen-treated Rad21-TEV primary neuron transduced with ERT2-TEV
2021-02-28 | GSE150129 | GEO