biostudies-arrayexpressMus musculushttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-15105The object of this study was to investigate how aKG impacts mouse intestinal stem cell (ISCs) function and fate decisions in vivo. Mice were treated for 7 days with twice daily aKG IP injections after which ISCs were FACS sorted and transcriptomically anayzled. This revealed a striking set of secretory genes upregulated in stem cells after aKG treatment.biostudies-arrayexpressLibrary Construction - From the resulting RNA, RNA-seq libraries were made using the Universal RNA-Seq with NuQuant kit(Tecan). cDNA was generated using a mixture of random and poly(T) priming from 15-16 ng of Total RNA. The cDNA is then fragmented, followed by end repaired, adapter ligation, strand selection and ribodepletion using AnyDeplete mouse probes(Tecan). The final library amplification step was performed with 18x cycles of PCR.Sequencing - The sample libraries were then pooled and converted to be compatible for the AVITI sequencer (Element Bioscience) by using Adept Rapid PCR-Plus protocol(Element Biosciences). The library was then sequenced with the AVITI Medium Output kit using 2x75 bp reads.Sample Collection - Lgr5+ISCs were FACS sorted and lyzed in immediately in Trizol.Nucleic Acid Extraction - Total RNA from sorted ISCs from dm-aKG or Ctrl treated mice(n=6) were isolated with Trizol. Total RNA was treated with DNase using the Heat&Run gDNA Removal(ArcticZymes) to remove residual DNAMINSEQE ScoreAssays and DataProcessed DataorganisationMAGE-TAB FilesSequence Alignment - Sequences aligning to ribosomal RNA were removed using SortMeRNA(v4.3.6). Remaining sequences were aligned to GRCm39 mouse genome using STAR(v2.7.11a).Data Transformation - Gene-level read counts were obtained using HTSeq(v2.0.2), setting minimum alignment quality to 20.MetabolomicsUnknownTranscriptomicsGenomicsProteomicsElement AVITIRNA-seq of coding RNAMus musculusOld mitochondria regulate niche renewal via alpha-ketoglutarate metabolism in stem cellsERP172171Onur DenizSimon AnderssonSimon Andersson, Hien Bui, Arto Viitanen, Daniel Borshagovski, Ella Salminen, Sami Kilpinen, Angelika Gebhart, Emilia Kuuluvainen, Swetha Gopalakrishnan, Nina Peltokangas, Martyn James, Kaia Achim, Eija Jokitalo, Petri Auvinen, Ville Hietakangas, Pekka KatajistofalseRNA-seq of Dm-aKG treated intestinal stem cells (ISCs) and controlsThe object of this study was to investigate how aKG impacts mouse intestinal stem cell (ISCs) function and fate decisions in vivo. Mice were treated for 7 days with twice daily aKG IP injections after which ISCs were FACS sorted and transcriptomically anayzled. This revealed a striking set of secretory genes upregulated in stem cells after aKG treatment.2025-05-02T00:00:00Z2026-05-31T00:35:19.623Z2025-05-01T16:16:59.555ZE-MTAB-15105ERP172171EFO_0002944EFO_0004170EFO_0004917EFO_0005518EFO_0003816EFO_0003738EFO_0004184