biostudies-arrayexpressOnur DenizMus musculushttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-15115To analyze aKG-induced Tet mediated changes to DNA hydroxymethylation in intestinal stem cellbiostudies-arrayexpressSequencing - The sample libraries were 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 High Output kit using 2x150 bp reads.Sample Collection - ISCs from 6 PBS and 6 dm-aKG treated mice were sortedNucleic Acid Extraction - total DNA was isolated using Quick-DNA microprep kit(Zymo). DNA was fractionated using Bioruptor NGS(Diagenode) after adding control DNAs from the NEBNext Enzymatic 5hmC-seq Kit(NEB-E3350S) to 250 ng of sample.Library Construction - The sonicated DNA libraries were constructed using NEBNext Primers for Epigenetics(Dual Index Primer Pairs Set 2B)(NEB-E3392S).OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesSequence Alignment - Alignment of sequence data and following methylation calls were performed with BSBolt(v1.4.8) on GRCm38.p6(mm10) mouse genome.Data Transformation - Methylation sites were called at a minimum read depth of three. For analysing differentially methylated regions (DMRs), methylation sites were filtered to contain only those where at least 5/6 of samples had non-missing values. Regions and their methylation levels were computed using Metilene(v0.2-8) with options -d 0.15 -m 5 -X 5 -Y 5 -M 500. In the DMR-file, \"g1\" and \"g2\" indicate aKG and control groups, respectively.UnknownTranscriptomicsGenomicsProteomicsElement AVITImethylation profiling by high throughput sequencingMus musculusOld mitochondria regulate niche renewal via alpha-ketoglutarate metabolism in stem cellsOnur 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 KatajistofalseDm-aKG treated Intestinal stem cells NEBNext Enzymatic 5hmC-seq (E5hmC-seq) sequencing and data processingTo analyze aKG-induced Tet mediated changes to DNA hydroxymethylation in intestinal stem cell2025-05-07T00:00:00Z2025-05-07T21:47:32.168Z2025-05-06T14:22:09.962ZE-MTAB-15115ERP172300EFO_0002944EFO_0004170EFO_0002761EFO_0004917EFO_0005518EFO_0003816EFO_0004184