2025-05-08
ENA first public
ERC000011
ENA-CHECKLIST
Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland Molecular and Integrative Bioscience Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
INSDC center name
public
INSDC status
ERS24441086
SRA accession
E-MTAB-15119_2:D2_BS
Submitter Id
4
month
age
ArrayExpress
broker name
stem cell young mitochondria
cell type
not collected
collection date
house mouse
common name
Protocols: Intestinal stem cells enriched for Old or Young mitochondria were FACS sorted. Cells form 3-4 mice of both genders(designated with M or F in sample metadata) were pooled for one biological replicate, to a total of four biological replicates. DNA was isolated using the Quick-DNA Microprep Plus Kit(D4074) according to manufacturers instructions  5-mC and 5-hmC modifications were determined using oxidative bisulfite sequencing(oxBS-Seq) with the NuGEN Ultralow Methyl-Seq with TrueMethyl®oxBs(M01512;Tecan). 300 ngs of genomic DNA were sonicated using a Covaris S220 sonicator(Covaris) to a mean size of 250-300bp. For quantitative assessment of oxidation the DNA was spiked with 1% of control DNA-duplexes, containing C, 5-mC and 5-hmC bases at known positions. The sonicated DNA from was split into two aliquots of 150ngs, one was oxidized, and bisulfite converted, the other was mock oxidized before bisulfite conversion. oxBS libraries required 10 PCR amplification cycles, BS libraries required 8 cycles. Library quality was assessed on an Agilent TapeStation D5000(Agilent Technologies, Santa Clara, CA).
description
adult
developmental stage
Lgr5(EGFP-CreERT2/+), Rosa26(Snap-Omp25/+)
genotype
not collected
geographic location (country and/or sea)
PK5677A_F, PK5683A_F, PK5595A_M
individual
not applicable
isolate
Mus musculus
organism
Mus musculus
organism
small intestine
organism part
Mus musculus
scientific_name
mixed sex
sex
C57BL/6J
strain
D2_BS
title