title: GSM9491726: ATAC-Seq, BMDM, 1st Phase, Healthy1; Mus musculus; ATAC-seq
library_construction_protocol: This in vitro model was adapted from Edgar et al.(Edgar et al. 2021) to mimic diabetic-trained and untrained BMDM states. Male C57BL/6J mice (8 weeks old) from the Laboratory Animal Center of National Bioindustry (Chongqing, China) were randomly allocated to control or diabetic groups. For diabetes induction, mice received low-dose streptozotocin (42-45 mg/kg/d; Solarbio, China) via intraperitoneal injection after a 12h fast, repeated daily for 5 days. One week post-final injection, mice with nonfasted blood glucose >16.9 mmol/L were deemed type 1 diabetic. After 6 weeks of hyperglycemia, bone marrow progenitors from both groups were isolated and cultured in 5 mmol/L glucose DMEM with recombinant murine M-CSF for 7 days (rest phase). Cells were then stimulated with 10 ng/mL IFN-γ and 100 ng/mL LPS for 16 hours (2nd phase). The trained BMDMs were analyzed for their epigenetic modifications and metabolic profiles. (1) Cell Lysis: Lyse the cells and keep the cells on the ice all the time. (2) DNA Transposition and Tagmentation: Add Tn5 transposase to the cell suspension after cell lysis and then purify it with Qiagen MinElute PCR Purification Kit. (3) DNA Fragments Enrichment: Determine PCR cycles based on the DNA concentration and then purify the products with Qiagen MinElute PCR Purification Kit. (4) Size Selecting: Select DNA fragments with agarose gel electrophoresi. Dissolve the products after gel extraction with elution buffer. (5) Library quality control; (6) Library circularization; (7) The library was amplified to make DNA nanoball (DNB); (8) Sequencing on DNBSEQ (DNBSEQ Technology) platform.