Illumina NovaSeq 6000 paired end sequencing; SPATIaL-seq of primary human mesenchymal stem  cells (MSC)-derived osteoblasts from healthy donors (differentiated with BPM2)
SPATIaL-seq of primary human mesenchymal stem  cells (MSC)-derived osteoblasts from healthy donors (differentiated with BPM2)
Primary bone-marrow derived human MSCs isolated from healthy donors were plated in osteogenic media at 15,000 cells/cm2 and the next day stimulated with recombinant human BMP2 in serum-free osteogenic media. Cells were harvested at 72 hours following BMP2 treatment. The initial 3C libraries were generated following a previously published protocol (Hughes et al., Nature genetics, 2014). The DNA was digested using DpnII, then re-ligated together using T4 DNA ligase, and finally isolated by phenol/chloroform extraction. The 3C libraries were sonicated to an average size of 300bp. Agilent SureSelect library capture protocol was then applied with capture probes targeting both ends of DpnII restriction fragments that overlap promoters of protein-coding, noncoding, antisense, snRNA, miRNA, snoRNA and lincRNA transcripts, totaling 36,691 RNA baited fragments. The bait list is provided in the file baits_1frag.bed.
Experimental Factor: individual
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