Transdifferentiated and control BJ fibroblasts (population doubling 20 to 30) were cross-linked with formaldehyde (1% final) for 5 min at room temperature or lysed in TRIzol (#15596018, Thermo Fisher Scientific) and snap-frozen for RNA isolation. Cross-linked cells were quenched with glycine (125 mM final) for 5 min, followed by two washes in cold PBS. Nuclei were then isolated from 20 million cells as previously described (78), and chromatin was sheared to 250-bp average size using a Covaris S220. Immunoprecipitations were performed using 500 μg of sheared chromatin lysate and 5 μg of antibodies preconjugated to protein G beads (Invitrogen): H3K27ac (39133, Active Motif), Flag (M2, F1804, Sigma-Aldrich), and hKLF4 (AF3640, R&D Systems). ChIP reactions were incubated for 16 hours at 4°C with rotation and then washed four times in wash buffer [50 mM Hepes-HCl (pH 8), 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% sodium deoxycholate, and 0.5% N-laurylsarcosine], followed by one wash in ChIP final wash buffer (1× tris-EDTA (TE) Buffer and 50 mM NaCl). Immunoprecipitated DNA was eluted from washed beads, reverse cross-linked overnight, purified, and used to construct libraries. Snap-frozen RNA samples were further extracted using chloroform and QIAGEN RNeasy Mini Kit (#74106) including deoxyribonuclease digestion. Purified RNA was then reverse-transcribed to complementary DNA (cDNA) using the High-Capacity cDNA Reverse Transcription Kit from Applied Biosystems (4368814). cDNA was then quantified and used to construct sequencing libraries.

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