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The nuclei were pelleted, resuspended in nucleus lysis buffer (50 mmol/L Tris-HCl [pH 8.1], 10 mmol/L EDTA, 1% SDS, and protease inhibitor cocktail), and incubated on ice for 10 min. Chromatin was sheared to a size range of 0.3 to 0.8 kb by sonication.
After washing 4 times with cold PBS, cells were lysed by incubating in nucleus lysis buffer.
After the cells were lysed by a nucleus lysis buffer, the lysates were sonicated.
Cell and nucleus lysis buffers (Magna ChIP™ G Kit, Millipore) were added to the cell pellets.
Nuclei were lysed using nucleus lysis buffer, and digested chromatin was sonicated to get equal sizes of chromatin fragments (average size about 500 base pairs).
A 1.25 ml of extraction buffer, 1.75 ml nucleus lysis buffer (0.2 M Tris HCl, 50 mM EDTA, 2 M NaCl, 2% hexadecyl-trimethyl-ammonium bromide pH 7.5), and 0.6 ml of 5% sarkosyl were used to dissolve the pellet.
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Briefly, 18 h culture from two blood agar plates was harvested and lysed in the Promega Nuclei Lysis Solution buffer (Promega, USA).
Cells were washed twice with cold PBS and subsequently incubated on ice for 10 min with cold nuclei lysis buffer (50 mM Tris HCl, 10 mM EDTA, 1% SDS) to which 1 mM protease inhibitors (Sigmafast, Sigma Aldrich, St Louis, MO) and 4 mM PMSF (Sigma Aldrich, St Louis, MO) was freshly added.
The cell nuclei were collected and lysed with Nuclei lysis buffer (50 mM Tris HCl, 10 mM EDTA (ethylenediaminetetraacetic acid), 1% SDS (sodium dodecyl sulfate)).
The only modification was that purified EBs were incubated with proteinase K for 1 hr at 60°C prior to addition of the Nuclei lysis solution.
Cells were lysed in Nuclei Lysis Solution and genomic DNA purification was done using the Wizard Genomic DNA Purification Kit (Promega) and following the manufacturer's instructions.
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