HiSeq X Ten paired end sequencing; The epigenetic pattern and genome-wide CTCF occupancy in HL-60 cells treated with ATRA
The epigenetic pattern and genome-wide CTCF occupancy in HL-60 cells treated with ATRA
10^7 HL-60 cells treated with 10 uM ATRA for 2 and 5 days were harvested for ChIP-seq. 10% whole cell lysates were saved as input after genomic DNA was broken into 200-500 bp by sonication. 1 μg IP grade antibodies of CTCF, H3K4me3 or H3K27me3 (CST, Boston, USA) were incubated with the rest of the lysate overnight, followed by 2 h protein-A beads incubation at 4 °C for target protein pull down.  The CTCF enriched or H3K4/27me3 modified DNA or input DNA were repaired to 3'-dA overhang and added the ligated adapter. The DNA library was eliminated the unligated adapters and selected the appropriate size for sequence using an Illumina X Ten platform.
Experimental Factor: immunoprecipitate
H3K27me3
Experimental Factor: compound
all-trans-retinoic acid
Experimental Factor: dose
10
Experimental Factor: time
2