GSM1203227: HKC8-H3K4me2; Homo sapiens; ChIP-Seq
HKC8 cell were collected when it reached to 80% confluence. Media were changed before fixing the cells to remove the dead cells. Cells were cross-linked with formaldehyde in a final concentration of 1% for 10 mins at room temperature.  A final concentration of 0.125M glycine was used in room temperature for 10 minutes to stop the reaction. Cells were scraped with ice cold PBS containing protease inhibitor.  The chromatin immunoprecipitation procedure was done with Invitrogen MAGnify™ Chromatin immunoprecipitation System following the manufacturer's protocols. Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit  (Illumina). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation.