GSM1159893: minusDHT_PCGEM1_hs17l4_3; Homo sapiens; OTHER
ChIRP was performed as described (Chu et al 2011) with minor modifications. Briefly, 60-mer antisense DNA probes targeting PRNCR1 and PCGEM1 full-length sequences were designed by http://www.singlemoleculefish.com/designer.html. A set of probes targeting LacZ RNA was also designed as the negative control. All probes were biotinylated using Label IT® Nucleic Acid Biotin Labeling Kit from Mirus Biotechnology. LNCaP cells were fixed with 1% formaldehyde for 10 min at room temperature. Crosslinking was then quenched with 125mM glycine for 5 min. The chromatin preparation, hybridization/elution, deep sequencing steps were essentially performed as described (Chu et al 2011) except that washing was conducted at 50 °C and 65°C. ChIRP complexes were washed and the DNA was extracted and purified by QIAquick Spin columns (Qiagen). For ChIRP-seq, extracted DNA was ligated to specific adaptors followed by deep sequencing.
GEO Accession
GSM1159893