GSM3640293: MN_CTCF (ChIPm-seq); Mus musculus; ChIP-Seq
The ChIPmentation protocol was adapted from Schmidl et al., 2015. ChIPmentation datasets were produced from 4-5 pairs of metanephros (approx. 7.5x105 cells) or from a fraction of forebrain micro-dissected from E13.5 embryos. Samples were dissociated in Collagenase (sterile filetered, C1764 Sigma). Fixation was done in a final concentration of 1% FA (w/o methanol) for 10 minutes at room temperature and cells were then stored at -80°C. Genotyping was done on brain or tail biopsies. Chromatin shearing was done using a Covaris E220 in 120 ul sonication buffer (0.25% SDS, duty cycle at 2%, peak incident power at 105W, with the amplifier engaged and a treatment of 8 minutes). The volume for the over-night IP (4°C, 25 rpm) was adjusted at 300 ul using a dilution buffer to lower the SDS concentration and buffer the pH (final concentration of 0.1% SDS, 20 mM HEPES). Following two LiCl wash, magnetic beads were then washed 2x in 1ml 10uM TrisHCl pH=7.4 and finally resuspended in 24 ul of pre-warmed tagmentation buffer (FC-121-1030, Illumina). 1 ul of TDE1 enzyme was added to the mix and the beads were incubated for 120” at 37°C. DNA purification, quantification and Nextera library construction were done following the published ChIPmentation protocol (Schmidl, 2015) using indexed Illumina adapters (FC-121-1011, Illumina).
GEO Accession
GSM3640293