GSM2970188: MEF 1X10^5 rep 2 G1; Mus musculus; OTHER
Cells were sorted by FACS into S and G1 phase portions Library preparation was done similar to Blecher-Gonen et al. (Blecher-Gonen et al. 2013) with some changes. Briefly, Sonicated DNA was subjected to a 50µl end repair reaction using 1µl End repair mix (E6050L, NEB), cleaned by 1.8X AmpureXP beads, followed by a 50µl A-tail reaction using 2µl Klenow fragment exo- (M0212L, NEB). The products were cleaned by 1.8X beads and were ligated by 2µl quick ligase (M2200, NEB) to 0.75µM illumina compatible forked indexed adapters. Ligation products were size selected by 0.7X PEG (considering the PEG in the ligation buffer) in order to remove free adaptors. 12-19 cycles of amplification were performed by PFU Ultra II Fusion DNA polymerase (600670, Agilent) with the following Primers:   P7 5'AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGAC 3',   P5 5' CAAGCAGAAGACGGCATACGAGAT 3'.   Amplified DNA was size selected for 300-700bp fragments by taking the supernatant after using 0.5X beads (which removed fragments greater than 700bp) followed by a 1.0X beads cleaning (which removed remaining primers and adapter dimers). The final quality of the library was assessed by Qubit and TapeStation. Libraries were pooled and sequenced on NextSeq (illumina) for 75 bp paired-end sequencing, generating 10M reads per each library (60M per experiment for triplicates of G1 and S).