GSM5048828: D-KO-RNA-seq-Rep3; Mus musculus; RNA-Seq
For RNA -seq: cells were lysed with Trizol reagent (Life Technologies) and RNA was extracted according to the manufacturer's instructions; For 4C-seq: cells were treated with DpnII and NlaIII as the first and second restriction enzymes, respectively. The primers were used to amplify the final 4C template for generating 4C-seq libraries and DNA was extracted according to the manufacturer's instructions; For ChIP-seq: cells were cross-linked with 1% formaldehyde. Sonication was carried out to shear the chromatin to yield DNA fragment sizes of 100 to 500 base pairs (bp). Samples were cleared and precleared for 1 hour with 40 μl of protein A/G agarose beads. Part of the precleared samples was used as input, and the remainder was immunoprecipitated with H3K27ac and H3K4me3 antibody and protein A/G agarose beads. The precipitated DNA and input DNA were sequenced using an Illumina sequencer. Reads were mapped to the mm10 reference genome using HISAT2 and further analyzed with HOMER package. RNA, ChIP-seq and 4C libraries were prepared for sequencing using standard Illumina protocols