GSM1696052: shSun2_RNAseq, replicate 2; Mus musculus; RNA-Seq
ChIP-seq: Cells were crosslinked with 1% formaldeyde for 10 min, then nuclei were isolated and lysed. Chromatin was sheared by sonication to a size of ~200-400 bp. Cleared lysates were precleared for 1 hour, then 10% saved as input, and lysates were incubated with Dynabeads Protein G pre-bound with the antibody of choice. After stringent washes, ChIP DNA was eluted from beads, and together with input chromtain was reverse-crosslinked with proteinase K. DNA was purified by phenol/chloroform extraction and ethanol precipitation. Hi-C: Hi-C experiments were conducted using HindIII according to the method described in Lieberman-Aiden, E. et al. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326, 289-93 (2009). RNA-seq: Xi-TgGFP TTFs (68-5-11) with the stable knock down of candidates were treated with 5'-azacytidine and etoposide at 0.3 uM each for 3 days. Strand specific RNA-seq, the library preparation, deep sequencing, and data analysis was followed as described in J. T. Kung et al., Locus-specific targeting to the X chromosome revealed by the RNA interactome of CTCF. Molecular cell 57, 361-375 (2015). All libraries were sequenced with Illumina Hiseq 2000 or 2500 using 50 cycles to obtain paired end reads. ChIP-seq: Libraries were constructed using the NEBNext ChIP-seq Library Preparation Kit with no modifications to the protocol. We used 16 cycles during the PCR step. Hi-C:  Sequencing libraries were constructed according to the method described in Lieberman-Aiden, E. et al. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326, 289-93 (2009). RNA-seq: Total RNA was harvested using trizol extraction, and ribosomal RNA was removed using RiboMinus. Strand-specific libraries were generated by performing reverse transcription with Superscript III, followed by second-strand synthesis using the NEBNext second-strand synthesis module supplemented with dUTP, and then libraries were generated using the NEBNext ChIP-seq Library Preparation Kit.
GEO Accession
GSM1696052