GSM1854059: Input_KSIC_c806; Mus musculus; ChIP-Seq
For RNA-Seq samples,  ~1 million cells were collected at the indicated time point and extracted with PrepEase RNA spin kit (Affymetrix). For ChIP-Seq sample preparation, PDA cells are treated  as indicated, fixed and quenched, sonicated to average fragment size of 250bp in 1% SDS lysis buffer, and incubated with 60ul Dynabeads protein G conjugated with 3-5ug of indicated antibodies. 2% pre-cleared chromatin prior to primary antibody addition was kept as input DNA. Magnetic beads were washed, chromatin was eluted, and reverse crosslinked ChIP DNA was dissolved in 10 mM Tris pH 8.0 buffer for further analysis. For RNA-Seq library construction, total RNA purified from mES and mEB was quantified by Ribogreen and quality assessed by Agilent BioAnalyzer 2000. 500ng RNA with integrity number (RIN) > 9.5 from each sample was used for library construction with TruSeq RNA Sample Prep Kit v2 (Illumina) according to manufacturer’s instructions.  For ChIP-Seq library construction, ChIP-Seq DNA samples were quantified and quality assessed by Ribogreen and Agilent Bioanalyzer. DNA fragments range from 200-600bp were selected constructed for ChIP-Seq library with TruSeq ChIP Sample Prep Kit (Illumina) according to manufacturer’s instructions. Multiplexed sequencing libraries were ran on a Hiseq2500 platform and more than 40million raw paired-end reads were generated for each sample.
GEO Accession
GSM1854059