title: GSM8558264: RNA-seq EB day 3 WT 2; Mus musculus; RNA-Seq
library_construction_protocol: Total RNA of samples were extracted with the TRIzol reagent (Invitrogen) according to the manufacturer's protocol. For ChIP-seq samples, cells were cross-linked with 1% formaldehyde for 8 minutes at room temperature. After washing, cells were sonicated with Diagenode Bioruptor in ChIP lysis buffer. For Hi-C samples, cells were cross-linked with 2% formaldehyde and incubated at room temperature for 10 minutes. Samples were sonicated using Covaris focused-ultrasonicator. RNA samples were prepared for transcriptome sequencing using the TruSeq library preparation kit (Illumina). The ChIP-seq libraries were constructed using the sparQ DNA Library Prep kit. The Hi-C libraries were constructed using Swift Biosciences Accel-NGS 2S Plus DNA Library Kit.