title: GSM4085043: SB_MDActrl_Nup93_3_S53_R1_001; Homo sapiens; OTHER
library_construction_protocol: For RNA-Seq, RNA was extracted following standard procedures based on Trizol and chloroform. The RNeasy Mini kit was used to purify RNA (Qiagen). Samples were incubated with DNAse I for 30 min to degrade genomic DNA. RNA was resuspended in RNAse-free water. The amount of RNA was quantified with Nanodrop. For Cut and Run, libraries were prepared according to published protocols [Skene and Henikoff_eLife_2017]. Briefly, cells were bound to concanavalin-A coated magnetic beads and incubated with the desired primary antibody after membrane permeabilization with digitonin. After washing, cells were incubated with protein A and Micrococcal Nuclease (pA-MN) on ice and Ca++ was added to start the reaction. DNA fragments were released by nuclease cleavage and finally extracted from the supernatant. Spike-in control of yeast DNA was added to each sample for normalization. mRNA-Seq libraries were prepared using the TruSeq RNA Library Preparation Kit according to the manufacturer's instructions (Illumina). stranded single-end mRNA-seq for RNA-Seq; regular library prep for Cut and Run