GSM3879688: WT  MEFs TNF 45min (caRNAseq); Mus musculus; RNA-Seq
Chromatin-associated RNA was isolated using TRIzol (Life Technologies) and purified using Direct-zol RNA Miniprep Kit (Zymo Research) according to the manufacturer's instructions. RNA concentrations were quantified using Epoch Spectrophotometer System (Biotek). 400ng of chromatin-associated RNA was subjected to library synthesis using KAPA Stranded RNA-Seq Kit with RiboErase. 400ng of total chromatin-associated RNA was subjected for ribosomal RNA depletion, fragmented using heat and magnesium, and reversed transcribed to double-stranded cDNA. The cDNA was end repaired, adenylate, and ligated with Illumina indexes prior to 12 cycles of PCR amplification. Sequencing was performed by the Broad Stem Cell Research Center core facility at the University of California, Los Angeles with single-end 50 bp sequencing
GEO Accession
GSM3879688