title: GSM3763078: ATAC-Seq Control KD, Rep 1; Mus musculus; ATAC-seq
design: -
library_construction_protocol: Mnase-Seq: DNA was extracted by phenol/chloroform extraction and mono/di-nucleosome fragments were gel-purified.  RNA-Seq: Total RNA was extracted from nuclei using Trizol (Invitrogen). Ribosomal RNA was removed prior to library construction by hybridizing to ribo-depletion beads that contain biotinylated capture probes (Ribo-Zero, Epicentre). RNA was then fragmented and libraries were prepared according to the TruSeq Stranded Total RNA Gold Kit (Illumina) using random hexamer priming.   Start-Seq: Total RNA was extracted from nuclei using Trizol (Invitrogen). Start-RNA libraries were prepared as described in (PMID:20007866) and size-selected (20-80 nt) to exclude full length snRNA species.  Ribo-Seq: Total RNA and ribosome-protected RNA from Cyclohexamide (CHX)-treated cells were isolated using the TruSeq Ribo Profile Mammalian Kit (Illumina) following the manufacturer's intructions.  ATAC-Seq:  DNA fragments were purified with 2 successive rounds of AMPure XP beads (1:3 ratio of sample to beads). MNase-Seq libraries were prepared using NuGen's Ovation Ultralow Library System V2.  RNA-Seq libraries were prepared according to the TruSeq Stranded Total RNA Gold Kit (Illumina) using random hexamer priming.  Ribo-Seq libraries were prepared according to TruSeq Ribo Profile Mammalian Library Prep Kit (Illumina).  Start-Seq libraries were prepared according to the TruSeq Small RNA Kit (Illumina). Illumina Spike-ins were used for normalization.  ATAC-Seq libraries were prepared according to NuGen's Ovation Ultralow Library System V2.