title: GSM3167423: CKO(GFP) genomes from ADAR1KO cells; Homo sapiens; RNA-Seq
library_construction_protocol: Viral ribonucleocapsids were purified from cellular RNA through CsCl density gradient centrifugation. Viral genomic RNA was extracted from ribonucleocapsids with Trizol and isopropanol-precipitated. 5 μl ribonucleocapsid RNA were fragmented for 7.5 min using the Ambion Fragmentation Reagent according to the manual. The samples were then diluted with nuclease-free H2O to a final volume of 100 μl, mixed with an equal volume of phenol/chloroform/isoamyl alcohol and phase-separated by centrifugation (12,000g, 4°C, 10 min). RNA was precipitated from the aqueous phase using sodium acetate / ethanol overnight at −20°C followed by centrifugation (20,000g, 4°C, 30 min). Pellets were washed with 70% (w/v) ethanol, dried and resuspended in 11 μl nuclease-free H2O. RNA libraries were prepared using 220-500 ng of total RNA according to the manufacturer's instructions for the TruSeq Stranded Total RNA Sample Prep Kit (Illumina, San Diego, CA).  The concentration and size distribution of the completed libraries was determined using an Agilent Bioanalyzer DNA 1000 chip (Santa Clara, CA) and Qubit fluorometry (Invitrogen, Carlsbad, CA). Libraries were sequenced at 8-14 million reads per sample following Illumina's standard protocol. The flow cells were sequenced as 300 × 2 paired end reads on an Illumina MiSeq using MiSeq v2 sequencing kit and MCS v2.6.2.1collection software.
attributes.tag: GEO Accession
attributes.value: GSM3167423