title: GSM6339607: HPDLC-3U; Homo sapiens; RNA-Seq
library_construction_protocol: RNA was isolated from each cells using TRIzol Reagent (Invitrogen, Carlsbad, CA). Cap analysis of gene expression (CAGE) allows genome-wide analysis of gene transcription start sites and quantitative study of RNA transcribed from them by DNAFORM (Yokohama, Kanagawa, Japan). In brief, RNA quality was assessed with a Bioanalyzer (Agilent, Santa Clara, CA) to ensure that the RNA integrity number was over 7.0, and A260/280 and 260/230 ratios were over 1.7. First-strand cDNAs were transcribed to the 5ʹ end of capped RNAs and attached to CAGE “barcode” tags, which upon sequencing were mapped to the mouse mm9 genomes using BWA software (v0.5.9) after discarding ribosomal or non-A/C/G/T base-containing RNAs. For tag clustering, CAGE-tag 5ʹ coordinates were input for CAGEr clustering using 20 bases as a maximal allowed distance between two neighboring tags and a minimum counts per million (CPM) value of 2 (Haberle et al., Nucleic Acids Research 2015 43:e51).