title: GSM2526394: WT-dlx5a-sox10; Danio rerio; RNA-Seq
library_construction_protocol: GFP/DsRed double-positive, double-negative, and single-positive populations were collected directly into RLT lysis buffer (Qiagen). Total RNA was immediately extracted using the RNeasy Micro kit (Qiagen) following the manufacturer’s protocol. The quality and quantity of extracted RNA were assessed on an Bioanalyzer Pico RNA chip (Agilent, Santa Clara, CA). cDNA was then made from the extracted RNA using the SMARTer kit (Clontech, Mountain View, CA), according to the manufacturer’s instructions. The number of amplification cycles for cDNA synthesis was estimated based on input amounts of RNA. The size and the amount of the resulting cDNA were then confirmed by Bioanalyzer. Sonication was performed on a S2 ultrasonicator (Covaris, Woburn, MA) according to Clontech’s recommended conditions. DNA libraries were constructed using the Kapa Hyper prep kit (Kapa Biosystems, Wilmington, MA) and NextFlex adapters (Bioo Scientific, Austin, TX). Libraries were visualized by Bioanalyzer analysis and quantified by qPCR (Kapa library quantification kit). Sequencing was performed on Illumina HiSeq 2000 (50-bp paired end reads) and NextSeq 500 (75-bp paired end reads) machines (Illumina, San Diego, CA). DNA libraries were constructed and sequencing was performed at the Norris Cancer Center Molecular Genomics Next Gen Sequencing Core at USC.