GSM6215134: Sample 57_Worm, 48h_3.13×10^-4g/L, rep4; Caenorhabditis elegans; RNA-Seq
RNA isolation was performed on all 60 samples in the next two days by following TRIzol™ Reagent (catalog number: 15-596-018, Invitrogen™, Waltham, Massachusetts, USA) protocol with slight modifications. Briefly, TRIzol and five 2 mm borosilicate glass beads (product number: CG-1101-01, Chemglass Life Sciences, Vineland, New Jersey, USA) were added to each thawing worm pellet, and a Bead Mill 4 Homogenizer (catalog number: 15-340-164, Fisherbrand™) was used for homogenization. Each RNA sample was resuspended in 40 µL nuclease-free water. The quantity and quality of RNA samples were measured using a NanoDrop 2000 Spectrophotometer (catalog number: ND-2000, Thermo Scientific™, Thermo Fisher Scientific). On the following day, RNA samples were aliquoted and sent to Scripps Research Genomics Core (La Jolla, California, USA) for shallow RNA-sequencing. cDNA library preparation and shallow RNA-Seq were performed at Scripps Research Genomics Core. Sample quality was assessed using a 2100 Bioanalyzer Instrument (part number: G2939BA, Agilent Technologies, Inc., Santa Clara, California, USA). Library preparation for RNA-Seq was performed via an early access kit, HTP RNA-Seq Library Prep, from iGenomX (now acquired by Twist Bioscience, South San Francisco, California, USA) with slight modifications. Briefly, PCR products 350–800 base pairs long were purified via 2% agarose gel electrophoresis, quantitated using Qubit dsDNA HS assay kit (catalog number: Q33231, Invitrogen™), and analyzed on a 4150 TapeStation System (part number: G2992AA, Agilent Technologies, Inc.).