Chunk #19 — Materials and methods — Differentiation of hESCs into cortical interneurons and analysis of ethanol-induced miRNA and mRNA transcriptomic changes by RNA-seq
mRNA-seq was applied to profile the mRNA transcriptome of hESC-derived cortical interneurons since high-quality total RNA samples (RINs > 7) were extracted from cultured cells. The Illumina® TruSeq® Stranded mRNA Library Prep Kit (Illumina, San Diego, CA, USA) was used to construct mRNA-seq libraries. Pooled cDNA libraries (up to 8) were sequenced (2 × 100 bp) on the HiSeq 2000 system (Illumina, San Diego, CA, USA). The mRNA-seq raw data was processed by Pipeliner [30], as described above. The mean total number of reads per sample was 25,524,900 and the mean mapping rate (aligned reads/reads sent to Aligner) was 75.1%. The quality of the mRNA-seq data was visualized using box plots (Fig. S5b). The mRNA-seq data has been deposited in the NCBI GEO database (accession number: GSE181049).
