Transcriptomic Analysis of Cell Phenotypes

The NucleoSpin RNA Mini kit (Macherey-Nagel, Düren, Germany) was used to extract total RNA and RNA integrity numbers (RIN) were measured using the Agilent 4200 Tapestation (Santa Clara, United States, cat. G2991BA). RIN values of samples considered within this study ranged from 9.3–10. No significant differences in RIN values were observed between the two phenotypes. Libraries preparation was carried out using the Illumina Stranded mRNA Prep kit. Sequencing of RNA libraries was performed in accordance with standard Illumina protocols within the Genomics Core Facility of the Center for Advanced Genomics Technology (Icahn School of Medicine at Mount Sinai, New York). Libraries were pooled and 100 bp, paired-end reads were sequenced on a NovaSeq 6000. FASTQ files were aligned to GENCODE v29 [23 (link)] using STAR (v2.6.1d) [24 (link)] and RSEM (v1.3.1) [25 (link)].