RNA-seq of PHACTR1 knockdown and overexpression in HT1080 stable cell lines

The PHACTR1 gene to a range of vascular and neurological diseases, underscoring its pivotal role in biology. As part of a larger multi-omics study, we performed bulk RNA-seq on stable HT1080 cell lines with overexpression or knockdown of PHACTR1, comparing them to scrambled control cells, to understand how PHACTR1 expression affects the transcriptome. Cell lines were generated by lentiviral transfection with viral particles produced in Lenti-X 293T cells. Stable cell lines were selected with puromycin and maintained in media containing the selection agent. RNA was extracted from cells (n=6 per condition) and RNA libraries were prepared using RNA with RIN score >9.8 using the KAPA Total RNA Library Preparation kit (Roche). Barcoded libraries were subsequently analyzed using an Illumina NovaSeq 6000 using NovaSeq 6000 S1 Reagent Kit v1.5 (300 cycles, Illumina) with paired-end lengths of 150 base pairs with a depth of >40 million reads. Fastq files were mapped onto the human GENECODE 29 version using STAR 2.7.5. The average reads/sample was 57M. No samples were excluded from analysis after quality control.