title: Scr control 1
design: RNA-Seq and data analysis. Total RNA from HeLa cells transduced with Scr or one of two shRNA against ZIP11 was isolated using TRIzol and frozen at -80C until analysis. Independent replicates for each sample were evaluated for quality and concentration at the Molecular Biology Core Lab at the University of Massachusetts Chan Medical School. Quality Control-approved samples were submitted to BGI Genomics for library preparation and sequencing. Libraries were sequenced using the BGISEQ-500 platform and reads were filtered to remove adaptor-polluted, low quality and high content of unknown base reads. About 99% of the raw reads were identified as clean reads (~65M). The resulting reads were mapped onto the reference human genome (hg38) using HISAT [73]. Transcripts were reconstructed using StringTie [74], and novel transcripts were identified using Cufflinks [75] and combined and mapped to the mm10 reference transcriptome using Bowtie2 [76]. Gene expression levels were calculated using RSEM [77]. DEseq2 [78] and PoissonDis [79] algorithms were used to identify differentially expressed genes (DEG). Gene Ontology (GO) analysis was performed on DEGs to cluster genes into function-based categories.