Identification of dysregulated transcripts in apob-1(RNAi);apob-2(RNAi) planarians

ApoB-1 and ApoB-2 are intestine-enriched regulators of lipoprotein secretion in planarians. The goal of this study was to identify differentially expressed transcripts in uninjured apob-1(RNAi);apob-2(RNAi) double knockdown planarians relative to egfp(RNAi) control animals. Overall design: Total RNA was isolated from uninjured egfp(RNAi) (control), apob-1(RNAi);apob-2(RNAi) (mild phenotype - "apob-M"), and apob-1(RNAi);apob-2(RNAi) (severe phenotype - "apob-S") planarians (fed three times, 4-6 biological replicates each). Library generation (NEB NEXT ULTRA) and RNA sequencing (2x150bp paired-end, Illumina HiSeq 4000) were conducted by Genewiz. Bioinformatic analysis was conducted using BBDuk, Bowtie2, and edgeR.