BRD4 isoform knockdown RNA-sequencing data for "Isoform-Specific BRD4 Epigenetic Reader Programs Uniquely Govern Cardiac Homeostasis and Hypertrophy"

NRVMs were subjected to negative control (siNC) or BRD4-S (siBRD4-S) knockdown as described above. 24 hours after initiating siRNA transfection, cells were subjected to control or 50 µM phenylephrine treatment for an additional 24 hours in serum-free NRVM media to induce hypertrophic stress. Total RNA was extracted using the Quick RNA Microprep kit as described above. RNA concentrations were measured on the Qubit fluorometer, and RNA integrity was determined with Bioanalyzer (Agilent). Only samples with RNA integrity score >8 were used for library prep (poly A enrichment) and next-generation sequencing, which was performed at Novogene Inc., Santa Clara, CA. Purified cDNA libraries were sequenced on NovaSeq6000 (PE150). Pair-end reads were trimmed, processed, and mapped to the rat genome (mRatBN7.2). Differentially expressed transcripts were determined using Cuffdiff. Kyoto encyclopedia of genes and genomes (KEGG) analysis was used to determine gene pathways that were significantly enriched (based on FDR<0.05) among differentially down-regulated transcripts. Gene set enrichment analysis (GSEA) was performed on differentially enriched KEGG pathways using set of functional categories retrieved from MSigDB. Experimental groups: baseline controls: siNC0PE1,siNC0PE2,siNC0PE3,siNC0PE4 baseline with phenylephrine: siNC24PE1,siNC24PE2,siNC24PE3,siNC24PE4 BRD4-S knockdown baseline: BRD4SA0PE1, BRD4SA0PE2, BRD4SA0PE3, BRD4SA0PE4 BRD4-S knockdown with phenylephrine: BRD4SA24PE1, BRD4SA24PE2, BRD4SA24PE3, BRD4SA24PE4