Ambion dynabeads mrna purification kit

Samples were processed and analyzed as previously described^{12 (link)} with minor modifications as indicated below:
RNA was extracted from Trizol-lysed cells and 1 μg of total RNA was used for each sample. Polyadenylated RNA was selected using Ambion Dynabeads mRNA Purification Kit (Life Technologies 61006) and fragmented with Fragmentation Buffer (Ambion, #AM8740). First strand synthesis was performed using Random Hexamer Primers (Invitrogen, #48190-011) and SuperScript II (Invitrogen, #18064-014). Second strand synthesis was performed using DNA Pol I (Invitrogen #18010-025) and RNA was removed using RNaseH (Invitrogen #18021-014).
Libraries were end-repaired, 3′ A-tailed, and ligated to NEBNext Multiplex Oligo Adaptors (NEB E7335S). Sequencing was performed on an Illumina NextSeq 500 by Stanford Functional Genomics Facility.
Reads were mapped to hg19 annotation using Tophat2^{38 (link)} (version 2.0.13) and transcript expression was quantified against RefSeq gene annotations using featureCounts^{39 (link)}. Differential testing and log2 fold change calculation was performed using DESeq2^{40 (link)} with default multiple hypothesis adjustment to reduce false positives (Benjamini-Hochberg, FDR = 0.1). Gene Ontology analyses were performed using DAVID^{41 (link),42 (link)}.