Deep Sequencing Analysis of Small Noncoding RNA and mRNA Targets of the Global Post-Transcriptional Regulator, Hfq
Figure 1
Strategy to identify Hfq targets.
RNA was co-immunoprecipitated with Hfq in extracts from ESP-grown Salmonella cells (wild-type and chromosomal hfqFLAG strain) using an anti-FLAG antibody. The extracted RNA was converted to 5′ monophosphate RNA, and subsequently into cDNA, followed by direct pyrosequencing. Our approach was validated by hybridization of cDNA to high density oligo microarrays. In addition, total RNA of the wild-type strain and its hfq deletion mutant was used for transcriptomic analysis using Salmonella SALSA microarrays.