Identification of PUF9-copurifying RNAs by microarray.

RNA co-precipitating with the PUF9::TAP fusion (specifically co-purifying) and the TAP tag-only control (non-specifically co-purifying) was isolated and cDNA was generated, incorporating either Cy3 or Cy5 dyes. The two samples were compared by hybridization with a microarray of shotgun genomic clones. Two biological replicates were performed, and probes showing greater intensity for the PUF9 channel are marked “X”. Probes of interest were end-sequenced and their internal sequences estimated by comparison with genomic sequence data. Probes were grouped by locus (right column) in cases were multiple positive probes were mapped to overlapping or adjacent genomic regions. Genes that were further tested as candidate PUF9 targets are shown in bold.