Compilation of expressed Salmonella sRNAs and their enrichment by Hfq coIP.

aGene names of Salmonella sRNAs that have been experimentally proven here, and in previous studies. Method of identification is given in the third column. sRNA names follow Salmonella and/or E. coli nomenclature referenced in (Hershberg et al., 2003; Padalon-Brauch et al., 2008; Papenfort et al., 2008), except STnc490, 500, 520, 540, 560, 570, 580, which have been newly predicted in this study (see Supplementary Table S3).bAlternative sRNA IDs. References in (Hershberg et al., 2003; Padalon-Brauch et al., 2008; Papenfort et al., 2008).cEvidence for sRNAs in Salmonella.(I) Conserved sRNA found in Salmonella cDNA libraries, and previously shown to be expressed in E. coli (relevant ref. in (Papenfort et al., 2008); Table 1).(II) sRNA previously predicted and validated on Northern blots in Salmonella by (Padalon-Brauch et al., 2008).(III) sRNA previously validated on Northern blots in Salmonella (Altier et al., 2000; Figueroa-Bossi et al., 2006; Fortune et al., 2006; Papenfort et al., 2006; Papenfort et al., 2008; Pfeiffer et al., 2007; Sharma et al., 2007; Viegas et al., 2007).(IV) sRNA predicted through cDNA sequencing and validated by Northern blot analysis in this study.(V) sRNA previously predicted by (Pfeiffer et al., 2007) is recovered in cDNA sequences and validated by Northern blot analysis in this study.(VI) IstR sRNAs (Vogel et al., 2004) were not recovered in cDNA sequences but their expression in Salmonella validated by Northern blot analysis in this study (Figure S5).dFlanking genes of the intergenic region in which the sRNA candidate is located.eOrientation of sRNA candidate (middle) and flanking genes (�� and �� denote location of a gene on the clockwise or the counterclockwise strand of the Salmonella chromosome).fGenomic location of sRNA candidate gene according to the Salmonella typhimurium LT2 genome. For STnc470 through STnc640 start and end of the entire intergenic region are given.gOut of 145,873 sequences in total.hOut of 122,326 sequences in total.iEnrichment factor calculated by the number of blastable reads from Hfq coIP over control coIP.jDenotes verification on Northern blot in this study for new RNA transcripts; the estimated size is given in nucleotides.kThe cDNA reads map antisense internally of the IS200 element. Based on sequence identity they map to all IS200 elements (tnpA_1 to tnpA_6).lSTnc250 and STnc570 contain small ORFs annotated as ypfM or yneM, respectively, in E. coli (Wassarman et al., 2001).