High-throughput detection of RNA processing in bacteria

BMC Genomics

Table 1 Library growth conditions and summary of the number and percentage of reads mapped to the Pseudomonas aeruginosa PAO1 reference sequence and including (+ RNA) or excluding (− RNA) rRNA, tRNA and tmRNA genes

Sample		including rRNA		excluding rRNA
Sample	Total Reads	Reads Mapped	Percent Mapped	Reads Mapped	Percent Mapped
pRNA-Seq LB Medium, 37 °C, OD₆₀₀ = 0.7 (A06027)	272,983,632	149,142,710	55%	51,067,158	19%
dRNA-Seq LB Medium, 37 °C, OD₆₀₀ = 0.7 (110817_SN865)	131,130,793	108,900,693	83%	29,801,108	23%
RNA-Seq Synthetic Cystic Fibrosis Medium, 37 °C, OD₆₀₀ = 0.7 (A03674)	54,000,716	51,910,678	96%	16,003,536	30%
RNA-Seq Artifical Sputum Medium, 37 °C, OD₆₀₀ not determined (A06026)	63,854,706	61,850,374	97%	6,802,731	11%
RNA-Seq LB Medium, 37 °C, OD₆₀₀ = 0.7 (PA0004)	75,437,354	72,729,310	96%	30,068,678	40%
RNA-Seq LB Medium, 34 °C, OD₆₀₀ = 0.7 (PA0001)	20,643,394	17,559,382	85%	3,352,489	16%

In all libraries but 110817_SN865, which consists of single end reads, the mapped reads are in proper pairs with a maximum insert size < 1000. A moderate drop in read quality (55% aligned reads) was observed with the dRNA-Seq library, which we attributed to the extra RNA manipulation steps required for library construction. We employed the same rigorous alignment quality thresholds with the dRNA-Seq library as with all other libraries to ensure that only high quality reads were mapped

ISSN: 1471-2164