File S1 - Effect of Bodily Fluids from Honey Bee (Apis mellifera) Larvae on Growth and Genome-Wide Transcriptional Response of the Causal Agent of American Foulbrood Disease (Paenibacillus larvae)

Figure S1. Average expression stability (A) and determination of the optimal number (B) of reference targets with geNormPLUS. Figure S2. Validation of microarray data with RTQ-PCR. (A) Log2-transformed expression ratio of T1 compared to C1. (B) Log2-transformed expression ratio of T4 compared to C4. White bars: RTQ-PCR experiment. Black bars: microarray experiment. T1: test sample collected one hour after spiking with larval fluids. T4: test sample collected four hours after spiking with larval fluids. C1: control sample collected one hour after spiking with BHIT-broth. C4: control sample collected four hours after spiking with BHIT-broth. +: differential expression (significant). -: equal expression (non-significant). Figure S3. Validation of microarray data with RTQ-PCR. (A) Log2-transformed expression ratio of C4 compared to C1. (B) Log2-transformed expression ratio of T4 compared to T1. White bars: RTQ-PCR experiment. Black bars: microarray experiment. T1: test sample collected one hour after spiking with hemolymph. T4: test sample collected four hours after spiking with hemolymph. C1: control sample collected one hour after spiking with BHIT-broth. C4: control sample collected four hours after spiking with BHIT-broth. +: differential expression (significant). -: equal expression (non-significant). Figure S4. Stacked percentage bar chart, showing the numbers of up- and down-regulated (putative) transporter encoding genes for T4–T1 (left) and C4–C1 (right), respectively, relative to the total numbers of (putative) transporter encoding genes within the P. larvae genome. The latter are indicated between square brackets. Round brackets: GO term numbers. GO terms were assigned with Blast2GO. White bars: down-regulation for T4–T1. Dark grey bars: up-regulation for T4–T1. Light grey bars: down-regulation for C4–C1. Black bars: up-regulation for C4–C1. Arrow heads: arbitrary GO term hierarchy (;◂>⊲>\raster="rg3"). Figure S5. Stacked percentage bar chart, showing the numbers of up- and down-regulated (putative) metabolic genes for T4–T1 (left) and C4–C1 (right), respectively, relative to the total numbers of (putative) metabolic genes within the P. larvae genome. C: carbohydrate metabolism. The latter are indicated between square brackets. Round brackets: KO numbers (KEGG pathways). KEGG pathways were assigned with KAAS. White bars: down-regulation for T4–T1. Dark grey bars: up-regulation for T4–T1. Light grey bars: down-regulation for C4–C1. Black bars: up-regulation for C4–C1. ∼: KO:00061; KO:00071; KO:00592. *: KO:00350; KO:00360; KO:00380; KO:00400. °: KO:00410; KO:00430; KO:00450; KO:00480. ?: KO:00740; KO:00760; KO:00770; KO:00780; KO:00790; KO:00670; KO:00860; KO:00130. ‘:KO:00900; KO:00903; KO:00281; KO:00523; KO:01053; KO:01055; KO:00960; KO:00232; KO:00521; KO:00401. ‘’: KO:00362; KO:00627; KO:00625; KO:00622; KO:00633; KO:00642; KO:00643; KO:00930; KO:00621; KO:00626; KO:00983. Figure S6. Stacked percentage bar chart, showing the numbers of up- and down-regulated genes for T4–T1 (left) and C4–C1 (right), respectively, relative to the total numbers of genes within the P. larvae genome. The latter are indicated between square brackets. Round brackets: COG functional category label. C: cellular processes and signaling. I: information storage and processing. M: metabolism. P: poorly characterized. White bars: down-regulation for T4–T1. Dark grey bars: up-regulation for T4–T1. Light grey bars: down-regulation for C4–C1. Black bars: up-regulation for C4–C1. Table S1. Reference genes used to normalize the results of the qRT-PCR experiment for microarray data validation. Table S2. Randomly selected genes used in the RTQ-PCR experiment to validate the microarray results. Table S3. Validation of microarray data by qRT-PCR. Table S4. Validation of microarray data by qRT-PCR. Table S5. GO-enrichment analysis for comparison C4–C1, showing the most specific over- and under-represented biological process GO-terms for both up- and down-regulation. Table S6. GO-enrichment analysis for comparison T4–T1, showing the most specific over- and under-represented biological process GO-terms for both up- and down-regulation. Table S7. Annotation and pathway analysis for both up- and down-regulated genes for C4–C1. Table S8. Annotation and pathway analysis for both up- and down-regulated genes for T4–T1. (PDF)