Xanthomonas perforans

RNA-Seq_XpAL65_Tomato_Leaf_surface_24hr_Rep_2

XpAL65 epiphytic populations were established by dip-inoculating tomato plants with a culture suspension (~10 CFU/ml) containing MgSO and Silwet. Plants were kept in the greenhouse, and 500-600 primary leaves were collected at 24 h post-infection, immediately submerged in 2 L RNA stabilization solution (10 mL water-saturated phenol (pH <7.0), 190 mL ethanol, 1.8 L water), sonicated for 10 minutes and centrifuged at 5,000 g for 10 min to collect bacterial cells. The cell pellets were suspended in residual supernatant and filtered through a 5-m filter. The cells in the filtrate were harvested by centrifugation at 5,000 g for 5 min, the supernatant was discarded, and the pellets were placed at 20 C. The cells collected from the 500600 leaves from 50 plants per replicate at a time point served as a biological replicate, and the procedure was repeated to provide three biological replicates for each time point. RNA was extracted using Trizol method. Samples were DNAse treated with Invitrogen DNAse (RNAse free). Library preparation was performed using Illuminas Stranded Total RNA Prep Ligation with Ribo-Zero Plus kit and 10bp unique dual indices. Sequencing was done on a NovaSeq X Plus, producing paired end 150bp reads. Demultiplexing, quality control, and adapter trimming was performed with bcl-convert (v4.2.4).

{'host': 'Tomato FL47', 'strain': 'AL65', 'sample_type': 'RNA Transcriptome', 'geo_loc_name': 'USA: Alabama', 'biosamplemodel': 'Microbe, viral or environmental', 'collection_date': '2024-10', 'isolation_source': 'Tomato Leaf', 'host_tissue_sampled': 'Tomato Leaf'}

RNA-Seq_XpAL65_Tomato_Leaf_surface_24hr_Rep_3

XpAL65 epiphytic populations were established by dip-inoculating tomato plants with a culture suspension (~10 CFU/ml) containing MgSO and Silwet. Plants were kept in the greenhouse, and 500-600 primary leaves were collected at 24 h post-infection, immediately submerged in 2 L RNA stabilization solution (10 mL water-saturated phenol (pH <7.0), 190 mL ethanol, 1.8 L water), sonicated for 10 minutes and centrifuged at 5,000 g for 10 min to collect bacterial cells. The cell pellets were suspended in residual supernatant and filtered through a 5-m filter. The cells in the filtrate were harvested by centrifugation at 5,000 g for 5 min, the supernatant was discarded, and the pellets were placed at 20 C. The cells collected from the 500600 leaves from 50 plants per replicate at a time point served as a biological replicate, and the procedure was repeated to provide three biological replicates for each time point. RNA was extracted using Trizol method. Samples were DNAse treated with Invitrogen DNAse (RNAse free). Library preparation was performed using Illuminas Stranded Total RNA Prep Ligation with Ribo-Zero Plus kit and 10bp unique dual indices. Sequencing was done on a NovaSeq X Plus, producing paired end 150bp reads. Demultiplexing, quality control, and adapter trimming was performed with bcl-convert (v4.2.4).

{'host': 'Tomato FL47', 'strain': 'AL65', 'sample_type': 'RNA Transcriptome', 'geo_loc_name': 'USA: Alabama', 'biosamplemodel': 'Microbe, viral or environmental', 'collection_date': '2024-10', 'isolation_source': 'Tomato Leaf', 'host_tissue_sampled': 'Tomato Leaf'}

RNA-Seq_XpAL65_Tomato_Leaf_surface_8hr_Rep_1

XpAL65 epiphytic populations were established by dip-inoculating tomato plants with a culture suspension (~10 CFU/ml) containing MgSO and Silwet. Plants were kept in the greenhouse, and 500-600 primary leaves were collected at 8 h post-infection, immediately submerged in 2 L RNA stabilization solution (10 mL water-saturated phenol (pH <7.0), 190 mL ethanol, 1.8 L water), sonicated for 10 minutes and centrifuged at 5,000 g for 10 min to collect bacterial cells. The cell pellets were suspended in residual supernatant and filtered through a 5-m filter. The cells in the filtrate were harvested by centrifugation at 5,000 g for 5 min, the supernatant was discarded, and the pellets were placed at 20 C. The cells collected from the 500600 leaves from 50 plants per replicate at a time point served as a biological replicate, and the procedure was repeated to provide three biological replicates for each time point. RNA was extracted using Trizol method. Samples were DNAse treated with Invitrogen DNAse (RNAse free). Library preparation was performed using Illuminas Stranded Total RNA Prep Ligation with Ribo-Zero Plus kit and 10bp unique dual indices. Sequencing was done on a NovaSeq X Plus, producing paired end 150bp reads. Demultiplexing, quality control, and adapter trimming was performed with bcl-convert (v4.2.4).

{'host': 'Tomato FL47', 'strain': 'AL65', 'sample_type': 'RNA Transcriptome', 'geo_loc_name': 'USA: Alabama', 'biosamplemodel': 'Microbe, viral or environmental', 'collection_date': '2024-10', 'isolation_source': 'Tomato Leaf', 'host_tissue_sampled': 'Tomato Leaf'}