biostudies-arrayexpressUnknownTranscriptomicsGenomicsProteomicsZhishuo WangDNBSEQ-G400RNA-seq of coding RNAArabidopsis thalianaArabidopsis thalianahttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-15957Plants utilize a two-tiered immune system, called pattern-triggered immunity (PTI) and effector-triggered immunity (ETI), to recognise and defend against pathogens. PTI acts as the first line of defense, limiting pathogen invasion, whereas ETI provides a stronger response that potentiates PTI signaling. Here, we performed a global transcriptome analysis to compare immune-induced gene expression during PTI and ETI in wild-type Col-0 and the rh3 mutant Arabidopsis thaliana plants. Adult leaves were inoculated with a mock solution (MgCl₂), the non-pathogenic strain Pseudomonas syringae pv. tomato (Pst) DC3000 hrcC⁻, or the effector-triggering strain Pst DC3000 (avrHopZ1a). Leaf samples were collected 8 hours post-inoculation, with three independent biological replicates performed per condition.biostudies-arrayexpressSample Collection - Tissue was collected by excising leaves at the petiole. Leaves were then packaged in aluminium foil and frozen in liquid nitrogen before storing at -80 degrees celcius.Sequencing - RNA sequencing was constructed by BGI, the protocol of which is proprietary.Nucleic Acid Extraction - (1) Grind tissue very fine in liquid nitrogen. (2) Add 0.5 ml RNA extraction buffer (warmed to ~80ºC) and 0.5 ml phenol:chloroform:isoamylalcohol mixture (25:24:1). Vortex vigorously. (3) Centrifuge max. speed for 5 min. at 4ºC, but do not put samples on ice. (4) Transfer the aqueous phase (upper phase) to a new tube. (5) Add 0.5 ml cold chloroform:isoamylalcohol (24:1) and vortex vigorously. (6) Centrifuge max. speed for 5 min. at 4ºC, but do not put samples on ice. (7) Repeat steps 4, 5, and 6. (8) Transfer the aqueous phase to a new tube on ice and add 1/3 volume of 8 M LiCl. Optional: If protocol was started with small amounts of tissue also add 25 µg glycogen (5 µl of 5 mg/ml stock) to visualize RNA pellet in step 10. (9) Incubate overnight at 4ºC. (10) Centrifuge max. speed for 15 min. at 4ºC. A small clear pellet of total RNA should be visible. From now on keep tubes on ice at all times. (11) Without disturbing the pellet, very carefully remove the supernatant with a pipette. (12) Wash RNA pellet gently with ice-cold (-20ºC) 0.5 ml of 70% ethanol. Do not resuspend pellet. (13) Centrifuge max. speed for 1 min. at 4ºC to make sure the RNA pellet stays in place.Discard supernatant without disturbing the RNA pellet. (14) Repeat step 13 to remove any remaining 70% ethanol. (15) Dry RNA pellet in the SpeedVac for 1 min. without heating. Do not dry longer than this!!! (16) Add 400 μl ddH2O (autoclaved) and keep on ice for 30-60 min. to rehydrate the RNA pellet. (17) Dissolve the RNA pellet by vigorously pipetting the solution up and down. (18) Add 40 μl NaAc pH5.2 and 1 ml of ice-cold (-20ºC) 96% ethanol. Invert to mix (do not vortex!!!). (19) Incubate at least 60 min. at -20ºC. (20) Centrifuge max. speed for 15 min. at 4ºC. A gel-like pellet of pure RNA should now be visible. (21) Without disturbing the pellet, very carefully remove the supernatant with a pipette. (22) Wash RNA pellet gently with ice-cold (-20ºC) 0.5 ml of 70% ethanol. Do not resuspend pellet!!! (23) Centrifuge max. speed for 1 min. at 4ºC to make sure the RNA pellet stays in place. Discard supernatant without disturbing the RNA pellet. (24) Repeat step 23 to remove any remaining 70% ethanol. (25) Dry RNA pellet in the SpeedVac for 1 min. without heating. Do not dry longer than this! (26) Add 25 μl ddH2O (autoclaved) and let sit on ice for 30 min. to rehydrate the RNA pellet. (27) Resuspend RNA pellet by pipetting up and down. (28) RNA was then purified further using an RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions; Buffers & Solutions: RNA extraction buffer (autoclave) consists of 100 mM Tris-HCl, pH 8.0, 100 mM LiCl, 10 mM EDTA, 1% SDS; Phenol:chloroform:isoamyl alcohol (25:24:1); Chloroform:isoamylalcohol (24:1); 8M LiCl (autoclave); 3M NaAC, pH 5.2 (autoclave); 70% Ethanol; 96% Ethanol (pure ethanol)Library Construction - Strand-specific RNA libraries were constructed by BGI, the protocol of which is proprietary.Sample Treatment - Four-week old plant leaves are infiltrated using a 1-mL needleless syringe containing 5 × 106 CFU/mL bacterial suspension. After 8 hours leaf tissue was harvested for analysis.Growth Protocol - Seeds were germinated on soil in 100% relative humidity. After 12 days seedlings were transplanted to larger pots (6 plants per pot) and grown for an additional 3 weeks. Plants were watered as required. Growth conditions: 16/8 hours light/dark cycle (120 mol m-2 s-1), 21/18 degrees Celsius day/night cycle, 65% relative humidity.OrganizationMINSEQE ScoreAssays and DataMAGE-TAB FilesZhishuo WangfalseGlobal transcriptomic profiling of PTI- and ETI-responsive genes in wild-type Col-0 and mutant rh3 Arabidopsis thaliana plantsPlants utilize a two-tiered immune system, called pattern-triggered immunity (PTI) and effector-triggered immunity (ETI), to recognise and defend against pathogens. PTI acts as the first line of defense, limiting pathogen invasion, whereas ETI provides a stronger response that potentiates PTI signaling. Here, we performed a global transcriptome analysis to compare immune-induced gene expression during PTI and ETI in wild-type Col-0 and the rh3 mutant Arabidopsis thaliana plants. Adult leaves were inoculated with a mock solution (MgCl₂), the non-pathogenic strain Pseudomonas syringae pv. tomato (Pst) DC3000 hrcC⁻, or the effector-triggering strain Pst DC3000 (avrHopZ1a). Leaf samples were collected 8 hours post-inoculation, with three independent biological replicates performed per condition.2026-03-18T00:00:00Z2026-03-18T21:19:32.578Z2025-11-01T18:11:36.982ZE-MTAB-15957ERP183506EFO_0002944EFO_0004170EFO_0003789EFO_0005518EFO_0003738EFO_0004184EFO_0003969