Gene Expression
Nebulas
Gene Expression NebulasSummary: We performed RNA-Seq of leaves of Oryza sativa L. ssp. japonica cv. Nipponbare 48 hours after inoculation with Xanthomonas oryzae pv. oryzae strain PXO99A heterologously expressing the Tal2a effector, the designer TAL effector dT280 which targets a sequence overlapping the predicted Tal2a binding sequence in UCH, or the Tal11b effector. Results provide insight into the genes differentially regulated in a Tal2a- and dT280-specific manner.
Overall Design: Examination of mRNA levels in Oryza sativa L. ssp. japonica cv. Nipponbare leaves at 48 hours after inoculation. Each leaf was considered a separate biological replicate.
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| Growth Protocol: | Oryza sativa L. ssp. japonica cv. Nipponbare plants to be inoculated were grown in LC-1 soil mixture (Sungro, Bellevue, WA) in PGC15 growth chambers (Percival Scientific, Perry, IA) in trays approximately 60 cm below a combination of fluorescent and incandescent bulbs providing approximately 1,000 μmoles/m2/s measured at 15 cm, under a cycle of 12 h of light at 28 °C and 12 h of dark at 25 °C. |
| Treatment Protocol: | Plants were inoculated at four weeks with bacterial suspensions in 10 mM MgCl2 at approximately OD600=0.9 by infiltration using a needleless syringe. A region from the leaf tip to about 5 cm from the tip was completely infiltrated with contiguous spots. Tissue was collected individually from each leaf after 48 hours. |
| Extract Protocol: | RNA was extracted with the Qiagen RNeasy kit and manufacturer's protocol. |
| Library Construction Protocol: | These libraries were prepped with the Illumina TruSeq RNA Sample Prep v2 kit |
| Molecule Type: | poly(A)+ RNA |
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| Library Layout: | SINGLE |
| Library Strand: | - |
| Platform: | ILLUMINA |
| Instrument Model: | Illumina HiSeq 2000 |
| Strand-Specific: | Unspecific |
| Data Resource | GEN Sample ID | GEN Dataset ID | Project ID | BioProject ID | Sample ID | Sample Name | BioSample ID | Sample Accession | Experiment Accession | Release Date | Submission Date | Update Date | Species | Race | Ethnicity | Age | Age Unit | Gender | Source Name | Tissue | Cell Type | Cell Subtype | Cell Line | Disease | Disease State | Development Stage | Mutation | Phenotype | Case Detail | Control Detail | Growth Protocol | Treatment Protocol | Extract Protocol | Library Construction Protocol | Molecule Type | Library Layout | Strand-Specific | Library Strand | Spike-In | Strategy | Platform | Instrument Model | Cell Number | Reads Number | Gbases | AvgSpotLen1 | AvgSpotLen2 | Uniq Mapping Rate | Multiple Mapping Rate | Coverage Rate |
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