@inbook{dalal_land_vasani_he_smith_rodriguez-welsh_perera_sederoff_2015, title={Methods for RNA Profiling of Gravi-Responding Plant Tissues}, volume={1309}, ISBN={9781493926961 9781493926978}, ISSN={1064-3745 1940-6029}, url={http://dx.doi.org/10.1007/978-1-4939-2697-8_9}, DOI={10.1007/978-1-4939-2697-8_9}, abstractNote={Plant transcriptional responses to gravity stimulation by reorientation are among the fastest measured in any tissue or species. Upon reorientation, changes in abundance of specific mRNAs can be measured within seconds or minutes, for plastid or nuclear encoded genes, respectively. Identifying fast gravity-induced transcripts has been made possible by the development of high-throughput technology for qualitative and quantitative RNA analysis. RNA profiling has undergone further rapid development due to its enormous potential in basic sciences and medical applications. We describe here the current and most widely used methods to profile the changes in an entire transcriptome by high-throughput sequencing of RNA fractions (RNAseq) and single gene transcript analysis using real-time quantitative reverse-transcriptase polymerase chain reaction (qRT-PCR).}, booktitle={Methods in Molecular Biology}, publisher={Springer New York}, author={Dalal, Jyoti and Land, Eric and Vasani, Naresh and He, Luyan and Smith, Caroline and Rodriguez-Welsh, Maria and Perera, Imara Y. and Sederoff, Heike}, year={2015}, pages={91–117} }
 @article{howard_hu_babaoglu_chandra_borghi_tan_he_winter-sederoff_gassmann_veronese_et al._2013, title={High-Throughput RNA Sequencing of Pseudomonas-Infected Arabidopsis Reveals Hidden Transcriptome Complexity and Novel Splice Variants}, volume={8}, ISSN={["1932-6203"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84885077606&partnerID=MN8TOARS}, DOI={10.1371/journal.pone.0074183}, abstractNote={We report the results of a genome-wide analysis of transcription in Arabidopsis thaliana after treatment with Pseudomonas syringae pathovar tomato. Our time course RNA-Seq experiment uses over 500 million read pairs to provide a detailed characterization of the response to infection in both susceptible and resistant hosts. The set of observed differentially expressed genes is consistent with previous studies, confirming and extending existing findings about genes likely to play an important role in the defense response to Pseudomonas syringae. The high coverage of the Arabidopsis transcriptome resulted in the discovery of a surprisingly large number of alternative splicing (AS) events--more than 44% of multi-exon genes showed evidence for novel AS in at least one of the probed conditions. This demonstrates that the Arabidopsis transcriptome annotation is still highly incomplete, and that AS events are more abundant than expected. To further refine our predictions, we identified genes with statistically significant changes in the ratios of alternative isoforms between treatments. This set includes several genes previously known to be alternatively spliced or expressed during the defense response, and it may serve as a pool of candidate genes for regulated alternative splicing with possible biological relevance for the defense response against invasive pathogens.}, number={10}, journal={PLOS ONE}, author={Howard, Brian E. and Hu, Qiwen and Babaoglu, Ahmet Can and Chandra, Manan and Borghi, Monica and Tan, Xiaoping and He, Luyan and Winter-Sederoff, Heike and Gassmann, Walter and Veronese, Paola and et al.}, year={2013}, month={Oct} }