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In this study, deep transcriptome RNA sequencing (RNA-Seq) of Brassica rapa was undertaken with two objectives: SNP detection and improved transcriptome annotation. We performed SNP detection on two varieties that are parents of a mapping population to aid in development of a marker system for this population and subsequent development of high-resolution genetic map. An improved Brassica rapa transcriptome was constructed to detect novel transcripts and to improve the current genome annotation. Deep RNA-Seq of two Brassica rapa genotypes—R500 (var. trilocularis, Yellow Sarson) and IMB211 (a rapid cycling variety)—using eight different tissues (root, internode, leaf, petiole, apical meristem, floral meristem, silique, and seedling) grown across three different environments (growth chamber, greenhouse and field) and under two different treatments (simulated sun and simulated shade) generated 2.3 billion high-quality Illumina reads. In this experiment, two pools were made, with one pool consisting of 66 samples collected from growth chamber and another pool consisting of 60 samples collected from greenhouse and field. 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Cell lysates were immunoprecipitated with TBK1 antibody. Antibody enriched protein samples were run on SDS-PAGE gels and submitted to UT Southwestern Proteomics Core Facility for Mass Spectrometry. Protein gel pieces were digested overnight with trypsin (Pierce) following reduction and alkylation with DTT and iodoacetamide (Sigma Aldrich. The samples then underwent solid-phase extraction cleanup with Oasis HLB microelution plates (Waters) and the resulting samples were analyzed by LC-MS-MS, using an Orbitrap Fusion Lumos mass spectrometer (Thermo Electron) coupled to an Ultimate 3000 RSLC-Nano liquid chromatography systems (Dionex)."}],"externalReference":[],"extraInfo":[],"format":[],"fulltext":[],"geolocation":[],"id":"50|_____OmicsDI::023fd1fcbb64f0f7df0671798a62f379","instance":[{"accessright":{"classid":"UNKNOWN","classname":"not available","schemeid":"dnet:access_modes","schemename":"dnet:access_modes"},"collectedfrom":{"key":"10|rest________::f63e28997bb5aee636a4d21ab2a0a5f9","value":"Omics Discovery Index (OmicsDI)"},"dateofacceptance":{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:datasetarchive","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"value":"2019-12-03"},"distributionlocation":"","hostedby":{"key":"10|omicsdi_____::7ab3f388bbf5200ebf5e501260ecddcc","value":"MassIVE Database (Mass Spectrometry Interactive Virtual Environment)"},"instancetype":{"classid":"0021","classname":"Dataset","schemeid":"dnet:publication_resource","schemename":"dnet:publication_resource"},"refereed":{"classid":"UNKNOWN","classname":"UNKNOWN","schemeid":"dnet:review_levels","schemename":"dnet:review_levels"},"url":["https://www.omicsdi.org/dataset/massive/MSV000084654"]}],"language":{"classid":"UNKNOWN","classname":"UNKNOWN","schemeid":"dnet:languages","schemename":"dnet:languages"},"lastupdatetimestamp":1597349577614,"oaiprovenance":{"originDescription":{"altered":true,"baseURL":"https%3A%2F%2Fwww.omicsdi.org%2Fws%2Fdataset%2Fsearch","datestamp":"","harvestDate":"2020-07-18T15:06:08.42Z","identifier":"","metadataNamespace":""}},"originalId":[""],"pid":[{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"qualifier":{"classid":"pdb","classname":"pdb","schemeid":"dnet:pid_types","schemename":"dnet:pid_types"},"value":"fakepdb"}],"relevantdate":[],"resourcetype":{"classid":"UNKNOWN","classname":"UNKNOWN","schemeid":"dnet:dataCite_resource","schemename":"dnet:dataCite_resource"},"resulttype":{"classid":"dataset","classname":"dataset","schemeid":"dnet:result_typologies","schemename":"dnet:result_typologies"},"source":[],"subject":[{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:datasetarchive","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"qualifier":{"classid":"UNKNOWN","classname":"UNKNOWN","schemeid":"dnet:subject_classification_typologies","schemename":"dnet:subject_classification_typologies"},"value":"Proteomics"}],"title":[{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:datasetarchive","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"qualifier":{"classid":"main title","classname":"main title","schemeid":"dnet:dataCite_title","schemename":"dnet:dataCite_title"},"value":"EGFR inhibition triggers an adaptive response by co-opting antiviral signaling pathways in lung cancer"}]}
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