02544nas a2200313   4500000000100000000000100001008004100002260000900043100001700052700001400069700001600083700001800099700001500117700001500132700001500147700001500162700001600177700001000193700001900203700001900222700001100241700001100252700001600263245012500279300001100404490000700415520179400422022001402216       2021                            d  c20211 aHuiyuan Wang1 aSheng Liu1 aXiufang Dai1 aYongkang Yang1 aYunjun Luo1 aYubang Gao1 aXuqing Liu1 aWentao Wei1 aHuihui Wang1 aXi Xu1 aAnireddy Reddy1 aPankaj Jaiswal1 aWei Li1 aBo Liu1 aLianfeng Gu00aPSDX: A Comprehensive Multi-Omics Association Database of  With a Focus on the Secondary Growth in Response to Stresses.  a6555650 v123 a<p>() is a model tree for the investigation of wood formation. In recent years, researchers have generated a large number of high-throughput sequencing data in . However, no comprehensive database that provides multi-omics associations for the investigation of secondary growth in response to diverse stresses has been reported. Therefore, we developed a public repository that presents comprehensive measurements of gene expression and post-transcriptional regulation by integrating 144 RNA-Seq, 33 ChIP-seq, and six single-molecule real-time (SMRT) isoform sequencing (Iso-seq) libraries prepared from tissues subjected to different stresses. All the samples from different studies were analyzed to obtain gene expression, co-expression network, and differentially expressed genes (DEG) using unified parameters, which allowed comparison of results from different studies and treatments. In addition to gene expression, we also identified and deposited pre-processed data about alternative splicing (AS), alternative polyadenylation (APA) and alternative transcription initiation (ATI). The post-transcriptional regulation, differential expression, and co-expression network datasets were integrated into a new Stem Differentiating Xylem (PSDX) database (http://forestry.fafu.edu.cn/db/SDX), which further highlights gene families of RNA-binding proteins and stress-related genes. The PSDX also provides tools for data query, visualization, a genome browser, and the BLAST option for sequence-based query. Much of the data is also available for bulk download. The availability of PSDX contributes to the research related to the secondary growth in response to stresses in , which will provide new insights that can be useful for the improvement of stress tolerance in woody plants.</p>
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