Project description:Long non-coding RNAs (lncRNAs) are essential regulators of a broad range of biological processes in plants. Spectacular progress in next-generation sequencing technologies has enabled genome-wide identification of lncRNAs in multiple plant species. In this study, genome-wide lncRNA sequencing technology was used to identify cold-responsive lncRNAs at the booting stage in rice by comparison of a tolerant variety, Kongyu131 (KY131), and a sensitive variety, Dongnong422 (DN422). GO and KEGG enrichment analysis were performed, focusing on the cis- and trans- target genes of differential lncRNAs. To identify cold-responsive genes, a meta-analysis was used to integrate cold-tolerant QTLs at the booting stage. In total, 13 cold-responsive target genes were obtained by KEGG enrichment analysis combined with meta-analysis, as confirmed by qRT-PCR. Finally, three of these genes were identified in response to cold stress. These results sought to provide new insight into cold-resistance research for rice.

2018-12-15 | GSE123900 | GEO

ICE1 regulation of the Arabidopsis Cold-Responsive Transcriptome

Project description:To understand the gene network that controls plant tolerance to cold stress, we carried out a near full genome transcript expression profiling in Arabidopsis using Affymetrix GeneChips that contain approximately 24,000 genes. For microarray analysis, Arabidopsis seedlings were cold treated at 0 C for 0 h, 3 h, 6 h, and 24 h. A total of 939 genes were statistically determined to be cold-regulated with 655 being up-regulated and 284 down-regulated. A large number of the early cold-responsive genes encode transcription factors that likely control late-responsive genes, which implies a multitude of transcriptional cascades. In addition, many genes involved in post-transcriptional and chromatin level regulation were also cold regulated suggesting their involvement in cold responsive gene regulation. A number of genes important for the biosynthesis or signaling of plant hormones, such as abscisic acid, gibberellic acid and auxin, are regulated by cold stress, which is of potential importance in coordinating cold tolerance with growth and development. We compared the cold-responsive transcriptomes of wild type and ice1, a mutant defective in an upstream transcription factor required for chilling and freezing tolerance. The transcript levels of many cold-responsive genes were altered in the ice1 mutant not only during cold stress conditions, but also before cold treatments. Our study provides a global picture of the Arabidopsis cold-responsive transcriptome and its control by ICE1, and thus will be valuable for understanding gene regulation under cold stress and the molecular mechanisms of cold tolerance. Keywords: Cold Stress response

2005-10-01 | GSE3326 | GEO

cold-responsive genes in tomato

Project description:cold-responsive genes in tomato Raw sequence reads

| PRJNA1201737 | ENA

sphingo-1-Identification of Sphingolipid regulated genes in cold stress response. Sphingolipids regulated genes.

Project description:rs07-05_sphingolipids-cold - sphingo-1 - The cold choc response seems to be partly triggered by Sphingolipid species. To date no gene response as been associated to sphingolipid signaling pathway in plant. Our aim is to identify among the cold induced genes the ones regulated by sphingolipids and to try to define a sphingolipid pathway specific group of genes. - 7ml of 5 days-old cells suspensions were incubated in presence of different sphingolipid pathway inhibitors, 30 min to 2 hours depending in the coumpound (all were resuspended in DMSO and control were done with DMSO). Then a 30 min cold choc was applied before cells were harvested and frozen in cold nitrogen. RNA were then extracted. FB1 and DMS were from Alexis , Myr from Cayman, TSP from matreya.

2012-03-28 | GSE36659 | GEO

sphingo-1-Identification of Sphingolipid regulated genes in cold stress response. Sphingolipids regulated genes.

2012-03-27 | E-GEOD-36659 | biostudies-arrayexpress

RNA-seq for Cold-treated bamboo

Project description:Identification of the Cold-responsive gene

2022-04-22 | GSE130314 | GEO

Identification of genes regulated by Bcl11b

Project description:Identification of genes regulated by Bcl11b

| PRJNA856979 | ENA