Differential gene expression in Miscanthus sinensis under chilling stress
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Illumina HiSeq 4000
ORGANISM(S): Miscanthus sinensis
SUBMITTER: Karolina Sobańska
PROVIDER: E-MTAB-15229 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:Iso-Seq (PacBio) sequencing was performed to generate a reference transcriptome library of M. sinensis.
2025-11-21 | E-MTAB-15228 | biostudies-arrayexpress
Project description:Cotton premature leaf senescence often occurred with an increasing frequency in many cotton growing areas and caused serious reduction in yield and quality of cotton has been one of the impontant factors that restrict severely the production of cotton.Our laboratory studies showed chilling stress is the key factor that induced A. alternatia infection, caused Alternaria disease and then lead to cotton leaf senescence, but the molecular mechanism of cotton premature leaf senscence is still unclear. We used microarrays to study molecular mechanism of chilling stress causing Alternaria alternata infection and leading to cotton leaf senescence and find the key genes during this process. Plants were grown in growth chamber with a 14/10 hours photoperiod, 28â/22â. Three-to-four leaves stage cotton plants were pre-treated by chilling stress with the low temperatures of 16/12â day/night for a fixed time length of 3 days. While, the normal growth plants were sustained growing at optimal temperature of 28/20â day/night. And then, both chilling stress pre-treated and normal growth cotton plants were inoculated with Alternaria. alternata isolate A1. The mock inoculations were performed with sterilized water. Cotton leaf Samples were respectively collected at 3, 6 days after inoculation (DAI) for RNA extraction and hybridization on Affymetrix microarrays. To that end, we collected 8 samples, i.e. chilling stress pre-treated cotton leaves: 3 DAI (C) and its mock control (D), 6 DAI (E) and its mock control (F); normal growth cotton leaves: 3 DAI (H) and its mock control (I), 6 DAI (J) and its mock control (K). All samples were arranged in completely randomized designed with three replications for each treatment.
2015-10-28 | E-GEOD-74412 | biostudies-arrayexpress
Project description:This study investigated changes in gene expression of controlled environment chilled (4C) grape overwintering buds as they accumulated from 0 to 2000 chilling hours. Keywords: time course, chilling, endodormancy release, axillary bud, grape A loop design with 3 biological replicates (RNA from buds collected at 0, 500, 1000, 1500, and 2000 hr of chilling in 2002, 2004, and 2005).
2010-05-18 | E-GEOD-9903 | biostudies-arrayexpress
Project description:In this study we used the Affymetrix Barley 1 GeneChip to investigate transcriptome responses of barley cv. Morex to low temperature, including triplicated measurements of cold, freeze/thaw cycles and de-acclimation over 33 days. Experiment Overall Design: Plants were grown at 20ºC for seven days and subject to a symmetrical cycle of acclimation, cold, freeze-thaw, and deacclimation. Chilling began by decreasing the temperature overnight from 20ºC to 4ºC at a rate of 1.3ºCâ¢h-1 and maintaining temperatures of 4 ºC in the day and 2ºC at night for 5 days. Freeze-thaw cycling lasted 12 days with day temperatures of 4ºC and night temperatures gradually decreasing from -2ºC the first night to -4ºC for three nights and -10ºC for four nights, then recovering to -4ºC for three nights and -2ºC for one night. This treatment was designed to allow daily freeze-thaw cycling and protein synthesis. Chilling conditions (4ºC day, 2ºC night) were resumed for five days, followed by deacclimation with increasing temperature to 20ºC overnight and maintaining for three days. Sampling was done at four different times, each at the 11th hour of light to avoid circadian effects: 1) before chilling treatment, 2) five days after initiation of chilling treatment, 3) eight days into freeze-thaw treatment and 4) three days into de-acclimation.
2008-06-15 | E-GEOD-6993 | biostudies-arrayexpress
Project description:We investigated effect of severe cold on transcriptome changes in two inbred maize lines, chilling-sensitive ETH-DL3 and chilling-tolerant ETH-DH7. Kernels were germinated in wet sand in darkness at 25C. Seedlings were transferred to growth chamber (day/night temperature 24/22C, photoperiod 14/10 h, light 250 umol quanta x m-2 x s-1) and grow in pots containing Knop's nutrient solution supplemented with Hoagland's micro-nutrients. After full development of the 3rd leaf (fully developed ligular region) plants were used in experiment. The experiment was begun at the start of the dark period. Half of the plants were transferred to cold chamber (day/night temperature 8/6C, photoperiod 14/10 h, light 250 umol quanta x m-2 x s-1) other half served as control (day/night temperature 24/22C, other parameters was the same as for cold treatment). After dark period (10h) and 200 minutes of light period samples were taken. Each sample consisted of the middle part of the 3rd leaf blade, pooled from three plants and frozen in liquid nitrogen. The experiment was replicated four times with two replications dye swapped.
2014-03-15 | E-MTAB-1315 | biostudies-arrayexpress
Project description:RNA-Seq was performed to study the change of gene expression before and after chilling treatment in rice. Different change patterns were identified. We have provided a complete view of transcriptome under cold stress condition, which will deepen our understanding of gene expression regulation in cold stress response as well as cold stress response mechanism for monocot plants. The mRNA profiles of 15-day-old rice seedlings with and without chilling treatment (4 °C for 33 h) were generated by deep sequencing using Illumina Hiseq 2000 platform.
2016-04-13 | E-GEOD-67373 | biostudies-arrayexpress
Project description:We take the one year old plant for chilling stress (4M-BM-0C, 10h) and controls.Use the Affymetrix poplar gene chip to decrypt the gene functions and mechanisms in Populus simonii leaves. We used microarrays to detail the global programme of gene expression during chilling stress (4M-BM-0C, 10h). Populus simonii leaves were taken from chilling stress (4M-BM-0C, 10h) and controls for RNA extraction and hybridization on Affymetrix microarrays.BH11269-2_Zdqe 13 and BH11269-2_Zdqe 14 from chilling stress (4M-BM-0C, 10h) treatments, CK1 and CK2 controls.
2014-05-16 | E-GEOD-43872 | biostudies-arrayexpress
Project description:We investigated chilling response of seedlings of three inbred maize lines: chilling tolerant S68911, chilling-sensitive S160 and moderate chilling-sensitive S50676. Kernels were germinated in wet sand in darkness at 25C. Seedlings were transferred to growth chamber (photoperiod 14/10h, temperature 24, light 250 umol quanta x m-2 x s-1), grown till the third-leaf stage and used in experiment. Chilling treatment started at the start of the dark period and lasted 38h (10h dark, 14h light,10h dark, 4h light). Growth conditions was as previously described but temperature was set to 14 (light/dark). At the same time control plants were grown as previously described. There were three biological replications of hybridization scheme.
2016-02-14 | E-MEXP-3508 | biostudies-arrayexpress
Project description:The aim of this study was to conduct global gene expression profiling and comparative analysis of two chilling tolerant rice varieties, Jumli Marshi and Sijung (spp. Japonica), during early chilling stress (24h, 10C). Leaf tissue from cv. Jumli Marshi and cv. Sijung plants grown under chilling stress conditions were harvested after 4 and 24 h. Control plants (0 h) were harvested at the beginning of the experiment, i.e., at mid-day. Three biological replicates were profiled for each time point and variety. In order to readily detect highly (saturated) as well as weakly (near background signal) expressed genes, scanning was done twice on the microarrays: at the PMT sensitivity level 100% (pmt100) and 10% (pmt10).
2014-11-30 | E-MTAB-3121 | biostudies-arrayexpress
Project description:Rice is sensitive to chilling stress, especially at the seedling stage. To elucidate the molecular genetic mechanisms of chilling tolerance in rice, comprehensive gene expressions of two rice genotypes (chilling-tolerant LTH and chilling-sensitive IR29) with contrasting responses to chilling stress were comparatively analyzed. Results revealed distinct global transcription reprogramming between the two rice genotypes under time-series chilling stress and subsequent recovery conditions. A set of genes with higher basal expression were identified in LTH, indicating their possible role in intrinsic tolerance to chilling stress. Under chilling stress, the major effect on gene expression was up-regulation in LTH and strong repression in IR29. Early responses to chilling stress in both genotypes featured commonly up-regulated genes related to transcription regulation and signal transduction, while functional categories for late phase chilling regulated genes were diverse with a wide range of functional adaptations to continuous stress. Following the cessation of chilling treatments, there was quick and efficient reversion of gene expression in LTH, while IR29 displayed considerably slower recovering capacity at the transcriptional level. In addition, the detection of differentially-regulated TF genes and enriched cis-elements demonstrated that multiple regulatory pathways, including CBF and MYBS3 regulons, were involved in chilling stress tolerance. In present study, comprehensive gene expression using an Affymetrix rice genome array revealed a diverse global transcription reprogramming between two rice genotypes under chilling stress and subsequent recovery conditions. The dominant change in gene expression at low temperature was up-regulation in the chilling-tolerant genotype and down-regulation in the chilling-sensitive genotype. Early responses to chilling stress common to both genotypes featured up-regulated genes related to transcription regulation and signal transduction, while functional categories of LR-chilling regulated genes were clearly diverse with a wide range of functional adaptations. At the end of the chilling treatments, there was quick and efficient reversion of gene expression in LTH, while IR29 displayed considerably slower recovery capacity at the transcriptional level. Finally, analysis of differentially-regulated TF genes and enriched cis-elements demonstrated that multiple regulatory pathways, including CBF and MYBS3 regulons, are involved in chilling stress tolerance. In this study, parallel transcriptomic analysis in two rice genotypes with contrasting chilling-tolerant phenotypes was performed to identify and characterize novel genes involved in chilling stress tolerance in rice.
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