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PROVIDER: PRJNA755748 | ENA |
REPOSITORIES: ENA
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Project description:Here we performed a transcriptomic study on the effect of sodium nitroprusside (SNP) on cucumber leaves under alkali stress using Solexa/Illumina's high-throughput digital gene expression (DGE) system. Two DGE libraries (from one NaHCO3-treated sample and one NaHCO3 + SNP-treated sample) were constructed, and the gene expression variations between the two samples were compared. Hundreds of differentially expressed genes were obtained by the comparison, and GO analysis of these genes suggested that many biological processes, molecular function, cellular components were related to SNPM-bM-^@M-^Ys mitigated effect on alkaline stress. The authenticity of the DGE data was further confirmed by analyzing real-time RT-PCR using several random-selected genes. The experiment had 2 treatments: 30 mM NaHCO3 (alkali stress treatment, indicated as Na) and 30 mM NaHCO3+100 M-NM-<M sodium nitroprusside (indicated as SNP). Samples from Na- and SNP-treated leaves, used for RNA isolation, were harvested, and the two corresponding tag libraries of samples were constructed in parallel. Illumina sequencing of transcripts from Na- and SNP-treated samples to get gene information for cucumber leaves in different treatments.
2013-11-26 | E-GEOD-42439 | biostudies-arrayexpress
Project description:Real-time quantitative PCR (RT–qPCR) is the favoured method for gene expression analysis in molecular biology due to its sensitivity, specificity, cost-effectiveness, and reproducibility. To obtain the accuracy and reliability of RT-qPCR, the use of reliable reference genes is inevitable. There were many reports about the physiological response of giant reed (Arundo donax L.) to abiotic stresses. However, there is little use in the validation of reference genes under different treatments. It still belongs to the blank that the research about selecting reference genes under salt and alkali. In this study, the expression stability of twenty-three candidate reference genes in leaves and roots were assessed under salt, drought, and alkali stresses using geNorm, NormFinder, BestKeeper, and Delta Ct algorithms. Our results showed that no one gene had an invariant expression under different conditions. For example, under drought stress, UPL3, UBC2, and APT1 were better reference genes in leaves, RPL5 and FPS2 were better in roots. Under alkali stress, GAPDH, APT1, and RPS5 were better reference genes in leaves; UPL3, ACT2, and SAMDC2 were better in roots. In addition, the expression of MSD1 was used to further confirm the validated reference genes under salt, drought, and alkali stresses. It was proved that the use of inappropriate reference genes in giant reed significantly altered the relative expression of target genes and even reversed the results. Consequently, our results provided guidelines for reference gene selection under salt, drought, and alkali stresses and a foundation for more accurate and widespread use of RT-qPCR in the giant reed.
2021-12-15 | GSE190890 | GEO
Project description:Here we performed a transcriptomic study on the effect of sodium nitroprusside (SNP) on cucumber leaves under alkali stress using Solexa/Illumina's high-throughput digital gene expression (DGE) system. Two DGE libraries (from one NaHCO3-treated sample and one NaHCO3 + SNP-treated sample) were constructed, and the gene expression variations between the two samples were compared. Hundreds of differentially expressed genes were obtained by the comparison, and GO analysis of these genes suggested that many biological processes, molecular function, cellular components were related to SNP’s mitigated effect on alkaline stress. The authenticity of the DGE data was further confirmed by analyzing real-time RT-PCR using several random-selected genes.
2013-11-26 | GSE42439 | GEO
Project description:Alkali-salinity exerts severe osmotic, ionic, and high-pH stresses to plants. Photosynthetic machinery is especially sensitive to saline-alkali stress. In addition, reversible protein phosphorylation also play crucial roles in plant salt resistance. While our knowledge on protein phosphorylation events in salt stress response is very limited. Few studies have been published involving photosynthetic protein phosphorylation modulation to improve salt resistance. In the present study, we investigated the Na2CO3-responsive characteristics in Puccinellia tenuiflora chloroplasts using stable isotope dimethyl labeled phosphoproteomic approach. A total of 161 unique phosphopeptides were identified, and 137 phosphopeptides were quantified by dimethyl labeling. Among them, 50 proteins were quantified as Na2CO3-responsive proteins with 57 phosphosites, including 33 increased and 14 decreased. Importantly, 26 phosphosites were newly identified as Na2CO3-responsive phosphoproteins in plants, which were supposed to be crucial for regulating photosynthesis, membrane and transporting, signaling, stress response, and protein synthesis and turnover. Among them, seven light harvesting proteins, six PSII proteins, five PSI proteins, three electron transfer chain proteins, and two Calvin cycle-related proteins were increased, but five ATP synthase subunits and sucrose-phosphate synthase were decreased at phosphorylation level. Besides, Na+/H+ antiporter, villin-2, and two thylakoid organization related proteins were increased at phosphorylation level. Two signaling related proteins and most protein species in charge of gene expression and protein turnover were enhanced at phosphorylation level at 24h after Na2CO3 treatment.
2021-08-30 | PXD005472 | Pride
Project description:Salt stress, especially saline-alkali stress, has seriously negative effect on citrus production. Ziyang xiangcheng (Citrus junos Sieb.) (Cj) has been reported as a saline-alkali stress and iron deficiency tolerant citrus rootstock. However, the molecular mechanism of its saline-alkali stress tolerance is still not clear. Two citrus rootstocks and one navel orange scion, Cj, Poncirus trifoliate (Poncirus trifoliata (L.) Raf.) (Pt) and ‘Lane Late’ navel orange (Citrus sinensis (L.) Osb.) (LL), were used in this study. The grafted materials Cj+LL and Pt+LL grown in calcareous soil were used to identify genes and pathways responsive to saline-alkali stress using RNA-seq. The seedlings of Cj and Pt grown in the solutions with different gradient pH value were used to perform a supplement experiment. Comprehensively analyzing the data of RNA-seq, physiology and biochemistry, agronomic traits and mineral elements of Cj+LL, Pt+LL, Cj and Pt, several candidate pathways and genes were identified to be highly regulated under saline-alkali stress. Here, we propose citrate is important for the tolerance to iron deficiency and the jasmonate (JA) biosynthesis and signal transduction pathway may play a crucial role in tolerance to saline-alkali stress in citrus by interacting with other plant hormones, calcium signaling, ROS scavenging system and lignin biosynthesis.
2018-07-06 | GSE98996 | GEO
Project description:Resequencing and comparative genomics for SNP/InDel indentification
| PRJDB1804 | ENA
Project description:Abstract: In order to understand the expression patterns of miRNAs in alfalfa under alkali stress, small RNA sequencing was performed on alfalfa roots at different time points under alkali stress, and miRNAs were identified and analyzed.
2023-05-08 | GSE231697 | GEO
Project description:SNP array of 7 HCCs and matched background liver in children with bile salt export pump deficiency
| EGAD00010000560 | EGA
Project description:To investigate possible genetic basis of alkali tolerance in rice, we generated an introgressed rice line (K83) with significantly enhanced tolerance to alkali stress than its recipient parental cultivar (Jijing88). By using microarray analysis, we examined global gene expression profiles in K83 and Jijing88, found more than 1,200 genes were constitutively differentially expressed in K83 compared with Jijing88, with 572 up- and 654 down-regulated. Upon alkali treatment, a total of 347 genes in K83 were found up- and 156 down-regulated in K83, compared with 591 and 187 respectively in Jijing88. Seven-day-old uniform-sized seedlings grown in hydroponic medium were transferred to fresh hydroponic medium alone or containing 50 mM alkali salts. Shoots were harvested 24 h after transfer and 10 shoots were pooled for microarray analysis.
2014-05-16 | E-GEOD-45724 | biostudies-arrayexpress
Project description:Soil alkalinity greatly affects plant growth and crop productivity. Although RNA-Seq analyses have been conducted to investigate genome-wide gene expression in response to alkaline stress in many plants, the expression of alkali-responsive genes in rice has not previously investigated. In this study, the transcriptomic data were compared between an alkaline-tolerant [WD20342 (WD)] and an alkaline-sensitive [Caidao (CD)] rice cultivar under control and alkaline stress conditions. A total of 962 important alkali-responsive (IAR) genes from highly differentially expressed genes (DEGs) were identified, including 28 alkaline-resistant cultivar-related genes, 771 alkaline-sensitive cultivar-related genes and 163 cultivar-non-specific genes. Gene ontology (GO) analysis suggested the enrichment of IAR genes involved in response to various stimuli or stresses. According to KEGG pathway analysis, the IAR genes were related primarily to plant hormone signal transduction and biosynthesis of secondary metabolites. Additionally, among these 962 IAR genes, 74 were transcription factors and 15 occurred with differential alternative splicing between the different samples after alkaline treatment. Our results provide a valuable resource on alkali-responsive genes and should benefit the improvement of alkaline stress tolerance in rice.
2018-07-12 | GSE104928 | GEO