Transcriptomic analysis revealed adverse effect of melatonin on root growth
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ABSTRACT:
PROVIDER: PRJNA580447 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR10365935_1.fastq.gz | Fastqsanger.gz | |||
| SRR10365935_2.fastq.gz | Fastqsanger.gz | |||
| SRR10365936_1.fastq.gz | Fastqsanger.gz | |||
| SRR10365936_2.fastq.gz | Fastqsanger.gz | |||
| SRR10365937_1.fastq.gz | Fastqsanger.gz |
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Project description:Purpose: We aimed to compare transcriptomic changes after high concentration melatonin treatment in Arabidopsis Methods: A total amount of 3 μg RNA was used for generation of sequencing libraries using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. After cluster generation, the library preparations were sequenced on an Illumina Hiseq platform and 125 bp/150 bp paired-end reads were generated. Clean reads were obtained by removing low quality reads, reads containing adapter and ploy-N from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. Index of the Arabidopsis genome was built using Bowtie v2.2.3 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.12. HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And then FPKM (Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced) of each gene was calculated based on the length of the gene and reads count mapped to this gene. Differential expression analysis of drought stress versus control condition was performed using the DESeq R package (1.18.0). Results:In total, eight samples with two biological replicates per genotype/treatment combination were used for RNA sequencing analysis. At least 2 G clean bases were generated for each sample. Comparative analysis revealed different networks which were modulated by melatonin and IAA in Arabidopsis seedlings
2021-12-21 | GSE139595 | GEO
Project description:Melatonin is a well-known agent that plays multiple roles in animals. Its possible function in plants is less clear. In the present study, we tested the effect of melatonin (N-acetyl-5-methoxytryptamine) on soybean growth and development. Both spraying of leaves and seed-coating with melatonin significantly promoted soybean growth as judged from leaf size and plant height. This enhancement was also observed in soybean production and their fatty acid content. Melatonin increased pod number, seed number and seed weight. However, the 100-seed weight was not influenced by melatonin application. Melatonin also improved soybean tolerance to salt and drought stresses. Transcriptome analysis revealed that melatonin up-regulated the expression of many genes and alleviated the inhibitory effects of salt stress on gene expressions. Further detailed analysis of the affected pathways documents that melatonin likely achieved its promotional roles in soybean through enhancement of genes involved in cell division, photosynthesis, carbohydrate metabolism, fatty acid biosynthesis and ascorbate metabolism. Our results demonstrate that melatonin has significant potential for improving of soybean growth and seed production. Further study should uncover more about the molecular mechanisms of melatoninM-bM-^@M-^Ys function in soybeans and other crops. Four different treatments were chosen, water, salt, 100M-BM-5M melatonin and salt plus 100M-BM-5M melatonin. The comparison of salt/melatonin-treated sample versus water-treated sample reveals salt or melatonin induced transcriptome changes. The comparison of melatonin plus salt treated sample versus salt-treated sample reveals melatonin induced changes when salt exists.
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Project description:To interpret the melatonin-mediated flooding response in soybeans, proteomic analysis was performed in root tips.
2020-12-07 | PXD022450 | Pride
Project description:Melatonin is a well-known agent that plays multiple roles in animals. Its possible function in plants is less clear. In the present study, we tested the effect of melatonin (N-acetyl-5-methoxytryptamine) on soybean growth and development. Both spraying of leaves and seed-coating with melatonin significantly promoted soybean growth as judged from leaf size and plant height. This enhancement was also observed in soybean production and their fatty acid content. Melatonin increased pod number, seed number and seed weight. However, the 100-seed weight was not influenced by melatonin application. Melatonin also improved soybean tolerance to salt and drought stresses. Transcriptome analysis revealed that melatonin up-regulated the expression of many genes and alleviated the inhibitory effects of salt stress on gene expressions. Further detailed analysis of the affected pathways documents that melatonin likely achieved its promotional roles in soybean through enhancement of genes involved in cell division, photosynthesis, carbohydrate metabolism, fatty acid biosynthesis and ascorbate metabolism. Our results demonstrate that melatonin has significant potential for improving of soybean growth and seed production. Further study should uncover more about the molecular mechanisms of melatonin’s function in soybeans and other crops.
2014-08-31 | GSE57960 | GEO
Project description:Melatonin promotes Arabidopsis root growth in an IAA dependent manner [7d]
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Project description:Melatonin promotes Arabidopsis root growth in an IAA dependent manner [72h]
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Project description:Purpose: We aimed to compare transcriptomic changes after melatonin (MT) and IAA treatments in Arabidopsis and dissected cross-talk between MT and IAA Methods: A total amount of 1 μg RNA was used for generation of sequencing libraries using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. After cluster generation, the library preparations were sequenced on an Illumina Hiseq2000 platform and paired-end reads were generated. Clean reads were obtained by removing low quality reads, reads containing adapter and ploy-N from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. Index of the Arabidopsis genome was built using Bowtie v2.2.3 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.12. HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And then FPKM (Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced) of each gene was calculated based on the length of the gene and reads count mapped to this gene. Differential expression analysis of drought stress versus control condition was performed using the DESeq R package (1.18.0). Results:In total, six samples with two biological replicates per genotype/treatment combination were used for RNA sequencing analysis. At least 2 G clean bases were generated for each sample. Comparative analysis identified coregulated genes by melatonin and IAA in Arabidopsis seedlings
2021-12-21 | GSE152813 | GEO
Project description:Purpose: We aimed to compare transcriptomic changes after melatonin (MT) and IAA treatments in Arabidopsis and dissected cross-talk between MT and IAA Methods: A total amount of 1 μg RNA was used for generation of sequencing libraries using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. After cluster generation, the library preparations were sequenced on an Illumina Hiseq2000 platform and paired-end reads were generated. Clean reads were obtained by removing low quality reads, reads containing adapter and ploy-N from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. Index of the Arabidopsis genome was built using Bowtie v2.2.3 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.12. HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And then FPKM (Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced) of each gene was calculated based on the length of the gene and reads count mapped to this gene. Differential expression analysis of drought stress versus control condition was performed using the DESeq R package (1.18.0). Results:In total, six samples with two biological replicates per genotype/treatment combination were used for RNA sequencing analysis. At least 2 G clean bases were generated for each sample. Comparative analysis identified coregulated genes by melatonin and IAA in Arabidopsis seedlings
2021-08-11 | GSE167524 | GEO
Project description:Intervention 1: Intervention group: Treatment with melatonin will be started on the evening of the first chemotherapy dose and continue through 1 month following the last dose of chemotherapy or 6 months after starting melatonin (each one goes earlier). During this period, patients will consume 20 mg of melatonin (4 capsules, each one contains 5mg melatonin) every evening. Melatonin capsule will be supplied by Zahravi Pharmaceutical Company. Intervention 2: Control group: Treatment with melatonin will be started on the evening of the first chemotherapy dose and continue through 1 month following the last dose of chemotherapy or 6 months after starting melatonin/placebo (each one goes earlier). During this period, patients will consume 4 capsules of placebo every evening. Placebo capsules will be supplied by Zahravi Pharmaceutical Company and will be the same as melatonin.
Primary outcome(s): Percent of grade 2 and 3 neuropathy according to National Cancer Institute’s Common Toxicity Criteria for adverse events (NCI-CTCAE V.4) will be compered among the two study groups (case and control), as the main outcome of the study. Timepoint: Prior to the start of study; during the chemotherapy (prior to receiving each cycle); 1 month after receiving the last dose of chemotherapy or 6 months after initiation of melatonin (each one happens earlier). Method of measurement: National Cancer Institute’s Common Toxicity Criteria for adverse events (NCI-CTCAE V.4) scale will be used by the oncologist to evaluate severity of neuropathy in the patients. According to this scale severity of neuropathy will be classified from 1 to 5.
Study Design: Randomization: Randomized, Blinding: Double blinded, Placebo: Used, Assignment: Parallel, Purpose: Prevention, Randomization description: Randomization will be done by block-permutation method, considering 8 blocks, each one consisting 10 patients. Random Allocation software will be used to allocate patients to drug or placebo group. Randomization and allocation will be done by one of the researchers who has no role in the treatment and evaluation of the patients, and also analysis of data, Blinding description: Randomization and allocation will be done by one of the researchers who has no role in the treatment and evaluation of the patients, and also analysis of data. Drug (melatonin) and placebo packaging will be similar and will not be distinguishable by physician and patients who receive them. During the study, melatonin and placebo will be supplied by the same company.
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Project description:Background: Melatonin is considered to be a polyfunctional master regulator in animals and higher plants. Exogenous melatonin inhibits plant infection by multiple diseases; however, the role of melatonin in cucumber green mottle mosaic virus (CGMMV) infection remains unknown. Results: In this study, we demonstrated that exogenous melatonin treatment can effectively control CGMMV infection. The greatest control effect was achieved by 3 days of root irrigation at a melatonin concentration of 50 µM. Exogenous melatonin showed preventive and therapeutic effects against CGMMV infection at early stage in tobacco and cucumber. We utilized RNA sequencing technology to compare the expression profiles of mock-inoculated, CGMMV-infected, and melatonin+CGMMV-infected tobacco leaves. Defense-related gene CRISP1 was specifically upregulated in response to melatonin, but not to salicylic acid (SA). Silencing CRISP1 enhanced the preventive effects of melatonin on CGMMV infection, but had no effect on CGMMV infection. We also found exogenous melatonin has preventive effects against another Tobamovirus, pepper mild mottle virus (PMMoV) infection. Conclusions: Together, these results indicate that exogenous melatonin controls two Tobamovirus infection and inhibition of CRISP1 enhanced melatonin control effects against CGMMV infection, which may lead to the development of a novel melatonin treatment for Tobamovirus control.
2022-12-30 | GSE221904 | GEO