Melatonin promotes Arabidopsis root growth in an IAA dependent manner [72h]
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ABSTRACT:
PROVIDER: PRJNA640533 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR12053493_1.fastq.gz | Fastqsanger.gz | |||
| SRR12053493_2.fastq.gz | Fastqsanger.gz | |||
| SRR12053494_1.fastq.gz | Fastqsanger.gz | |||
| SRR12053494_2.fastq.gz | Fastqsanger.gz | |||
| SRR12053495_1.fastq.gz | Fastqsanger.gz |
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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
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Project description:Melatonin promotes Arabidopsis root growth in an IAA dependent manner [7d]
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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.
2014-08-31 | E-GEOD-57960 | biostudies-arrayexpress
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.
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