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Series GSE145208 Query DataSets for GSE145208
Status Public on Apr 01, 2021
Title A dynamic network reveals the novel characteristics of miRNA regulation over time in response to the ABA hormone in Arabidopsis (microRNA)
Organism Arabidopsis thaliana
Experiment type Non-coding RNA profiling by high throughput sequencing
Summary MicroRNAs (miRNAs) participate in post-transcriptional regulation as short non-coding RNAs together with the transcription factors (TFs) and other regulatory factors such as alternative splicing (AS), which constitute complex gene regulatory networks. Following stimulation with ABA in Arabidopsis, we performed RNA-seq and small RNA-seq simultaneously at consecutive time points, and found that miRNAs respond rapidly under stress condition. Further functional analyses revealed that miRNAs classified according to different response time points play a role by binding different target genes. Systematic analysis including the static network of TF-target, TF-miRNA, miRNA-target and the time series DEGs and DE-miRNAs revealed a miRNA-mRNA dynamic regulatory network. We found that miRNAs in miRNA-containing feed-forward loops (M-FFLs) could enhance co-expression and crosstalks between different FFLs of network. Additionally, the differential transcript usage (DTU) and differential alternative splicing (DAS) analysis increased regulatory diversity between miRNA and its target genes. Collectively, our findings highlighted the systematical and precise post-transcriptional regulation of miRNAs in plant.
Overall design Totally fifty-six samples, two treatments with seven time points and two replicates, and each sample has two files of paired-end data.
Contributor(s) Gao Z, Yu R, Li L, Deng XW, He H
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Submission date Feb 12, 2020
Last update date Apr 01, 2021
Contact name Xu Zhao Gao
Organization name Peking University
Department College of Biological Sciences
Lab Plant molecular genetics and agricultural biotechnology research laboratory
Street address The Summer Palace Road No. 5
City Beijing
State/province Beijing
ZIP/Postal code 100871
Country China
Platforms (1)
GPL19580 Illumina NextSeq 500 (Arabidopsis thaliana)
Samples (28)
GSM4308493 miRNA ABA_0.5h-1
GSM4308494 miRNA ABA_0.5h-2
GSM4308495 miRNA ABA_1h-1
This SubSeries is part of SuperSeries:
GSE145209 A dynamic network reveals the novel characteristics of miRNA regulation over time in response to the ABA hormone in Arabidopsis
BioProject PRJNA606322
SRA SRP248471

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE145208_miRNA_process.txt.gz 59.2 Kb (ftp)(http) TXT
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Raw data are available in SRA
Processed data are available on Series record

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