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Transcriptome Phase Distribution Analysis Reveals Diurnal Regulated Biological Processes and Key Pathways in Rice Flag Leaves and Seedling Leaves
Wenying Xu, Institute of Genetics and Developmental Biology, Department of Chinese Academy of Sciences, Beijing, China (x_wenying@yahoo.com)
Experiment design (40 hybridizations)
developmental stage name
•Seedling leaf •Flag Leaf
time
•Time 1 •Time 2 •Time 3 •Time 4 •Time 5 •Time 6 •Time 7 •Time 8 •Time 9 •Time 10

This experiment has been imported by PLEXdb from NCBI GEO (GSE28124)

Series_summary:
Plant diurnal oscillation is a 24-hour period ba...[complete overview]

Experiment     Expression     Hybridizations & Samples     Quality Control     Compare Treatments     Downloads    

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Experiment Name: Transcriptome Phase Distribution Analysis Reveals Diurnal Regulated Biological Processes and Key Pathways in Rice Flag Leaves and Seedling Leaves
Accession No: OS64
Microarray: Rice57k
Visibility: public
Experiment Type:
Experiment Factor(s):
developmental stage name
•Seedling leaf   •Flag Leaf
time
•Time 1   •Time 2   •Time 3   •Time 4   •Time 5   •Time 6   •Time 7   •Time 8   •Time 9   •Time 10
Quality Control: biological replicates
Treatment summary:
 developmental stage name  time  # replicates
 Seedling leaf  Time 1  2
 Seedling leaf  Time 2  2
 Seedling leaf  Time 3  2
 Seedling leaf  Time 4  2
 Seedling leaf  Time 5  2
 Seedling leaf  Time 6  2
 Seedling leaf  Time 7  2
 Seedling leaf  Time 8  2
 Seedling leaf  Time 9  2
 Seedling leaf  Time 10  2
 Flag Leaf  Time 1  2
 Flag Leaf  Time 2  2
 Flag Leaf  Time 3  2
 Flag Leaf  Time 4  2
 Flag Leaf  Time 5  2
 Flag Leaf  Time 6  2
 Flag Leaf  Time 7  2
 Flag Leaf  Time 8  2
 Flag Leaf  Time 9  2
 Flag Leaf  Time 10  2
Total hybridizations: 40
Description: This experiment has been imported by PLEXdb from NCBI GEO (GSE28124)

Series_summary:
Plant diurnal oscillation is a 24-hour period based variation. The correlation between diurnal genes and biological pathways was widely revealed by microarray analysis in different species. Rice (Oryza sativa) is the major food staple for about half of the world's population. The rice flag leaf is essential in providing photosynthates to the grain filling. However, there is still no comprehensive view about the diurnal transcriptome for rice leaves. In this study, we applied rice microarray to monitor the rhythmically expressed genes in rice seedling and flag leaves. We developed a new computational analysis approach and identified 6,266 (10.96%) diurnal probe sets in seedling leaves, 13,773 (24.08%) diurnal probe sets in flag leaves. About 65% of overall transcription factors were identified as flag leaf preferred. In seedling leaves, the peak of phase distribution was from 2:00am to 4:00am, whereas in flag leaves, the peak was from 8:00pm to 2:00am. The diurnal phase distribution analysis of gene ontology (GO) and cis-element enrichment indicated that, some important processes were waken by the light, such as photosynthesis and abiotic stimulus, while some genes related to the nuclear and ribosome involved processes were active mostly during the switch time of light to dark. The starch and sucrose metabolism pathway genes also showed diurnal phase. We conducted comparison analysis between Arabidopsis and rice leaf transcriptome throughout the diurnal cycle. In summary, our analysis approach is feasible for relatively unbiased identification of diurnal transcripts, efficiently detecting some special periodic patterns with non-sinusoidal periodic patterns. Compared to the rice flag leaves, the gene transcription levels of seedling leaves were relatively limited to the diurnal rhythm. Our comprehensive microarray analysis of seedling and flag leaves of rice provided an overview of the rice diurnal transcriptome and indicated some diurnal regulated biological processes and key functional pathways in rice.

Series_overall_design:
we generate rice diurnal gene expression profiles of seedling leaves and flag leaves using 57K Affymetrix rice whole genome array.
keywords: rice (Oryza sativa L.), seedling leaves, flag leaves, diurnal, molecular functions, microarray


PLEXdb Curator's Note:
We have changed the sample names from the original at GEO to clarify the 10 time points as shown below.
Sample1=Time 1= DAY 1-8:00am
Sample1=Time 2= DAY 1-12:00am
Sample1=Time 3= DAY 1-4:00pm
Sample1=Time 4= DAY 1-8:00pm
Sample1=Time 5= DAY 2-0:00am
Sample1=Time 6= DAY 2-4.00am
Sample1=Time 7= DAY 2-8:00am
Sample1=Time 8= DAY 2-12:00am
Sample1=Time 9= DAY 2-4:00pm
Sample1=Time 10= DAY 2-8:00pm

Publication: 'Transcriptome phase distribution analysis reveals diurnal regulated biological processes and key pathways in rice flag leaves and seedling leaves.', Xu W, Yang R, Li M, Xing Z, Yang W, Chen G, Guo H, Gong X, Du Z, Zhang Z, Hu X, Wang D, Qian Q, Wang T, Su Z, Xue Y.
PLoS One 2011 Mar 2;6(3):e17613.
pubmed: 21407816
Created: 2011-07-18 14:05:46
Last Update: 2011-07-18 21:05:33
Released: 2011-07-18
GEO Accession GSE28124
Submitter: PLEXdb Curator
Name: Wenying Xu
Institution: Institute of Genetics and Developmental Biology, Department of Chinese Academy of Sciences, Beijing, China
Head of Laboratory: Yongbiao Xue
email(s):
Homepage:

 
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