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Browse RicePLEX Experiment Data

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Expression data for reproductive development in rice
Sanjay Kapoor , University of Delhi South Campus (kapoors@genomeindia.org )
Experiment design (45 hybridizations)
developmental stage name
•Root, 7-day-old Seedling •Mature leaf •Y Leaf •SAM •Young inflorescence (P1, upto 3 cm) •Inflorescence (P2, 3 - 5 cm) •Inflorescence (P3, 5 - 10 cm) •Inflorescence (P4, 10 - 15 cm) •Inflorescence (P5, 15 - 22 cm) •Inflorescence (P6, 22 - 30 cm) •Seed (S1, 0 - 2 dap) •Seed (S2, 3 - 4 dap) •Seed (S3, 5 - 10 dap) •Seed (S4, 11 - 20 dap) •Seed (S5, 21 - 29 dap)

This experiment has been imported from NCBI GEO(GSE6893). Series_summary: "Plants initially undergo a period of vegetative development, in whic...[complete overview]

Experiment     Expression     Hybridizations & Samples     Quality Control     Compare Treatments     Downloads    

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Experiment Name: Expression data for reproductive development in rice
Accession No: OS5
Microarray: Rice57k
Visibility: public
Experiment Type:
Experiment Factor(s):
developmental stage name
•Root, 7-day-old Seedling   •Mature leaf   •Y Leaf   •SAM   •Young inflorescence (P1, upto 3 cm)   •Inflorescence (P2, 3 - 5 cm)   •Inflorescence (P3, 5 - 10 cm)   •Inflorescence (P4, 10 - 15 cm)   •Inflorescence (P5, 15 - 22 cm)   •Inflorescence (P6, 22 - 30 cm)   •Seed (S1, 0 - 2 dap)   •Seed (S2, 3 - 4 dap)   •Seed (S3, 5 - 10 dap)   •Seed (S4, 11 - 20 dap)   •Seed (S5, 21 - 29 dap)
Quality Control:
Treatment summary:
 developmental stage name  # replicates
 Root, 7-day-old Seedling  3
 Mature leaf  3
 Y Leaf  3
 SAM  3
 Young inflorescence (P1, upto 3 cm)  3
 Inflorescence (P2, 3 - 5 cm)  3
 Inflorescence (P3, 5 - 10 cm)  3
 Inflorescence (P4, 10 - 15 cm)  3
 Inflorescence (P5, 15 - 22 cm)  3
 Inflorescence (P6, 22 - 30 cm)  3
 Seed (S1, 0 - 2 dap)  3
 Seed (S2, 3 - 4 dap)  3
 Seed (S3, 5 - 10 dap)  3
 Seed (S4, 11 - 20 dap)  3
 Seed (S5, 21 - 29 dap)  3
Total hybridizations: 45
Description: This experiment has been imported from NCBI GEO(GSE6893).

Series_summary:
"Plants initially undergo a period of vegetative development, in which it produces leaves from shoot apical meristem (SAM) and roots from the root apical meristem. Later in development, the SAM undergoes a change in fate and enters reproductive development called as floral transition, producing flowers and seeds. Our understanding of the molecular and genetic mechanisms that underlie reproductive development in plants has increased tremendously in the past decade, essentially through the work on Arabidopsis. In this study, we have analyzed the spatial and temporal gene expression in various tissues/organs and developmental stages of rice using microarray technology to identify the genes differentially expressed during various stages of reproductive development."

Series_Overall Design:
"Various rice tissues/organs (seedling root, mature leaf and Y leaf) and stages of reproductive (panicle and seed) development were used for RNA extraction and hybridization on Affymetrix microarrays. Three biological replicates of each sample were used for microarray analysis. We sought to obtain developmental and temporal gene expression profiles at each stage to identify the differentially expressed genes. Different stages of panicle and seed development have been categorized according to panicle length and days after pollination, respectively, based on landmark developmental events as follows: up to 0.5 mm, shoot apical meristem and rachis meristem (SAM); 0-3 cm, floral transition and floral organ development (P1); 3-10 cm, meiotic stage (P2 and P3); 10-15 cm, young microspore stage (P4); 15-22 cm, vacuolated pollen stage (P5); 22-30 cm, mature pollen stage (P6); 0-2 dap, early globular embryo (S1); 3-4 dap, middle and late globular embryo (S2); 5-10 dap, embryo morphogenesis (S3); 11-20 dap, embryo maturation (S4); 21-29, dormancy and desiccation tolerance (S5). These stage specifications are approximations based on information from Itoh et al., 2005, Plant Cell Physiol, 46, 23-47."
Publication: 'F-box proteins in rice. Genome-wide analysis, classification, temporal and spatial gene expression during panicle and seed development, and regulation by light and abiotic stress.', Jain M, Nijhawan A, Arora R, Agarwal P et al.
Plant Physiol 2007 Apr;143(4):1467-83.
pubmed: 17293439
Created: 2009-01-27 16:53:16
Last Update: 2009-03-11 13:33:29
GEO Accession GSE6893
Submitter: PLEXdb Curator
Name: Sanjay Kapoor
Institution: University of Delhi South Campus
Head of Laboratory:
email(s):
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