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Browse RicePLEX Experiment Data

Choose an experiment:
Dissecting the developmental transcriptomes of rice
Weibo,Xie, Organization name: Huazhong Agricultural University, Department: College of Life Science and Technology Lab, National Key Laboratory of Crop Genetic Improvement, Street address: Luoshi Road, City: Wuhan, State/province: Hubei, ZIP/Postal code: 470070, C (not in GEO)
Experiment design (190 hybridizations)
cultivar
•Minghui63 •Zhenshan97
organism part name
•callus1 •callus2 •callus3 •callus4 •callus5 •callus6 •callus7 •callus8 •germinating_seed •plumule1 •radicle1 •plumule2 •radicle2 •seedling3 •seedling4 •seedling5 •shoot •root •leaf1 •sheath1 •leaf2 •sheath2 •panicle4 •stem1 •leaf3 •stem2 •panicle5 •palea/lemma •stamen •spikelet •endosperm1 •endosperm2 •endosperm3 •leaf4 •seedling1 •seedling2 •panicle1 •panicle2 •panicle3

This experiment has been imported by PLEXdb from NCBI GEO (GSE19024)

Series_summary:
In this study, we collected 39 tissues/organs co...[complete overview]

Experiment     Expression     Hybridizations & Samples     Quality Control     Compare Treatments     Downloads    

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Experiment Name: Dissecting the developmental transcriptomes of rice
Accession No: OS32
Microarray: Rice57k
Visibility: public
Experiment Type:
Experiment Factor(s):
cultivar
•Minghui63   •Zhenshan97
organism part name
•callus1   •callus2   •callus3   •callus4   •callus5   •callus6   •callus7   •callus8   •germinating_seed   •plumule1   •radicle1   •plumule2   •radicle2   •seedling3   •seedling4   •seedling5   •shoot   •root   •leaf1   •sheath1   •leaf2   •sheath2   •panicle4   •stem1   •leaf3   •stem2   •panicle5   •palea/lemma   •stamen   •spikelet   •endosperm1   •endosperm2   •endosperm3   •leaf4   •seedling1   •seedling2   •panicle1   •panicle2   •panicle3
Quality Control: biological replicates,technical replicates
Treatment summary:
 cultivar  organism part name  # replicates
 Minghui63  callus1  2
 Minghui63  callus2  2
 Minghui63  callus3  2
 Minghui63  callus4  2
 Minghui63  callus5  2
 Minghui63  callus6  0
 Minghui63  callus7  0
 Minghui63  callus8  0
 Minghui63  germinating_seed  2
 Minghui63  plumule1  2
 Minghui63  radicle1  2
 Minghui63  plumule2  2
 Minghui63  radicle2  2
 Minghui63  seedling3  2
 Minghui63  seedling4  2
 Minghui63  seedling5  2
 Minghui63  shoot  2
 Minghui63  root  2
 Minghui63  leaf1  2
 Minghui63  sheath1  2
 Minghui63  leaf2  2
 Minghui63  sheath2  2
 Minghui63  panicle4  2
 Minghui63  stem1  2
 Minghui63  leaf3  2
 Minghui63  stem2  2
 Minghui63  panicle5  2
 Minghui63  palea/lemma  2
 Minghui63  stamen  2
 Minghui63  spikelet  2
 Minghui63  endosperm1  2
 Minghui63  endosperm2  2
 Minghui63  endosperm3  2
 Minghui63  leaf4  2
 Minghui63  seedling1  6
 Minghui63  seedling2  6
 Minghui63  panicle1  6
 Minghui63  panicle2  6
 Minghui63  panicle3  6
 Zhenshan97  callus1  2
 Zhenshan97  callus2  2
 Zhenshan97  callus3  2
 Zhenshan97  callus4  2
 Zhenshan97  callus5  2
 Zhenshan97  callus6  2
 Zhenshan97  callus7  2
 Zhenshan97  callus8  2
 Zhenshan97  germinating_seed  2
 Zhenshan97  plumule1  2
 Zhenshan97  radicle1  2
 Zhenshan97  plumule2  2
 Zhenshan97  radicle2  2
 Zhenshan97  seedling3  2
 Zhenshan97  seedling4  2
 Zhenshan97  seedling5  2
 Zhenshan97  shoot  2
 Zhenshan97  root  2
 Zhenshan97  leaf1  2
 Zhenshan97  sheath1  2
 Zhenshan97  leaf2  2
 Zhenshan97  sheath2  2
 Zhenshan97  panicle4  2
 Zhenshan97  stem1  2
 Zhenshan97  leaf3  2
 Zhenshan97  stem2  2
 Zhenshan97  panicle5  2
 Zhenshan97  palea/lemma  2
 Zhenshan97  stamen  2
 Zhenshan97  spikelet  2
 Zhenshan97  endosperm1  2
 Zhenshan97  endosperm2  2
 Zhenshan97  endosperm3  2
 Zhenshan97  leaf4  2
 Zhenshan97  seedling1  6
 Zhenshan97  seedling2  6
 Zhenshan97  panicle1  6
 Zhenshan97  panicle2  6
 Zhenshan97  panicle3  6
Total hybridizations: 190
Description: This experiment has been imported by PLEXdb from NCBI GEO (GSE19024)

Series_summary:
In this study, we collected 39 tissues/organs covering the life cycle of the rice from two indica varieties Minghui 63 and Zhenshan 97, and the Affymetrix GeneChip Rice Genome Array was used to investigate the transcriptomes of these organs. The objective was to develop a genomic resource of genome-wide dynamic transcriptome of the rice plant, which could be used as the reference gene expression map for rice and other cereals. Also, the dataset is used to identify the candidates of genes with potential functions in regulating the development of rice or breeding practice. Keywords: rice, expression profiling, life cycle, development, inflorescence

Series_overall_design:
To dissect the developmental transcriptomes of rice, a total of 39 tissues covering the entire tissue culture process and life cycle were sampled from two indica varieties Minghui 63 and Zhenshan 97. And the Affymetrix Genechip rice Genome Array was used to investigate their dynamic transcriptomes. Two independent biological replicates were sampled from most tissues, except two seedling and three panicle tissues, for which three independent biological replicates each with two technical replicates were sampled, resulting in a dataset of 190 microarrays.


PLEXdb Curator's Note:
The following 5, seedling1, seedling2, panicle1, panicle2 and panicle3 have 3 biological replications each and 2 technical replication within each of these biological replications. When importing from GEO and data normalization, we have considered this combination as 6 replications per treatment and have presented so in our visualizations after analysis.

*** We want our readers to be aware of this fact, that the 6 replications are a combination biological and technical reps for the above 5 tissues.

Publication: 'A dynamic gene expression atlas covering the entire life cycle of rice', Wang L, Xie W, Chen Y, Tang W, Yang J, Ye R, Liu L, Lin Y, Xu C, Xiao J, Zhang Q.
The Plant Journal (2010) 61, 752–766
pubmed: 20003165
Created: 2010-03-04 11:33:36
Last Update: 2010-03-13 16:27:45
Released: 2010-03-18
GEO Accession GSE19024
Submitter: PLEXdb Curator
Name: Weibo,Xie
Institution: Organization name: Huazhong Agricultural University, Department: College of Life Science and Technology Lab, National Key Laboratory of Crop Genetic Improvement, Street address: Luoshi Road, City: Wuhan, State/province: Hubei, ZIP/Postal code: 470070, C
Head of Laboratory: --
email(s):
Homepage:

 
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