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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

Experimenter:

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):	not in GEO
Homepage:	http://www.ncpgr.cn


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