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Status
Public on Aug 01, 2015
Title
The landscape of gene expression in Arabidopsis
Sample organism
Arabidopsis thaliana Experiment type
Expression profiling by array
Summary
Transcriptome datasets from thousands of samples of the model plant Arabidopsis thaliana have been collectively generated by multiple individual labs. Although integration and meta-analysis of these samples has become routine in the plant research community, it is often hampered by the lack of metadata or differences in annotation styles by different labs. In this study, we carefully selected and integrated 6,057 Arabidopsis microarray expression samples from 304 experiments deposited to NCBI GEO. Metadata such as tissue type, growth condition, and developmental stage were manually curated for each sample. We then studied global expression landscape of the integrated dataset and found that samples of the same tissue tend to be more similar to each other than to samples of other tissues, even in different growth conditions or developmental stages. Root has the most distinct transcriptome compared to aerial tissues, but the transcriptome of cultured root is more similar to those of aerial tissues as the former samples lost their cellular identity. Using a simple computational classification method, we showed that the tissue type of a sample can be successfully predicted based on its expression profile, opening the door for automatic metadata extraction and facilitating re-use of plant transcriptome data. As a proof of principle we applied our automated annotation pipeline to 708 RNA-seq samples from public repositories and verified accuracy of our predictions with samples’ metadata provided by authors.
Overall design
6057 published Arabidopsis microarray samples from about 300 series assayed on the GPL198 were re-analyzed. Metadata were re-annotated and MAS5.0 was used to normalize the CEL files.
Contributor(s)
He F , Yoo S , Wang D , Kumari S , Gerstein M , Ware D , Maslov S Citation(s)
27015116 Submission date
Jun 18, 2015
Last update date
Mar 27, 2016
Contact name
Eduard Akhunov
Organization name
Kansas State University
Department
Plant Pathology
Street address
2245 Buckingham St, Apt 10
City
Manhattan
State/province
Kansas
ZIP/Postal code
66503
Country
USA
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GSE9996
Data table header descriptions Sample name title source name organism characteristics: Tissue characteristics: Developmental Stage characteristics: Ecotype characteristics: Genotype characteristics: Treatment characteristics: Original series ID characteristics: Replicate Group molecule label platform
Data table Sample name title source name organism characteristics: Tissue characteristics: Developmental Stage characteristics: Ecotype characteristics: Genotype characteristics: Treatment characteristics: Original series ID characteristics: Replicate Group molecule label platform GSM253153
Reanalysis of GSM253153
2h before the end of the night
Arabidopsis thaliana
leaf
6.3
Col-0
wild type
abiotic stress
GSE10016
GSE10016_1
total RNA
biotin
GPL198
GSM253154
Reanalysis of GSM253154
end of the night A
Arabidopsis thaliana
leaf
6.3
Col-0
wild type
abiotic stress
GSE10016
GSE10016_2
total RNA
biotin
GPL198
GSM253155
Reanalysis of GSM253155
end of the night B
Arabidopsis thaliana
leaf
6.3
Col-0
wild type
abiotic stress
GSE10016
GSE10016_2
total RNA
biotin
GPL198
GSM253156
Reanalysis of GSM253156
end of the night C
Arabidopsis thaliana
leaf
6.3
Col-0
wild type
abiotic stress
GSE10016
GSE10016_2
total RNA
biotin
GPL198
GSM253157
Reanalysis of GSM253157
2h into an extended night
Arabidopsis thaliana
leaf
6.3
Col-0
wild type
abiotic stress
GSE10016
GSE10016_5
total RNA
biotin
GPL198
GSM253158
Reanalysis of GSM253158
4h into an extended nightA
Arabidopsis thaliana
leaf
6.3
Col-0
wild type
abiotic stress
GSE10016
GSE10016_6
total RNA
biotin
GPL198
GSM253159
Reanalysis of GSM253159
4h into an extended nightB
Arabidopsis thaliana
leaf
6.3
Col-0
wild type
abiotic stress
GSE10016
GSE10016_6
total RNA
biotin
GPL198
GSM253160
Reanalysis of GSM253160
6h into an extended night
Arabidopsis thaliana
leaf
6.3
Col-0
wild type
abiotic stress
GSE10016
GSE10016_8
total RNA
biotin
GPL198
GSM253161
Reanalysis of GSM253161
8h into an extended nightA
Arabidopsis thaliana
leaf
6.3
Col-0
wild type
abiotic stress
GSE10016
GSE10016_9
total RNA
biotin
GPL198
GSM253162
Reanalysis of GSM253162
8h into an extended nightB
Arabidopsis thaliana
leaf
6.3
Col-0
wild type
abiotic stress
GSE10016
GSE10016_9
total RNA
biotin
GPL198
GSM253163
Reanalysis of GSM253163
24h into an extended nightB
Arabidopsis thaliana
leaf
6.3
Col-0
wild type
abiotic stress
GSE10016
GSE10016_11
total RNA
biotin
GPL198
GSM253164
Reanalysis of GSM253164
24h into an extended nightC
Arabidopsis thaliana
leaf
6.3
Col-0
wild type
abiotic stress
GSE10016
GSE10016_11
total RNA
biotin
GPL198
GSM253165
Reanalysis of GSM253165
48h into an extended nightB
Arabidopsis thaliana
leaf
6.3
Col-0
wild type
abiotic stress
GSE10016
GSE10016_13
total RNA
biotin
GPL198
GSM253166
Reanalysis of GSM253166
48h into an extended nightC
Arabidopsis thaliana
leaf
6.3
Col-0
wild type
abiotic stress
GSE10016
GSE10016_13
total RNA
biotin
GPL198
GSM265418
Reanalysis of GSM265418
"Arabidopsis, root, longitudinal zone 1, standard conditions, rep 1"
Arabidopsis thaliana
root
0.7
Col-0
wild type
abiotic stress
GSE10497
GSE10497_1
total RNA
biotin
GPL198
GSM265419
Reanalysis of GSM265419
"Arabidopsis, root, longitudinal zone 1, standard conditions, rep 2"
Arabidopsis thaliana
root
0.7
Col-0
wild type
abiotic stress
GSE10497
GSE10497_1
total RNA
biotin
GPL198
GSM265420
Reanalysis of GSM265420
"Arabidopsis, root, longitudinal zone 2, standard conditions, rep 1"
Arabidopsis thaliana
root
0.7
Col-0
wild type
abiotic stress
GSE10497
GSE10497_3
total RNA
biotin
GPL198
GSM265421
Reanalysis of GSM265421
"Arabidopsis, root, longitudinal zone 2, standard conditions, rep 2"
Arabidopsis thaliana
root
0.7
Col-0
wild type
abiotic stress
GSE10497
GSE10497_3
total RNA
biotin
GPL198
GSM265422
Reanalysis of GSM265422
"Arabidopsis, root, longitudinal zone 3, standard conditions, rep1"
Arabidopsis thaliana
root
0.7
Col-0
wild type
abiotic stress
GSE10497
GSE10497_5
total RNA
biotin
GPL198
GSM265423
Reanalysis of GSM265423
"Arabidopsis, root, longitudinal zone 3, standard conditions, rep 2"
Arabidopsis thaliana
root
0.7
Col-0
wild type
abiotic stress
GSE10497
GSE10497_5
total RNA
biotin
GPL198
6061 1001 Kbytes .Supplementary file Size Download File type/resource GSE69995_re-analyzed_data_matrix.txt.gz
201.6 Mb
(ftp) (http) TXT
Processed data are available on Series record
