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Sample GSM431930 Query DataSets for GSM431930
Status Public on Jul 22, 2009
Title Root- +Fe-P biological rep2
Sample type RNA
 
Source name Root segments derived from 11-d-old rice (Oryza sativa) seedlings under +Fe-P conditions
Organism Oryza sativa
Characteristics tissue: Root
Treatment protocol For –Fe+P treatment, FeCl3 and citric acid were removed. For +Fe-P treatment, NaH2PO4 was removed. While for –Fe–P treatment, FeCl3, citric acid, and NaH2PO4 were removed.
Growth protocol Rice seeds were germinated in distilled water for 2 d. After germination, 25 seedlings were transferred to a plastic net floating on the Yoshida nutrient solution (Yoshida et al., 1976).
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using RNAzol (Campro Scientific) and glass beads according to the manufacturer’s instructions.
Label biotin
Label protocol The One-Cycle Target Labeling and Control Reagent kit (Affymetrix 900493) and the protocols optimized by Affymetrix were used to prepare biotinylated complementaryRNA (cRNA; from 5 mg of total RNA) for microarray hybridization (n = 2 per group).
 
Hybridization protocol Microarray analysis was carried out using an Affymetrix technology platform and Affymetrix GeneChip rice genome array. Briefly, fragmented cRNA was mixed with spiked controls and applied to Affymetrix Test chips, and good quality samples were then used to hybridize with the rice GeneChip. The hybridization, probe array washing and staining, and washing procedures were executed as described in the Affymetrix protocols.
Scan protocol Probe arrays were scanned with a Hewlett-Packard Gene Array Scanner (Leiden Genome Technology Center).
Description Gene expression data from 10-d-old rice (Oryza sativa) seedlings under +Fe-P conditions
Data processing Data analysis was carried out using Avadis 4.3 (Strand Genomics) and Partek Genomics suite software, version 6.3. Raw intensity data were initially normalized using the MAS5 algorithm, which allowed probe identifier present calls to be determined.
 
Submission date Jul 21, 2009
Last update date Jul 21, 2009
Contact name Luqing Zheng
E-mail(s) zluqing@gmail.com
Organization name Colledge of Life Sciences, Zhejiang University
Street address 388 Yuhangtanghe Road
City Hangzhou
ZIP/Postal code 310058
Country China
 
Platform ID GPL2025
Series (1)
GSE17245 Transcriptome analysis of iron and phosphorus interaction in rice seedlings

Data table header descriptions
ID_REF
VALUE Signal
ABS_CALL indicating whether the transcript was present (P), absent (A), or marginal (M)
DETECTION P-VALUE

Data table
ID_REF VALUE ABS_CALL DETECTION P-VALUE
AFFX-BioB-5_at 405.795 P 0.00499819
AFFX-BioB-M_at 509.257 P 8.14279e-05
AFFX-BioB-3_at 271.103 P 0.000296708
AFFX-BioC-5_at 1004.28 P 5.16732e-05
AFFX-BioC-3_at 985.131 P 4.42873e-05
AFFX-BioDn-5_at 2759.84 P 4.42873e-05
AFFX-BioDn-3_at 6658.81 P 5.16732e-05
AFFX-CreX-5_at 15110.1 P 5.16732e-05
AFFX-CreX-3_at 19037.9 P 4.42873e-05
AFFX-DapX-5_at 2182.15 P 4.42873e-05
AFFX-DapX-M_at 3367.57 P 5.16732e-05
AFFX-DapX-3_at 3700.01 P 4.42873e-05
AFFX-LysX-5_at 198.231 P 6.02111e-05
AFFX-LysX-M_at 345.474 P 0.0125468
AFFX-LysX-3_at 598.437 P 5.16732e-05
AFFX-PheX-5_at 309.423 P 6.02111e-05
AFFX-PheX-M_at 271.197 P 0.000195116
AFFX-PheX-3_at 441.062 P 0.000296708
AFFX-ThrX-5_at 561.507 P 0.000126798
AFFX-ThrX-M_at 758.568 P 4.42873e-05

Total number of rows: 57381

Table truncated, full table size 2169 Kbytes.




Supplementary file Size Download File type/resource
GSM431930_R+Fe-P-2.CEL.gz 4.5 Mb (ftp)(http) CEL
GSM431930_R+Fe-P-2.CHP.gz 627.4 Kb (ftp)(http) CHP
Raw data provided as supplementary file
Processed data included within Sample table
Processed data provided as supplementary file

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