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Sample GSM431926 Query DataSets for GSM431926
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 492.052 P 0.002867
AFFX-BioB-M_at 431.58 P 0.000389797
AFFX-BioB-3_at 306.521 P 7.00668e-05
AFFX-BioC-5_at 1276.57 P 5.16732e-05
AFFX-BioC-3_at 1127.57 P 4.42873e-05
AFFX-BioDn-5_at 2194.35 P 4.42873e-05
AFFX-BioDn-3_at 6308.33 P 5.16732e-05
AFFX-CreX-5_at 16239.2 P 4.42873e-05
AFFX-CreX-3_at 19123.5 P 4.42873e-05
AFFX-DapX-5_at 275.332 P 0.000856509
AFFX-DapX-M_at 1264.17 P 0.000340305
AFFX-DapX-3_at 2941.65 P 5.16732e-05
AFFX-LysX-5_at 151.299 P 0.00179445
AFFX-LysX-M_at 372.422 P 0.0239288
AFFX-LysX-3_at 660.472 P 0.00010954
AFFX-PheX-5_at 188.064 P 0.00255552
AFFX-PheX-M_at 151.752 P 0.0103167
AFFX-PheX-3_at 318.186 P 0.000389797
AFFX-ThrX-5_at 139.432 A 0.102165
AFFX-ThrX-M_at 272.367 P 0.00159257

Total number of rows: 57381

Table truncated, full table size 2162 Kbytes.




Supplementary file Size Download File type/resource
GSM431926_R+Fe+P-2.CEL.gz 4.6 Mb (ftp)(http) CEL
GSM431926_R+Fe+P-2.CHP.gz 628.2 Kb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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