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Sample GSM5060850 Query DataSets for GSM5060850
Status Public on Feb 04, 2021
Title SD_WT
Sample type RNA
Source name wild-type rice leaves,short day conditions
Organism Oryza sativa
Characteristics growth conditions: short day
tissue: leaves
genotype: wild type Zhonghua11
Growth protocol 5-day-old seedlings of hd1-3 mutant and the wild-type Zhonghua11 after germination were grown in artificial climate chamber for 30 days. The growth conditions were set as 11.5 h light/ 12.5 h dark, 28℃ for short-day conditions and 15 h light/ 9 h dark, 28℃ for long-day conditions, respectively.
Extracted molecule total RNA
Extraction protocol Leaves of 35-day-old rice plants were collected. For short-day conditions, the samples were collected at 3 h after light; for long-day conditions, the samples were collected at 5 h after light. Total RNAs were extracted using TRIzol method and mRNAs were purified using mRNA purification kit.
Label biotin
Label protocol Biotinylated RNA were prepared according to the standard Affymetrix protocol.
Hybridization protocol Affymetrix gene chip hybridization, washing, staining, and scanning were carried out according to manufacturer's instructions.
Scan protocol GeneChips were scanned using Affymetrix Scanner 3000 with default settings.
Data processing The microarray data were analyzed using MAS5 algorithm.
Submission date Feb 03, 2021
Last update date Feb 04, 2021
Contact name Xuan Ma
Organization name Tianjin Normal University
Department College of Life Sciences
Street address Binshui West Road
City Tianjin
ZIP/Postal code 300387
Country China
Platform ID GPL2025
Series (1)
GSE166053 Microarray comparative analysis of wild-type and hd1-3 mutant rice

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

Data table
AFFX-BioB-5_at 513.724 P 0.0020226
AFFX-BioB-M_at 458.848 P 0.000195116
AFFX-BioB-3_at 446.133 P 4.42873e-05
AFFX-BioC-5_at 1636.55 P 4.42873e-05
AFFX-BioC-3_at 1770.16 P 4.42873e-05
AFFX-BioDn-5_at 2574.42 P 4.42873e-05
AFFX-BioDn-3_at 6543.75 P 5.16732e-05
AFFX-CreX-5_at 19686.3 P 5.16732e-05
AFFX-CreX-3_at 23715.7 P 4.42873e-05
AFFX-DapX-5_at 2894.98 P 4.42873e-05
AFFX-DapX-M_at 5355.22 P 7.00668e-05
AFFX-DapX-3_at 10148.3 P 4.42873e-05
AFFX-LysX-5_at 432.163 P 4.42873e-05
AFFX-LysX-M_at 811.74 P 0.000195116
AFFX-LysX-3_at 1909.25 P 4.42873e-05
AFFX-PheX-5_at 781.028 P 5.16732e-05
AFFX-PheX-M_at 891.295 P 4.42873e-05
AFFX-PheX-3_at 919.728 P 4.42873e-05
AFFX-ThrX-5_at 640.039 P 7.00668e-05
AFFX-ThrX-M_at 1207.23 P 4.42873e-05

Total number of rows: 57381

Table truncated, full table size 2170 Kbytes.

Supplementary file Size Download File type/resource
GSM5060850_SD_WT.CEL.gz 4.8 Mb (ftp)(http) CEL
GSM5060850_SD_WT.CHP.gz 310.7 Kb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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