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Sample GSM5060853 Query DataSets for GSM5060853
Status Public on Feb 04, 2021
Title LD_Mut
Sample type RNA
Source name hd1-3 mutant rice leaves,long day conditions
Organism Oryza sativa
Characteristics growth conditions: long day
tissue: leaves
genotype: hd1-3 mutant
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 520.64 P 0.000445901
AFFX-BioB-M_at 499.436 P 7.00668e-05
AFFX-BioB-3_at 539.365 P 4.42873e-05
AFFX-BioC-5_at 1565.05 P 5.16732e-05
AFFX-BioC-3_at 1563.16 P 4.42873e-05
AFFX-BioDn-5_at 2793.42 P 4.42873e-05
AFFX-BioDn-3_at 7437.75 P 4.42873e-05
AFFX-CreX-5_at 20067.5 P 5.16732e-05
AFFX-CreX-3_at 25470.7 P 4.42873e-05
AFFX-DapX-5_at 1704.43 P 4.42873e-05
AFFX-DapX-M_at 3734.87 P 6.02111e-05
AFFX-DapX-3_at 7349.66 P 4.42873e-05
AFFX-LysX-5_at 245.549 P 4.42873e-05
AFFX-LysX-M_at 530.121 P 0.000169227
AFFX-LysX-3_at 1239.25 P 4.42873e-05
AFFX-PheX-5_at 528.215 P 4.42873e-05
AFFX-PheX-M_at 619.634 P 5.16732e-05
AFFX-PheX-3_at 647.004 P 4.42873e-05
AFFX-ThrX-5_at 350.374 P 4.42873e-05
AFFX-ThrX-M_at 863.842 P 4.42873e-05

Total number of rows: 57381

Table truncated, full table size 2174 Kbytes.

Supplementary file Size Download File type/resource
GSM5060853_LD_Mut.CEL.gz 4.8 Mb (ftp)(http) CEL
GSM5060853_LD_Mut.CHP.gz 310.5 Kb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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