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Sample GSM5060851 Query DataSets for GSM5060851
Status Public on Feb 04, 2021
Title SD_Mut
Sample type RNA
Source name hd1-3 mutant rice leaves,short day conditions
Organism Oryza sativa
Characteristics growth conditions: short 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 573.097 P 0.000509415
AFFX-BioB-M_at 541.295 P 7.00668e-05
AFFX-BioB-3_at 511.56 P 5.16732e-05
AFFX-BioC-5_at 1644.38 P 5.16732e-05
AFFX-BioC-3_at 1589.18 P 5.16732e-05
AFFX-BioDn-5_at 2718.28 P 4.42873e-05
AFFX-BioDn-3_at 7769.52 P 5.16732e-05
AFFX-CreX-5_at 20476.4 P 4.42873e-05
AFFX-CreX-3_at 24372.1 P 4.42873e-05
AFFX-DapX-5_at 3674.7 P 4.42873e-05
AFFX-DapX-M_at 7646.39 P 6.02111e-05
AFFX-DapX-3_at 13842.5 P 4.42873e-05
AFFX-LysX-5_at 662.203 P 4.42873e-05
AFFX-LysX-M_at 1215.94 P 0.000146581
AFFX-LysX-3_at 2898.17 P 4.42873e-05
AFFX-PheX-5_at 1052.67 P 4.42246e-05
AFFX-PheX-M_at 1347.24 P 5.16732e-05
AFFX-PheX-3_at 1385.5 P 4.42873e-05
AFFX-ThrX-5_at 887.096 P 4.42873e-05
AFFX-ThrX-M_at 1837.64 P 4.42873e-05

Total number of rows: 57381

Table truncated, full table size 2168 Kbytes.

Supplementary file Size Download File type/resource
GSM5060851_SD_Mut.CEL.gz 4.7 Mb (ftp)(http) CEL
GSM5060851_SD_Mut.CHP.gz 311.8 Kb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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