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Sample GSM5060852 Query DataSets for GSM5060852
Status Public on Feb 04, 2021
Title LD_WT
Sample type RNA
Source name wild-type rice leaves,long day conditions
Organism Oryza sativa
Characteristics growth conditions: long 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 379.65 P 0.00159257
AFFX-BioB-M_at 454.873 P 8.14279e-05
AFFX-BioB-3_at 522.435 P 5.16732e-05
AFFX-BioC-5_at 1316.68 P 5.16732e-05
AFFX-BioC-3_at 1425.08 P 4.42873e-05
AFFX-BioDn-5_at 2437.05 P 4.42873e-05
AFFX-BioDn-3_at 6503.58 P 5.16732e-05
AFFX-CreX-5_at 17509.8 P 5.16732e-05
AFFX-CreX-3_at 21758 P 4.42873e-05
AFFX-DapX-5_at 1923.83 P 4.42873e-05
AFFX-DapX-M_at 3796.69 P 7.00668e-05
AFFX-DapX-3_at 7416.23 P 4.42873e-05
AFFX-LysX-5_at 262.976 P 4.42873e-05
AFFX-LysX-M_at 462.371 P 0.000340305
AFFX-LysX-3_at 1161.89 P 4.42873e-05
AFFX-PheX-5_at 535.03 P 7.00668e-05
AFFX-PheX-M_at 558.094 P 4.42873e-05
AFFX-PheX-3_at 644.119 P 4.42873e-05
AFFX-ThrX-5_at 411.231 P 8.14279e-05
AFFX-ThrX-M_at 840.959 P 4.42873e-05

Total number of rows: 57381

Table truncated, full table size 2173 Kbytes.

Supplementary file Size Download File type/resource
GSM5060852_LD_WT.CEL.gz 4.7 Mb (ftp)(http) CEL
GSM5060852_LD_WT.CHP.gz 310.3 Kb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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