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Sample GSM3018038 Query DataSets for GSM3018038
Status Public on Jun 06, 2018
Title Osfuct mutant_leaf_4weeks_rep3
Sample type RNA
 
Source name Leaf at the tillering stage_transgenic
Organism Oryza sativa
Characteristics cultivar: Oryza sativa japonica Dongjin
genotype/variation: alpha1,3-fucosyltransferase mutant
age: 4 weeks; tillering stage
tissue: leaf
Treatment protocol No treatment
Growth protocol Rice seeds were sterilized and germinated on 2N6 media in a growth chamber with a 16 hr light (28°C), 8 hr dark (26°C) photoperiod for 7 dats. The seedling were transferred to individual pots and grown in a greenhouse under the controlled conditions
Extracted molecule total RNA
Extraction protocol Total RNA from frozen wild-type and mutant leaves was prepared as previously described [Davis, KR & Ausubel, FM (1989) Mol. Plant-Microbe Interact 2: 363-368). Genomic DNA contamination was removed by DNase I at 37°C for 30 min and cDNA was generated by commercial cDNA synthesis kit according to the manufacturer's guidelines.
Label Cy3
Label protocol Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.
 
Hybridization protocol Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.
Scan protocol Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.
Description PM_HM_ABFT9
Data processing The raw data (.probe file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).
 
Submission date Feb 20, 2018
Last update date Jun 06, 2018
Contact name Yeon-Ki Kim
E-mail(s) kim750a11@gmail.com
Phone 82-31-321-6351
Organization name GreenGene Biotech Inc.
Department GreenGene Biotech Inc.
Lab Genomics & Genetics Ins.
Street address 38-2 Namdong
City Yongin
State/province Kyonggido
ZIP/Postal code 449-728
Country South Korea
 
Platform ID GPL14568
Series (1)
GSE110873 The lack of α1,3-fucosyltransferase (Osfuct) affects in anther and pollen development in rice (Oryza sativa)

Data table header descriptions
ID_REF
VALUE RMA-normalized, averaged gene-level signal intensity

Data table
ID_REF VALUE
Os03g0388900 5286.72
Os09g0502900 62.9506
Os08g0511900 7167.2
Os05g0457200 2853.25
Os04g0643200 7433.98
Os12g0221400 198.551
Os04g0499300 8201.79
Os11g0592400 229.932
Os06g0186500 55.4124
Os02g0503100 342.29
Os05g0130100 181.433
Os02g0187100 611.055
Os05g0196100 5103.34
Os01g0628700 71.4939
Os05g0490800 775.166
Os04g0137500 5183.77
Os01g0195400 6126.28
Os06g0141000 1531.99
Os03g0805600 2055.25
Os06g0259000 65.9421

Total number of rows: 31588

Table truncated, full table size 635 Kbytes.




Supplementary file Size Download File type/resource
GSM3018038_PM-HM-ABFT9_508872A06_081211_532.probe.gz 1.9 Mb (ftp)(http) PROBE
GSM3018038_PM_HM_ABFT9_532_nm_norm_RMA.pair.gz 2.1 Mb (ftp)(http) PAIR
Processed data included within Sample table
Processed data provided as supplementary file

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