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Status |
Public on Mar 16, 2021 |
Title |
GlcAC_1 |
Sample type |
RNA |
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Source name |
rice embryo
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Organism |
Oryza sativa |
Characteristics |
tissue: embryo condition: Glc/AC
|
Treatment protocol |
Approximately 150~200 surface-sterilized embryos were placed on a single layer of 3 mm Whatman paper soaked in 10 mM calcium chloride (CaCl2) solution containing 60 mM of either glucose or mannitol and incubated for 24 h at 28°C in the dark for aerobic germination. For anaerobic germination, 150~200 surface-sterilized rice embryos were submerged in orange conical tubes containing 50 mL of the aforementioned incubation media and flushed with N2 gas and incubated under the same conditions as aerobic germination. To induce energy starvation in cells, rice embryos were germinated aerobically as described above, except that 0.08 mM of the uncoupler 2,4-dinitrophenol (DNP; Sigma Aldrich, St. Louis, MO, USA) was added to the incubation media.
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Growth protocol |
Rice embryos were harvested from whole rice seeds (Oryza sativa L. cv. Dongjin),
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Extracted molecule |
total RNA |
Extraction protocol |
Rice embryos were ground to a fine powder with liquid nitrogen using a mortar and pestle, and extracted with TLE (0.2 M Tris, 0.1 M LiCl, and 5 mM EDTA; pH 8.2) and phenol-chloroform-isoamylalcohol solution. Total RNA was extracted with TRIZOL® reagent (Invitrogen, UK) and RNeasy plant mini kit (Qiagen, Hilden, Germany), according to the manufacturer’s instructions. The quantity and purity of the extracted RNA were assessed by measuring the OD260/280 using a NanoDrop spectrophotometer. For microarray experiments, total RNA was re-purified using low-elution Qiagen RNeasy columns (Qiagen), according to the manufacturer’s instructions. Total RNA was also used for the synthesis of the first strand cDNA for real-time quantitative reverse transcriptase PCR (qRT-PCR).
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Label |
biotin
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Label protocol |
Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).
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Hybridization protocol |
Samples were hybridized with Affymetrix RJpGene-1_1-st-v1 (Affymetrix) and scanned at GreenGene biotech.
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Scan protocol |
Array scanning was performed according to the manufacturer's instruction (Affymetrix)
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Description |
RMA expression value derived from Expression Console software; core-exon analysis
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Data processing |
Raw data were processed with the Exon Array Computational Tool (ExACT) (Affymetrix) for background correction and normalization. Data analysis and statistical evaluations were performed with customized R codes (version 2.3.1, http://www.r-project.org/). We extracted a probeset as present with default options apt-probeset-summarize with options: -p RJpGene-1_1-st.pgf -b RJpGene-1_1-st.bgp --qc-probesets RJpGene-1_1-st.qcc -m RJpGene-1_1-st.mps -a rma-sketch
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Submission date |
Mar 15, 2021 |
Last update date |
Mar 16, 2021 |
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 |
|
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Platform ID |
GPL25932 |
Series (1) |
GSE168915 |
Comparison of transcriptomic adjustments to availability of sugar, cellular energy, and oxygen in germinating rice embryos |
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