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Sample GSM5172281 Query DataSets for GSM5172281
Status Public on Mar 16, 2021
Title Mtl_2
Sample type RNA
 
Source name rice embryo
Organism Oryza sativa
Characteristics tissue: embryo
condition: Mtl
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.
Growth protocol Rice embryos were harvested from whole rice seeds (Oryza sativa L. cv. Dongjin),
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).
Label biotin
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).
 
Hybridization protocol Samples were hybridized with Affymetrix RJpGene-1_1-st-v1 (Affymetrix) and scanned at GreenGene biotech.
Scan protocol Array scanning was performed according to the manufacturer's instruction (Affymetrix)
Description RMA expression value derived from Expression Console software; core-exon analysis
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
 
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
 
Platform ID GPL25932
Series (1)
GSE168915 Comparison of transcriptomic adjustments to availability of sugar, cellular energy, and oxygen in germinating rice embryos

Data table header descriptions
ID_REF
VALUE log2 RMA signal

Data table
ID_REF VALUE
16196373 0.87455
16321349 1.65466
16233704 1.10495
16213615 5.17437
16340733 11.25383
16241463 7.24952
16196365 0.73579
16233706 0.40098
16343342 4.8216
16252573 1.02408
16312016 1.15861
16171809 6.05054
16157001 1.72763
16319462 2.30574
16156999 0.30327
16192105 4.1373
16212914 8.14785
16125445 7.17612
16342091 1.53085
16240715 6.64558

Total number of rows: 36643

Table truncated, full table size 604 Kbytes.




Supplementary file Size Download File type/resource
GSM5172281_Mtl_2.ga.cel.gz 4.9 Mb (ftp)(http) CEL
GSM5172281_Mtl_2.ga.rma-gene-full.chp.gz 250.1 Kb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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