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Sample GSM2905105 Query DataSets for GSM2905105
Status Public on Apr 20, 2020
Title wild type # 628
Sample type RNA
Source name roots, wild type, ammonium sufficient condition, 18 day-old sample
Organism Oryza sativa Japonica Group
Characteristics cultivar: Nipponbare
tissue: roots
growth period: 18 days
genotype: wild type
Treatment protocol Germinated seeds were hydroponically grown under one-quarter strength basal nutrient solution lacking a nitrogen (N) source with 1 mM of ammonium for 18 days.
Growth protocol We grew samples using two different conditions. Growth condition 1 for SAMPLE 1-17: The conditions in the greenhouse at Tohoku University, Sendai, Japan were: 14 h of light at 26oC and 10 h of darkness at 23oC without humidity control; light strength, 810 μmol∙m-2∙sec-1; light source, metal halide lamp (05:30 - 18:30) and sunlight. WT-, heterozygous Osgs1;1-, and homozygous Osgs1;2 seeds were sterilized in 3 steps: (i) seeds were immersed in 60oC water for 10 min and then washed in flowing water for 10 min, (ii) immersed in 70% ethanol for 30 sec and washed immediately, and (iii) immersed in 2% hypochlorous acid for 20 min and then washed in water for 20 min. Then they were incubated at 30oC for 2 days in the dark. Germinated seeds were hydroponically grown for 18 days in one-quarter strength basal nutrient solution that lacked an N source and contained 150 mM NaH2PO4•2H2O, 75 mM K2SO4, 75 mM CaCl2•2H2O, 100 mM MgCl2•H2O, 11.25 mM Fe•EDTA, 12.5 mM H3BO3, 2.25 mM MnSO4•5H2O, 0.075 mM CuSO4•5H2O, 0.175 mM ZnSO4•7H2O, and 0.025 mM Na2MoO4•2H2O and 1.0 mM NH4Cl to harvest root samples. Growth condition: Plants were hydroponically grown for 18 days.
Extracted molecule total RNA
Extraction protocol Total RNA isolation was performed using RNeasy Plant Mini Kit (QIAGEN, Valencia, CA, USA) according to the manufacturer's instruction.
Label biotin
Label protocol Biotinylated cRNA was labeled using a biotinylated nucleotide analog/ribonucleotide mix using GeneChip 3’ IVT Express Kit (Affymetrix, Santa Clara, CA, USA).
Hybridization protocol Following fragmentation, 12.5 ug of cRNA were hybridized for 16 h on GeneChip Rice Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 (Affymetrix).
Scan protocol GeneChips were scanned using the GeneChip scanner 3000 integrated with Affymetrix® Microarray Suitesoftware.
Description The sample was grown and harvested at Tohoku university. For details, see metadata as described in Kusano et al.
Data processing The microarray data normalization and background correction was performed using robust multi-array average (RMA) with Bioconductor package 'simpleaffy' by using R/Bioconductor.
Submission date Dec 27, 2017
Last update date Apr 20, 2020
Contact name Miyako Kusano
Organization name RIKEN CSRS
Street address 1-7-22, Suehiro, Tsurumi
City Yokohama
State/province Kanagawa
ZIP/Postal code 230-0045
Country Japan
Platform ID GPL2025
Series (1)
GSE49789 Microarray analysis of gene expression in rice lacking cytosolic glutamine synthetase 1;1 and 1;2 grown under the ammonium sufficient condition

Data table header descriptions
VALUE log2-RMA signal

Data table
AFFX-BioB-3_at 7.444061242
AFFX-BioB-5_at 7.840165508
AFFX-BioB-M_at 7.712110881
AFFX-BioC-3_at 9.190320638
AFFX-BioC-5_at 8.899006734
AFFX-BioDn-3_at 11.16637336
AFFX-BioDn-5_at 10.08282546
AFFX-CreX-3_at 13.07556141
AFFX-CreX-5_at 12.80563861
AFFX-DapX-3_at 9.498200858
AFFX-DapX-5_at 7.81044496
AFFX-DapX-M_at 8.98933631
AFFX-LysX-3_at 6.932246814
AFFX-LysX-5_at 5.464285525
AFFX-LysX-M_at 5.769411059
AFFX-Mgr-actin-3_at 5.226809999
AFFX-Mgr-actin-5_at 5.58461692
AFFX-Mgr-actin-M_at 5.265975735
AFFX-Mgr-ef1a-3_at 5.81235074
AFFX-Mgr-ef1a-3_x_at 5.229825229

Total number of rows: 57381

Table truncated, full table size 1728 Kbytes.

Supplementary file Size Download File type/resource
GSM2905105_SK069.CEL.gz 4.7 Mb (ftp)(http) CEL
Processed data included within Sample table

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