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Sample GSM1754947 Query DataSets for GSM1754947
Status Public on Sep 15, 2015
Title Developing seed at 72HAF control, biological rep1
Sample type RNA
 
Source name Wheat seeds 72 hours after fertilization - control
Organism Triticum aestivum
Characteristics stress: control
time: 72HAF
tissue: developing seed
Treatment protocol Drought stress treatment was initiated by discontinuing watering on the drought treatment plants while control plants were regularly watered twice daily. Stress treatment was applied at 48 HAF and relieved at 96 HAF (Fig. S1).
Growth protocol Winter wheat cultivar Redland, PI 502907 (Triticum aestivum L.) seedlings were vernalized at 4°C for 6 weeks and then transplanted to a one gallon pot of soil-sand mixture (3:1, v/v) and grown in a growth chamber under the following conditions: relative humidity, 50–70%; 16-h light/8-h dark photoperiod; 21°C daytime temperature and 18°C nights. Plants were watered regularly twice daily at the rate of 100ml/ per pot. Because, wheat has an asynchronous fertilization pattern for ovlues in the inflorescence, each floret needs to be specifically marked for timing the fertilization and stress induction. After spikes developed, unfertilized ovules were monitored and observed for the fertilization process. Closed wheat spikes with anthers outside were marked as fertilized. Drought stress was imposed 24h after the fertilization (HAF).
Extracted molecule total RNA
Extraction protocol Total RNA were isolated from seeds of drought-stressed and control plants at 24, 48 and 72 HAF from. Total RNA was isolated using a Trizol (Invitrogen, Carlsbad, CA) protocol and purified using an RNeasy MinElute Cleanup Kit (Qiagen, Hilden, Germany). Total RNA quality and concentration were determined on a 2100 Bioanalyzer (Agilent, Santa Clara, CA).
Label Biotin
Label protocol 15 µg of total RNA was used to synthesize cDNA using Affymetrix One-Cycle cDNA Synthesis Kit according to the manufacturer’s instructions (Affymetrix, Santa Clara, CA).
 
Hybridization protocol Hybridization was done on a GeneChip Wheat Genome Array.
Scan protocol GeneChip Scanner 3000 (Affymetrix, Santa Clara, CA)
Description Gene expression of developing seeds
Endosperm - Whole seed
Wheat_72HAF_c1
Data processing Affymetrix GeneChip Operating Software generated the images and probe set signal values as CEL files, and the CEL files were processed with the affy package using the robust multiarray analysis (RMA) to generate normalized signal values. The RMA signal values were log2 transformed. To detect differentially expressed genes, the transformed RMA expression values were analyzed with an empirical Bayes linear model. A probeset was considered differentially expressed when it satisfied two conditions, up-regulation or down-regulation more than 2-fold after drought treatment; and a false discovery rate-adjusted P-value was less than <0.05.
 
Submission date Jul 01, 2015
Last update date Sep 15, 2015
Contact name Kevin Begcy
E-mail(s) kevinbegcy@gmail.com
Organization name University of Florida
Street address 1535 Fifield Hall
City Gainesville
State/province Florida
ZIP/Postal code 32611
Country USA
 
Platform ID GPL3802
Series (1)
GSE70443 Early seed development in wheat under control and drought stress

Data table header descriptions
ID_REF
VALUE log2-transformed RMA signal

Data table
ID_REF VALUE
AFFX-BioB-3_at 5.587475811
AFFX-BioB-5_at 5.280277981
AFFX-BioB-M_at 5.439635495
AFFX-BioC-3_at 9.49452854
AFFX-BioC-5_at 8.945394043
AFFX-BioDn-3_at 11.34837558
AFFX-BioDn-5_at 10.59433984
AFFX-CreX-3_at 13.03391134
AFFX-CreX-5_at 12.79845016
AFFX-DapX-3_at 1.815559404
AFFX-DapX-5_at 1.796280888
AFFX-DapX-M_at 2.160713298
AFFX-LysX-3_at 2.018762396
AFFX-LysX-5_at 1.833586411
AFFX-LysX-M_at 2.05713975
AFFX-PheX-3_at 3.22723146
AFFX-PheX-5_at 2.032630466
AFFX-PheX-M_at 1.758371091
AFFX-r2-Bs-dap-3_at 2.09919744
AFFX-r2-Bs-dap-5_at 2.175631481

Total number of rows: 61290

Table truncated, full table size 1861 Kbytes.




Supplementary file Size Download File type/resource
GSM1754947_Wheat_72HAF_c1.CEL.gz 4.5 Mb (ftp)(http) CEL
Processed data included within Sample table

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