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Sample GSM1754946 Query DataSets for GSM1754946
Status Public on Sep 15, 2015
Title Developing seed at 48HAF drought, biological rep2
Sample type RNA
 
Source name Wheat seeds 48 hours after fertilization - drought
Organism Triticum aestivum
Characteristics stress: drought
time: 48HAF
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_48HAF_s2
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 3.967133978
AFFX-BioB-5_at 4.205913825
AFFX-BioB-M_at 3.862874578
AFFX-BioC-3_at 7.420420679
AFFX-BioC-5_at 6.931202965
AFFX-BioDn-3_at 9.659493706
AFFX-BioDn-5_at 8.829172906
AFFX-CreX-3_at 11.89664257
AFFX-CreX-5_at 11.55551648
AFFX-DapX-3_at 1.777867177
AFFX-DapX-5_at 1.943911811
AFFX-DapX-M_at 1.823983076
AFFX-LysX-3_at 1.746269375
AFFX-LysX-5_at 1.662390094
AFFX-LysX-M_at 1.861078501
AFFX-PheX-3_at 3.072845605
AFFX-PheX-5_at 1.736703715
AFFX-PheX-M_at 1.649614654
AFFX-r2-Bs-dap-3_at 1.524000707
AFFX-r2-Bs-dap-5_at 1.924770017

Total number of rows: 61290

Table truncated, full table size 1861 Kbytes.




Supplementary file Size Download File type/resource
GSM1754946_Wheat_48HAF_s2.CEL.gz 4.1 Mb (ftp)(http) CEL
Processed data included within Sample table

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