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Series GSE116473 Query DataSets for GSE116473
Status Public on Jun 30, 2020
Title Expression data of four wheat genotypes viz. HD2967, K307, K9107 and Chotilarma (CL) in response to nitrogen chronic limitation
Organism Triticum aestivum
Experiment type Expression profiling by array
Summary The transcriptome profile was examined in four wheat genotypes in roots and shoots under nitrogen stressed condition which indicates genotype specific transcript data-set apart from the common transcripts. Unique genes was identified for nitrogen uptake and utilization process.
We used microarrays to detail the gene expression and identify the candidate genes related to uptake and utilization of nitrogen in root and shoot tissues of wheat genotypes.
 
Overall design We collected seedlings from four wheat genotypes viz., HD2967, K9107, K307 and Chotilarma (CL) grown for 15 days in pots containing mixture of vermiculite and perlite in a ratio 2:1. Three sets of pots for each genotype were grown in two different conditions : control including 8mM Ca(NO3)2 and nitrogen starved condition 0.08mM Ca(NO3)2 as source. Total RNA isolated from these tissue samples and amplified RNA were purified and labeled by biotin with GeneChip® IVT labeling kit. The biotinylated cDNAs were fragmented and hybridized to the Affymetrix GeneChip® Wheat Genome Array (Affymetrix, Inc., Carlsbad, CA) for 16 hours. Normalization of the microarray data was conducted using Robust Multichip Average (RMA) algorithm with Affymetrix® GeneChip® Command Console® Software (AGCC) used to analyze the data. Transcriptome profiling was detected in all four different wheat genotypes for N+ and N- plants. Each array dataset was then imported into Agilent GeneSpring software 14.5 for analysis. The signal intensities of the samples were transformed into log2-ratio data. Normalized data with a p-value of ≤ 0.1 that passed a Student’s t- test was used to identify differentially expressed genes.
 
Contributor(s) Mandal PK, Sinha S, Singh A
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Submission date Jul 01, 2018
Last update date Jul 01, 2020
Contact name Pranab kumar Mandal
E-mail(s) pranab.mandal@icar.gov.in
Phone 011-25841787
Organization name Indian council of Agriculture Research
Department National Research Centre on Plant Biotechnology
Lab Dr. P.K. Mandal
Street address LBS building, Pusa Campus
City New Delhi
State/province Delhi
ZIP/Postal code 110012
Country India
 
Platforms (1)
GPL3802 [wheat] Affymetrix Wheat Genome Array
Samples (48)
GSM3239721 HD2967 Nitrogen stressed shoot, Rep 3
GSM3239722 HD2967 Nitrogen stressed shoot, Rep 1
GSM3239723 HD2967 Nitrogen stressed root, Rep 1
Relations
BioProject PRJNA478766

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE116473_RAW.tar 224.8 Mb (http)(custom) TAR (of CEL, CHP)
Processed data included within Sample table
Processed data provided as supplementary file
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