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E-GEOD-69821 - Transcriptome analysis during seed development provides insights into altered gene expression in Glycine max

Status
Released on 11 August 2015, last updated on 20 August 2015
Organism
Glycine max
Samples (12)
Arrays (2)
Protocols (7)
Description
The temporal expression profile of Glycine max seeds was carried out to identify genes that are differentially expressed (DE) during seed development. Using the Affymetrix chip, we have for the first time provided a holistic view of the transcriptional landscape during seed development in four different developmental stages in Glycine max. cv. Pusa 16. The analysis of the differential expression patterns and functional category enrichment of DE genes highlighted specific and common significant coordination and enrichment of various biological processes during seed development which have led to the identification of few candidate genes related to inositol metabolism and especially in phytate biosynthesis. In conclusion, we have shown here a logical approach to identify possible candidate genes for fine tuning the metabolic flux for phytate generation, which may be altered by metabolic engineering in developing a low phytate phenotype. Seeds of Glycine max grown at 28/26°C, 16h/8h light/dark were collected at different developmental stages( 0-4mm, 4-8mm, 8-12mm and 12-16mm ) and analyzed. Samples in triplicates from each developmental stage were used for data generation on Affymetrix Chip, each time the earlier developmental stage was considered as control Vs the treatment, corresponding to the later developmental stage. For each biological replicates, RNA was extracted from 20 seeds collected from 5 different plants, grown in the same conditions using the Trizol method. RNA integrity was analyzed using bio analyzer (with RIN value more than 8).
Experiment type
transcription profiling by array 
Contacts
Archana Sachdev <arcs_bio@yahoo.com>, A Dahuja, A Hada, A Marathe, A Sachdev, C Viswanathan, M Jolly, M Punjabi, N Basak, R D Rai, R Kansal, V Krishnan, V Pandey
MIAME
PlatformsProtocolsVariablesProcessedRaw
Files
Investigation descriptionE-GEOD-69821.idf.txt
Sample and data relationshipE-GEOD-69821.sdrf.txt
Raw data (1)E-GEOD-69821.raw.1.zip
Processed data (1)E-GEOD-69821.processed.1.zip
Array designsA-AFFY-59.adf.txt, A-GEOD-13674.adf.txt
Links