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Series GSE42550 Query DataSets for GSE42550
Status Public on Jul 29, 2014
Title Transcription factors and glyoxylate cycle genes prominent in the transition of soybean cotyledons to the first functional leaves of the seedling
Organism Glycine max
Experiment type Expression profiling by high throughput sequencing
Summary To understand the genetic mechanisms involved in the functional transition of cotyledons from non-photosynthetic storage tissue to metabolically active photosynthetic tissue during soybean seedling development, we constructed seven different RNA-Seq libraries using cotyledons from each developmental stage separately. Analysis of RNA-Seq data from different developmental stages revealed the differential expression of many genes including transcription factors. In this study, we focused on NAC and YABBY transcription factors which showed a conspicuous expression pattern during soybean seedling development. Their expression gradually increases from stage 1 to stage 4 of soybean germinating cotyledons. The highest level of expression was found at stage 4. Then it gradually decreased as the germinating cotyledons develop a mature seedling. We investigated the differential expression of NAC and YABBY regulated genes between stage 3 (before the functional transition) and stage 6 (after the functional transition) using our RNA-Seq data. Based on our RNA-Seq data, we found that 10 genes are up-regulated and 21 genes are down-regulated by NAC transcription factor. Similarly we found that 19 genes are up-regulated and 27 genes are down-regulated by YABBY transcription factor.
Overall design High-throughput sequencing using Illumina HiSeq 2000 (RNA-Seq) was performed on seven developmental stages of soybean seedlings, with two biological replicates per stage.
Contributor(s) Shamimuzzaman M, Vodkin LO
Citation(s) 25070765, 25635113
Submission date Nov 27, 2012
Last update date May 15, 2019
Contact name Lila O. Vodkin
Phone 217-244-6147
Organization name University of Illinois
Department Crop Sciences
Lab Lila Vodkin
Street address 1201 W. Gregory Dr.
City Urbana
State/province IL
ZIP/Postal code 61801
Country USA
Platforms (1)
GPL15008 Illumina HiSeq 2000 (Glycine max)
Samples (14)
GSM1044984 R76_Germinating_Cotyledons_Stage1_BR1
GSM1044985 R84_Germinating_Cotyledons_Stage1_BR2
GSM1044986 R77_Germinating_Cotyledons_Stage2_BR1
BioProject PRJNA182292
SRA SRP017324

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Supplementary file Size Download File type/resource
GSE42550_RAW.tar 8.9 Mb (http)(custom) TAR (of TXT)
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Raw data are available in SRA
Processed data provided as supplementary file

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