Gene Expression Nebulas
A data portal of transcriptomic profiles analyzed by a unified pipeline across multiple species

Gene Expression Nebulas

A data portal of transcriptome profiles across multiple species
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PRJNA182292

PRJNA182292: Transcription factors and glyoxylate cycle genes prominent in the transition of soybean cotyledons to the first functional leaves of the seedling

Source: NCBI / GSE42550
Submission Date: Nov 27 2012
Release Date: Jul 29 2014
Update Date: May 15 2019

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.

GEN Datasets:
GEND000267
Strategy:
Species:
Tissue:
Development Stage:
Protocol
Growth Protocol: Plants were grown in optimal greenhouse conditions. Germinating cotyledons were collected at stated days after planting
Treatment Protocol: Tissue was fresh frozen in liquid nitrogen for 10 min and then stored at -80°C.
Extract Protocol: Total RNA was extracted from tissues using phenol:chloroform and a lithium chloride precipitation (Gonzalez and Vodkin 2007). Sequencing was performed by the Keck Center (University of Illinois) using an Illumina HiSeq 2000.
Library Construction Protocol: RNA libraries were prepared for sequencing using standard Illumina protocols
Sequencing
Molecule Type: poly(A)+ RNA
Library Source:
Library Layout: SINGLE
Library Strand: -
Platform: ILLUMINA
Instrument Model: Illumina HiSeq 2000
Strand-Specific: Unspecific
Samples
Basic Information:
Sample Characteristic:
Biological Condition:
Experimental Variables:
Protocol:
Sequencing:
Assessing Quality:
Analysis:
Publications
Transcription factors and glyoxylate cycle genes prominent in the transition of soybean cotyledons to the first functional leaves of the seedling.
Functional & integrative genomics . 2014-07-29 [PMID: 25070765]
Direct detection of transcription factors in cotyledons during seedling development using sensitive silicon-substrate photonic crystal protein arrays.
Plant physiology . 2015-01-29 [PMID: 25635113]