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Series GSE54903 Query DataSets for GSE54903
Status Public on May 16, 2014
Title RNA-Seq Profiling of a Defective Seed Coat Mutation in Glycine max Reveals Differential Expression of Proline Rich and Other Cell Wall Protein Transcripts
Organism Glycine max
Experiment type Expression profiling by high throughput sequencing
Summary The plant cell wall performs a number of essential functions including providing shape to many different cell types and serving as a defense against potential pathogens. The net pattern mutation creates breaks in the seed coat of soybean (Glycine max) because of ruptured cell walls. Using RNA-Seq, we examined the seed coat transcriptome from three stages of immature seed development in two pairs of isolines with normal or defective seed coat phenotypes due to the net pattern. The genome-wide comparative study of the transcript profiles of these isolines revealed 364 differentially expressed genes in common between the two varieties that were further divided into different broad functional categories. Genes related to cell wall processes accounted for 19% of the differentially expressed genes in the middle developmental stage of 100-200 mg seed weight. Within this class, the cell wall proline-rich and glycine-rich protein genes were highly differentially expressed in both genetic backgrounds. Other genes that showed significant expression changes in each of the isoline pairs at the 100-200 mg seed weight stage were xylem serine proteinase, fasciclin-related genes, auxin and stress response related genes, TRANSPARENT TESTA 1 (TT1) and other transcription factors. The mutant appears to shift the timing of either the increase or decrease in the levels of some of the transcripts. The analysis of these data sets reveals the physiological changes that the seed coat undergoes during the formation of the breaks in the cell wall.
 
Overall design Examination of soybean isolines in two different genetic background at three different seed weight stages: Seed coats of Clark standard (CS, wild type) & Clark defective (CD, seed coat mutant), Harosoy Standard (HS) & Harosoy defective (HD) at 50-100mg, 100-200mg and 400-500mg.
 
Contributor(s) Kour A, Boone AM, Vodkin L
Citation(s) 24828743
Submission date Feb 12, 2014
Last update date May 15, 2019
Contact name Lila O. Vodkin
E-mail l-vodkin@illinois.edu
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 (2)
GPL11192 Illumina Genome Analyzer II (Glycine max)
GPL15008 Illumina HiSeq 2000 (Glycine max)
Samples (12)
GSM1326387 R121_RNASeq_Clark_standard
GSM1326388 R40_RNASeq_Clark_standard
GSM1326389 R120_RNASeq_Clark_standard
Relations
BioProject PRJNA238008
SRA SRP037713

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
GSE54903_R114_116_Harosoy_seedcoat_400_500mg_RNASeq_RPKM_data.txt.gz 1.0 Mb (ftp)(http) TXT
GSE54903_R115_117_Harosoy_seedcoat_50_100mg_RNASeq_RPKM_data.txt.gz 1.0 Mb (ftp)(http) TXT
GSE54903_R120_118_Clark_seedcoat_400_500mg_RNASeq_RPKM_data.txt.gz 1.0 Mb (ftp)(http) TXT
GSE54903_R121_119_Clark_seedcoat_50_100mg_RNASeq_RPKM_data.txt.gz 1.1 Mb (ftp)(http) TXT
GSE54903_R19_20_Harosoy_Seedcoat_100_200mg_RNASeq_RPKM_data.txt.gz 1.1 Mb (ftp)(http) TXT
GSE54903_R40_17_Clark_Seedcoat_100_200mg_RNASeq_RPKM_data.txt.gz 1.1 Mb (ftp)(http) TXT
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