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SRX5125913: GSM3508935: Replicate 3 for wild type (Col-0); Arabidopsis thaliana; RNA-Seq
1 ILLUMINA (Illumina HiSeq 2500) run: 48.9M spots, 2.4G bases, 1.1Gb downloads

Submitted by: NCBI (GEO)
Study: Compared gene expression during seed germination (12 hai) in the nac25 (KO2) and nac1L (KO1) null mutants and wild-type (Columbia-0) controls using deep sequencing of RNA populations (RNA-seq).
show Abstracthide Abstract
A key component of seed germination is the interplay of mechanical forces governing embryo growth and the surrounding restraining endosperm tissue. Endosperm cell separation is therefore thought to play a critical role in the control of this developmental transition. Here we demonstrate that in Arabidopsis thaliana seeds, endosperm cell expansion is a key component of germination. Endosperm cells expand to accommodate embryo growth prior to germination. We show that this is an actively regulated process supported by spatiotemporal control of the cell expansion gene EXPANSIN 2 (EXPA2). The NAC transcription factors NAC25 and NAC1L were identified as upstream regulatory effectors of EXPA2 expression, GA-mediated endosperm expansion and seed germination. The DELLA protein RGL2 repressed activation of EXPA2 promoter by NAC. Our findings demonstrate a key role of this gene network in regulating endosperm cell-expansion to control the seed to seedling transition. Overall design: Three genotypes were analyzed: WT (Arabidopsis thaliana Col-0), nac25 (KO2; loss-of-function mutant) and nac1L (KO1; loss-of-function mutant). Seeds from each genotype (20mg) were imbibed in agarose (0,6%) plates and collected for RNA extraction after 12h. Three biological replicates per genotype were used.
Sample: Replicate 3 for wild type (Col-0)
SAMN10581419 • SRS4139035 • All experiments • All runs
Instrument: Illumina HiSeq 2500
Strategy: RNA-Seq
Selection: cDNA
Layout: SINGLE
Construction protocol: RNA extraction was carried out as described previously (protocol 2 in Oñate-Sánchez and Vicente-Carbajosa, 2008) except that: in step 2, the mix containing the sample, phenol and chloroform was applied to a Phase Lock (5-PRIME) eppendorf previous to centrifugation to prevent organic contamination of the aqueous phase. RNA isolation was followed by RNA cleanup by the RNeasy mini kit (Qiagen). Stranded library for HiSeq Sequencing v4 Chemistry
Experiment attributes:
GEO Accession: GSM3508935
Runs: 1 run, 48.9M spots, 2.4G bases, 1.1Gb
Run# of Spots# of BasesSizePublished


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