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SRX1418378: GSM1930282: 10-day-old wild type rep. 1; Arabidopsis thaliana; RNA-Seq
1 ILLUMINA (Illumina HiSeq 2500) run: 33.7M spots, 5.1G bases, 2.6Gb downloads

Submitted by: NCBI (GEO)
Study: Transcriptomics analysis of developing wild type and val1 mutant Arabidopsis embryos
show Abstracthide Abstract
Developing Arabidopsis seeds accumulate oils and seed storage proteins synthesized by the pathways of primary metabolism. Seed development and metabolism are positively regulated by transcription factors belonging to the LAFL regulatory network. The VAL gene family encodes repressors of the seed maturation program in germinating seeds, although they are also expressed during seed maturation. VAL1 functions as a repressor of seed metabolism, as val1 mutant seeds accumulated elevated levels of storage proteins compared to the wild type. Two VAL1 splice variants were identified through RNA sequencing analysis: a full-length and a truncated form lacking the plant-homeodomain-like domain associated with epigenetic repression. None of the transcripts encoding the core LAFL network transcription factors were affected in val1 embryos. Instead, activation of VAL1 by FUSCA3 appears to result in repression of a subset of seed maturation genes downstream of core LAFL regulators as 39% of transcripts in the FUSCA3 regulon were de-repressed in the val1 mutant. The LEC1 and LEC2 regulons also responded but to a lesser extent. Additional 832 transcripts that were not LAFL targets were de-repressed in val1 mutant embryos. These transcripts are candidate targets of VAL1, acting through epigenetic and/or transcriptional repression. Overall design: 2 genotypes, 7 time points, 3 biological and 4 technical replicates
Sample: 10-day-old wild type rep. 1
SAMN04240701 • SRS1152449 • All experiments • All runs
Instrument: Illumina HiSeq 2500
Strategy: RNA-Seq
Selection: cDNA
Layout: PAIRED
Construction protocol: RNA was extracted from frozen embryos using phenol/chloroform and LiCl precipitation and purified by using the Qiagen RNeasy Plant Mini kit. RNA quality and integrity analysis was performed by the Virginia Bioinformatics Institute (Virginia Tech, Blacksburg, VA). Reverse transcription of mRNA, library preparation, and paired-end RNA-Seq generating 75-bp reads, including removing low quality reads and adapter sequence trimming, was performed by Beckman Coulter Genomics (Danvers, MA) using established protocols.
Experiment attributes:
GEO Accession: GSM1930282
Runs: 1 run, 33.7M spots, 5.1G bases, 2.6Gb
Run# of Spots# of BasesSizePublished


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