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SRX2823835: GSM2627925: Rice GSK5 rep1; Oryza sativa Japonica Group; RNA-Seq
1 ILLUMINA (Illumina HiSeq 2000) run: 31.2M spots, 9.4G bases, 3.8Gb downloads

Submitted by: NCBI (GEO)
Study: The novel quantitative trait locus qTGW3 encodes a GSK3-like kinase and negatively regulates grain size and weight in rice
show Abstracthide Abstract
qTGW3 encodes a GLYCOGEN SYNTHASE KINASE 3 (GSK3)/SHAGGY-like family protein kinase GSK5. We demonstrate that GSK5 interacts with and phosphorylates the AUXIN RESPONSE FACTOR (ARF) transcription factor ARF4. Both GSK5 and ARF4 are mainly expressed in reproductive tissues, and loss-of-function mutation of ARF4 also increases rice grain length and weight. ARF4 functions as a transcriptional repressor in plants and RNA-Seq analysis reveals that, compared to the wild-type plants, totally 887 and 1179 genes were up-regulated in the GSK5 and ARF4 mutants, respectively. Among them, 373 genes were commonly up-regulated in both mutants. In contrast, there were 681 and 669 genes were down-regulated in the GSK5 and ARF4 mutants, respectively. Among them, 288 genes were commonly up-regulated in both mutants. These results showed that GSK5 and ARF4 have overlapping roles and regulate a common set of genes during rice grain development. Overall design: Rice grain (7-8 days after flowering) mRNA profiles of wild type (WT), GSK5-edited and ARF4-edited plants were generated by deep sequencing, in triplicate, using Illumina GAIIx.
Sample: Rice GSK5 rep1
SAMN07124410 • SRS2200435 • All experiments • All runs
Library:
Instrument: Illumina HiSeq 2000
Strategy: RNA-Seq
Source: TRANSCRIPTOMIC
Selection: cDNA
Layout: PAIRED
Construction protocol: Rice grains were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols
Experiment attributes:
GEO Accession: GSM2627925
Links:
Runs: 1 run, 31.2M spots, 9.4G bases, 3.8Gb
Run# of Spots# of BasesSizePublished
SRR556073031,165,0519.4G3.8Gb2017-05-19

ID:
4059677

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