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SRX4781136: GSM3408861: leaf_poly(A)+ rep4; Arabidopsis thaliana; RNA-Seq
1 ILLUMINA (HiSeq X Ten) run: 43.3M spots, 13G bases, 4.7Gb downloads

Submitted by: NCBI (GEO)
Study: Global identification of Arabidopsis lncRNAs reveals the regulation of MAF4 by a natural antisense RNA
show Abstracthide Abstract
Long non-coding RNAs (lncRNAs) have emerged as important regulators of gene expression and plant development. Here, we identified 6,510 lncRNAs in Arabidopsis under normal or stress conditions. We found that the expression of natural antisense transcripts (NATs) that are transcribed in the opposite directionof protein-coding genes often positively correlates with and is required for theexpression of their cognate sense genes. We further characterized MAS, a NAT-lncRNA produced from the MADS AFFECTING FLOWERING4 (MAF4) locus.MAS is induced by cold and indispensable for the activation of MAF4 transcriptionand suppression of precocious flowering. MAS activates MAF4 by interacting with WDR5a, one core component of the COMPASS-like complexes, and recruiting WDR5a to MAF4 to enhance histone 3 lysine 4 trimethylation (H3K4me3). Our study greatly extends the repertoire of lncRNAs in Arabidopsis and reveals a role for NAT-lncRNAs in regulating gene expression in vernalization response and likely in other biological processes Overall design: To globally identify lncRNAs in Arabidopsis, we reconstructed an Arabidopsis transcriptome using high depth strand-specific RNA sequencing (ssRNA-seq). We generated cDNA libraries for rRNA-depleted total, polyadenylated [poly(A)+] and non-polyadenylated [poly(A)-] RNAs in whole cell extract, nuclear and cytosolic fractions that were prepared from Arabidopsis grown under normal or stress conditions
Sample: leaf_poly(A)+ rep4
SAMN10150220 • SRS3861605 • All experiments • All runs
Instrument: HiSeq X Ten
Strategy: RNA-Seq
Selection: cDNA
Layout: PAIRED
Construction protocol: Total RNA was extracted with TRIzol (Invitrogen) and treated with DNase I (Ambion). Polyadenylated [poly(A)+] RNAs were isolated from total RNA through two rounds of purification with oligo(dT) beads (QIAGEN). Libraries for RNA-seq were generated using NEXTflex Rapid Directional qRNA-Seq Kit (dUTP based) according to the manufacturer's instructions.
Experiment attributes:
GEO Accession: GSM3408861
Runs: 1 run, 43.3M spots, 13G bases, 4.7Gb
Run# of Spots# of BasesSizePublished


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