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SRX5001297GSM3466701: dc5F_2mm_1_RNAseq; Zea mays; RNA-Seq
1 ILLUMINA (Illumina HiSeq 2500) run: 25.9M spots, 1.3G bases, 749.5Mb downloads

Submitted by: NCBI (GEO)
Study: Transcriptome and sRNA profiling of Maize dcl5 CRISPR null alleles
show Abstracthide Abstract
Small RNAs play important roles during plant development by regulating transcript levels of target mRNAs, maintaining genome integrity, and reinforcing DNA methylation. Dicer-like 5 (Dcl5) is proposed to be responsible for precise slicing to generate diverse 24-nt phased, secondary small interfering RNAs (phasiRNAs), which are exceptionally abundant in meiotic anthers of maize, rice, and other grasses 1. Importance and functions of these phasiRNAs remain unclear. Here we used the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) Cas9 system to mutate Dcl5. We report that dcl5 mutants have few or no 24-nt phasiRNAs, develop short anthers and defective tapetal cells, and exhibit temperature-sensitive male fertility. We propose that DCL5 and 24-nt phasiRNAs are critical for fertility under growth regimes for optimal yield. Overall design: RNA and sRNA-seq libraries were made from meiotic anthers of multiple Maize dcl5 null alleles along with the fertile siblings.
Sample: dc5F_2mm_1_RNAseq
SAMN10413929 • SRS4036013 • All experiments • All runs
Organism: Zea mays
Library:
Instrument: Illumina HiSeq 2500
Strategy: RNA-Seq
Source: TRANSCRIPTOMIC
Selection: cDNA
Layout: SINGLE
Construction protocol: Total RNA for sRNA-seq and RNA-seq libraries was isolated using the PureLink Plant RNA Reagent (ThermoFisher) following the manufacturer's instructions. Total RNA quality was assessed by denaturing agarose gel electrophoresis and quantified by the Qubit RNA BR Assay Kit (ThermoFisher). For small RNA library preparation, 20 to 30 nt RNAs were excised from a 15% polyacrylamide/urea gel, and ~25 ng of sRNA used for library construction with the TruSeq Small RNA Prep Kit (Illumina) following the manufacturer's instructions. For RNA-seq, 2 μg of total RNA was treated with DNase I (New England BioLabs) and then cleaned with RNA Clean and Concentrator-5 (Zymo Research). The TruSeq Stranded Total RNA with RiboZero-Plant Kit (Illumina) was used for library construction with 500 ng of treated RNA, following the manufacturer's instructions.
Experiment attributes:
GEO Accession: GSM3466701
Links:
Runs: 1 run, 25.9M spots, 1.3G bases, 749.5Mb
Run# of Spots# of BasesSizePublished
SRR818130125,879,1431.3G749.5Mb2018-12-18

ID:
6743851

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