Dataset features

Specifications


Application: RNA-seq analysis, sRNA-seq analysis
Number of samples: 12
Release date: May 26 2012
Last update date: Jun 20 2017
Access: Public
Taxon: Arabidopsis thaliana, Oryza sativa, Zea mays
Dataset link Small RNA sequencing in maize hybrids and inbreds

Experimental Protocol


sRNA libraries were derived from RNA isolated from the seedling shoot apex and developing ear tissues from B73, Mo17, B73xMo17 and Mo17xB73. The shoot apex was chosen because it is enriched for meristematic tissue where cell proliferation occurs, rates of organ initiation are determined, and organ size is specified. The developing ear was examined because it is enriched in meristematic tissue and is undergoing rapid growth, and also because the mature ear shows the highest degree of heterosis. Total RNA was isolated and separated on a 15% TBE-Urea polyacrylamide gel. Using a 10-bp ladder, the sRNA fraction representing 10-40-bp was excised. sRNA libraries were prepared according to Lu et al. (2007) or manufacturer's instructitions (Illumina). A combination of Perl scripts and FASTX toolkit scripts were used to remove adapters, collapse identical sequences and count reads per sequence. Supplementary processed data text files contain the distinct sRNA sequences for all of the genotypes analyzed in that experiment. Abundance (reads per million) was calculated for each distinct sequence by dividing the number of reads of distinct sRNA in a library by the total number of sRNA reads for that library and multiplying this by 1 million. Genome builds: B73 genome, maizesequence.org release 4a.53 (October, 2009); Mo17 whole genome shotgun clones.

Repositories


GEO

GSE37411

ArrayExpress

E-GEOD-37411

ENA

SRP012317

BioProject

PRJNA159733

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Contact


Wesley Barber
Wesley T Barber