Dataset features

Specifications


Application: RNA-seq analysis, sRNA-seq analysis
Number of samples: 12
Release date: Jun 8 2009
Last update date: Jun 11 2013
Access: Public
Taxon: Oryza sativa
Dataset link Endogenous small RNAs of meristematic and a terminally differentiated tissue of rice.

Experimental Protocol


Total RNA was extracted from root apices, shoot apices, developing inflorescence and mature leaf. Three samples from each tissue were taken to represent replicates and small RNAs from these were ligated to a common 5' RNA adapter and a replicate-specific 3' adapter. These replicate samples were then identified from within single 454 data sets using the 3' adapter sequence. It should be noted that there was a strong frequency bias observed between the RNA sequence and the particular 3' adapter used in the sequencing. This resulted in both increased or decreased read counts for the known miRNA sequences in a 3' adapter dependent fashion. Use of the three samples for each tissue as replicates is therefore problematic.

Repositories


GEO

GSE16350

ArrayExpress

E-GEOD-16350

BioProject

PRJNA115305

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Contact


Cameron Johnson