Dataset features

Specifications


Application: RNA-seq analysis
Number of samples: 42
Release date: Jul 17 2016
Last update date: Oct 16 2016
Access: Public
Dataset link Widespread and adaptive alterations in genome-wide gene expression associated with ecological divergence of two Oryza species

Experimental Protocol


We selected accessions representing typical Oryza rufipogon and O. nivara, which were sampled exclusively from South and Southeast Asia where the two species overlap. We chose to collect three types of tissues, i.e., flag leaves at the heading stage (2–7 cm above the primary branch) (L), panicles at the heading stage (H) and panicles at the flowering stage (10–15 cm above the primary branch) (F). Sample collection was repeated twice in two consecutive years (2009 and 2010) under the same controlled conditions. A total of 36 samples were sequenced by Illumina’s digital gene expression (DGE) system, with each type of tissues collected from six individuals of each species as biological replicates. To access the quality of DGE technology, we also selected six samples representing three tissues from each of two individuals (one individual per species) for paired-end RNA-Seq sequencing.

Repositories


GEO

GSE71044

ArrayExpress

E-GEOD-71044

ENA

SRP061274

BioProject

PRJNA290171

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Contact


Jie Guo