Dataset features

Specifications


Application: Gene expression microarray analysis
Number of samples: 18
Release date: Dec 22 2014
Last update date: Dec 24 2014
Access: Public
Dataset link Plant root transcriptome profiling of Azospirillum-rice cooperation

Experimental Protocol


For each of the four condition, three replicates were analysed on an oligo microarray produced by NimbleGenTM (Madison, WI, USA). The microarray was derived of the one previously described in Yuan et al. 2005 . This microarray is composed of about 385,000 60mer probes selected for their GC content, Tm and number of cycles needed to synthesize the oligo. This chip contains 90,000 probes representing 45,000 genes (two probes per gene) of rice Oryza sativa ssp. japonica, based on the TIGR rice genome annotation version 3.1 genes (Chaparro et al. 2007) and 201 691 oligomers corresponding to previously described copies of LTR retrotranposons available on the retrOryza database (www.retroryza.fr). Probes represent 1,000 bp of the LTR-retrotransposon flanking regions at the 3’ and 5’ side. The oligonucleotides have been designed at the 3’ end of the genes to detect the readings of reverse transcriptase. On the other hand, the LTR-retrotransposons are represented throughout their length at the rate of a probe every 500 bp.

Repositories


GEO

GSE59137

ArrayExpress

E-GEOD-59137

BioProject

PRJNA254488

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