Transcriptome of Oryza glaberrima in response to Meloidogyne graminicola

Dataset name : Transcriptome of Oryza glaberrima in response to Meloidogyne graminicola 
Organism : O. glaberrima TOG5681
Referent people : Anne-Sophie Petitot (anne-sophie.petitot@ird.fr)
Unit : DIADE
Description : Gene expression profiling of the resistant rice Oryza glaberrima (TOG5681) in response to the root-knot nematode Meloidogyne graminicola, a major pest of rice (Oryza sativa L.) in Asia and in Central America. Dual RNA-seq, that is the simultaneous sequencing of the two organisms, was performed on M. graminicola-infected rice plants. RNA-seq data were obtained from 8 libraries coming from two biological replicates (1 and 2) of the following samples: mock-inoculated rice root tips (Oryza glaberrima accession TOG5681) as plant controls (TogC) and M. graminicola infected rice root tips (Oryza glaberrima accession TOG5681) collected at 2 dpi, 4 dpi, and 8 dpi (days post-inoculation) (Tog2dpi, Tog4dpi, Tog8dpi).
Lab Protocol : Rice seeds were germinated on sand wetted with Hoagland solution for 7 days and then transferred to plastic tubes containing SAP (Sand and Absorbent Polymer) substrate wetted with Hoagland solution. Three days after transplanting into SAP substrate, the plants were inoculated with 400 J2 (M.graminicola juveniles at the stage J2). One day after inoculation, plants were transferred to a 50-ml hydroponic culture system containing Hoagland solution, to synchronize the infection process. Roots tips (1-2 mm) or visible galls were dissected by hand and collected at 2, 4, and 8 dpi. Root tips from non-inoculated plants were collected at the same time as the 2-dpi plants, and were considered as control. Samples were immediately frozen in liquid nitrogen and stored at -80°C until further use. One biological replicate contains a pool of root tips or galls collected from a mean of 25 plants. Total RNA was extracted from rice root samples using the RNeasy Plant mini kit (Qiagen, France), with addition of an on-column DNase I digestion. RNA integrity was determined by the RIN (RNA integrity number) using the Agilent RNA 6000 Nano chip. Individually indexed libraries were prepared using the TruSeq RNA sample Preparation v2 kit according to the manufacturer's instructions (Illumina Inc., USA). The libraries were sequenced at the Centre National de Séquençage (Genoscope, Evry, France) on a HiSeq2000 system (Illumina Inc.) generating 100 bp paired-end reads. 
Sequencing platform : Illumina Hiseq
Production data : 2015
Bioinformatic pipeline : Mapping against MSU7 using TopHat2 and count files generated by htseq-count (i-trop, Alexis Dereeper) 
DOI : https://doi.org/10.1093/aob/mcw256
ENA/SRA accession number : ERS715982