|
| Status |
Public on Feb 04, 2017 |
| Title |
Rhizophagus NPC exudate time point 24h replicate 3 |
| Sample type |
SRA |
| |
|
| Source name |
germinating spores
|
| Organism |
Rhizophagus irregularis |
| Characteristics |
strain: DAOM197198
treatment: rice NPC Root exudates
growth time post induction: 24 hours
|
| Treatment protocol |
germinating spores were treated with root exudates and collected 1 hour, 24 hours and 7 days in the same previous conditions.
|
| Growth protocol |
80 000 spores were germinated in 40ml of liquid M medium for 2 days in the dark with 2% CO2 before treatment (T0)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Spores were crushed with a motar and a pestle in liquid nitrogen and mRNA were extracted using RNeasy plant kit (Qiagen), according to the manufacturer instructions.
Samples were sequenced at the Genome and Transriptome platform (Toulouse, France - GeT). mRNA were isolated with polyT beads before processing, libraries were constructed according to the manufacturer's protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Sample 15
|
| Data processing |
For gene expression analysis, we used additional triplicates Illumina libraries from treated samples (germinating spores of R.irregularis with wt/npc rice root exudates at time 0, 1h, 24h , 7d). Reads were mapped to the Gloin1 assembly (Tisserant et al., PNAS, 2013) for calculating gene expression by using RNA-seq functionality of the CLC Genomic Workbench suite. To find the genes significantly upregulated during symbiosis, RPKM (Reads Per Kilobase of exon per Million fragments mapped - Mortazavi et al., 2008) and proportion-based test statistics (Baggerly et al., 2003) with a False Discovery Rate (FDR) correction for multiple testing (Benjamini & Hochberg, 1995) were calculated (settings: minimum mapped read length fraction = 0.95; minimum similarity = 0.98). According to CLC recommendation, genes were considered as significantly up regulated when meeting the requirements of "total difference reads mapped" >10 (parameter proposed by CLC WorkBench to select only significantly expressed genes), RPKM fold change>2 and FDR corrected p value<0.05.
Genome_build: Gloin1 (GCA_000439145.2)
Supplementary_files_format_and_content: Analysis2.xlsx reports processed data.
|
| |
|
| Submission date |
Feb 04, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Christophe Roux |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Toulouse/CNRS
|
| Lab |
Plant Science Laboratory - Joint Unit University of Toulouse/CNRS 5546
|
| Street address |
Chemin de Borde Rouge
|
| City |
Castanet-Tolosan |
| ZIP/Postal code |
F-31326 |
| Country |
France |
| |
|
| Platform ID |
GPL19734 |
| Series (1) |
| GSE65595 |
Rhizophagus irregularis gene regulation in response to rice root exudates |
|
| Relations |
| BioSample |
SAMN03328975 |
| SRA |
SRX864892 |
