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| Status |
Public on Dec 01, 2016 |
| Title |
Gene expression changes in Tulasnella calospora - Serapias vomeracea mycorrhizal protocorms at stage P2 compared to asymbiotic, achlorophyllous Serapias vomeracea protocorms |
| Organisms |
Serapias vomeracea; Tulasnella calospora |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Illumina HiSeq technology was used to generate mRNA profiles from Serapias vomeracea-Tulasnella calospora mycorrhizal protocorms compared to asymbiotic protocorms . Protocorms were harvested at stage P2 and used for RNA extraction. Reads of 150bp were generated and aligned to a de novo transcriptome assembly from Serapias vomeracea using CLC Genomics Workbench 9.
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| Overall design |
mRNA profiles from Serapias vomeracea-Tulasnella calospora mycorrhizal protocorm and asymbiotic, achlorophyllous Serapias vomeracea protocorms were generated by 150bp Illumina HiSeq2500 sequencing. Three biological replicates were sequenced for mycorrhizal and asymbiotic samples. Asymbiotic samples (containing only plant-derived reads) were used to generate a reference de novo assembly (Trinity software) and reads from all samples were then aligned to this reference.
Please note that the raw data for Mycorrhizal protocorm_plantP2* samples are same as GSM2311257-GSM2311259 raw data, but re-analyzed on the plant side in the current study as they are dual transcriptome from symbiotic tissue containing both fungal and plant reads.
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| Contributor(s) |
Fochi V, Perotto S, Singan VR, Grigoriev IV, Kohler A, Martin F |
| Citation(s) |
27859287 |
| |
| Submission date |
Sep 20, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Annegret Kohler |
| E-mail(s) |
[email protected]
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| Phone |
+33 (0)383 394072
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| Organization name |
INRAE
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| Department |
UMR 1136
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| Lab |
Interactions Arbres/Micro-organismes
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| Street address |
Centre INRAE Grand Est Nancy
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| City |
Champenoux |
| ZIP/Postal code |
54280 |
| Country |
France |
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| Platforms (2) |
| GPL22437 |
Illumina HiSeq 2500 (Serapias vomeracea; Tulasnella calospora) |
| GPL22451 |
Illumina HiSeq 2500 (Serapias vomeracea) |
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| Samples (6)
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| Relations |
| BioProject |
PRJNA343607 |
| SRA |
SRP090173 |
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