|
| Status |
Public on Mar 01, 2018 |
| Title |
Poplar Mycorrhizal roots-late-2 |
| Sample type |
SRA |
| |
|
| Source name |
Mycorrhizal roots
|
| Organism |
Cenococcum geophilum 1.58 |
| Characteristics |
tissue: Mycorrhizal roots
|
| Growth protocol |
Populus tremula x Populus alba; INRA clone 717-1B4 was micropropagated in vitro in Murashige and Skoog (MS) medium, with hormone supplements to synchronize rhizogenesis. In parallel, MNM medium with low phosphorus and nitrogen was covered with cellophane membranes and inoculated with ten to twelve agar disks containing fungal mycelium at 25 °C for 20 days. Following this, two hybrid poplar plants per dish were transferred onto the fungal mycelium. The Petri dishes were incubated in a growth chamber at 25 °C with 16 h light/ day for 60 days. Pure cultures of C. geophilum grown in identical conditions were used as free-living mycelium controls.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from mycorrhizal roots and fungal controls were extracted with the RNeasy Plant Mini kit (Qiagen, Courtaboeuf, France), including a DNase I (Qiagen) treatment, according to the manufacturer’s instructions to eliminate traces of genomic DNA. Assays for the quantification and integrity check were conducted using an Experion Automated Electrophoresis Station (Bio-Rad, Hercules, CA, USA) or Agilent 2100 Bioanalyzer system (Agilent, Santa Clara, CA, USA).
cDNA libraries were prepared for sequencing using standard Illumina protocols by the Joint Genome Institue (JGI)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Cenococcum geophilum 1.58-Populus tremula x alba INRA 717-1B4
This sample is from 60d old mycorrhizal poplar roots. It is the second of three biological replicates used in this experiment.
PoplarECMlate-2
|
| Data processing |
Illumina sofware was used by the JGI to generate fastq raw data files
Raw fastq file reads were filtered and trimmed using the JGI QC pipeline. Filtered reads from each library were aligned to the reference genome using HISAT version 0.1.4-beta, featureCounts was used to generate the raw gene counts file using gff3 annotations. Only primary hits assigned to the reverse strand were included in the raw gene counts.Further FPKM and TPM normalized gene counts were calculated.
Genome_build: Cenococcum geophilum 1.58 (https://genome.jgi.doe.gov/Cenge3/Cenge3.home.html)
Supplementary_files_format_and_content: tab-delimited text file including JGI Cenge3 Protein IDs, raw counts,FPKM and TPM normalised values
|
| |
|
| Submission date |
Jan 05, 2018 |
| Last update date |
Mar 01, 2018 |
| Contact name |
Annegret Kohler |
| E-mail(s) |
[email protected]
|
| Phone |
+33 (0)383 394072
|
| Organization name |
INRAE
|
| Department |
UMR 1136
|
| Lab |
Interactions Arbres/Micro-organismes
|
| Street address |
Centre INRAE Grand Est Nancy
|
| City |
Champenoux |
| ZIP/Postal code |
54280 |
| Country |
France |
| |
|
| Platform ID |
GPL24474 |
| Series (1) |
| GSE108831 |
Gene expression changes in Cenococcum geophilum 1.58-Populus tremulaxalba INRA 717-1B4 ectomycorrhizal roots compared to Cenococcum geophilum free-living mycelium |
|
| Relations |
| BioSample |
SAMN08299276 |
| SRA |
SRX3537828 |
