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| Status |
Public on Dec 15, 2021 |
| Title |
ectomycorrhizal root tips 14d-3 |
| Sample type |
SRA |
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| Source name |
ectomycorrhizal root tips 14d
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| Organism |
Laccaria bicolor |
| Characteristics |
tissue: ectomycorrhizal root tips
time: 14 days
strain: S238N
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| Growth protocol |
Laccaria bicolor S238N and Populus tremula x alba 717-1B4 in vitro co-cultures were made according to the sandwich system , with small modifications. In brief, L. bicolor was pre-cultured in dark at 25°C for one week on sugar-reduced Pachlewski agar medium P20. P. tremula x alba micro-cuttings were stimulated to root for 1 week on solid Murashige and Skoog (MS) medium supplemented with 2 mg/L IBA (Indol-3-butyric acid) and subsequently transferred to cellophane covered MS plates. After three weeks of incubation at 25°C with a 16h photoperiod, poplar explants were transferred to cellophane covered P20 medium supplemented with 0.1% MES. To allow plant-fungal interaction, the cellophane covered with L. bicolor pre-cultures was placed in an inverted position on the roots. Control plates, containing no plants (i.e. free-living mycelium (FLM)) were prepared and handled the same way as co-cultures. All plates were incubated at 20°C with a 16h photoperiod. Samples (100 mg fresh weight) for RNA extraction were taken in triplicate at 0, 3, 7, 14 and 21 days of (co-)culture from FLM, EcM (i.e. all fungal and mixed plant-fungal material within 0.5 cm distance of a root) and extramatrical mycelium (i.e. all fungal material at a distance of > 0.5 cm of a root), snap frozen in liquid nitrogen and stored at -80°C.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from fungal and mixed plant-fungal biomass (100 mg) using the RNeasy Plant Mini Kit (Qiagen). Biomass was ground in liquid nitrogen prior to extraction and an on column DNAse I treatment was included in the protocol. For samples containing poplar roots (EcM), extraction buffer RLC was supplemented with 2% PEG (polyethylene glycol) 8000.
Preparation of libraries from total RNA (TruSeq Stranded mRNA Kit Illumina) and 2 x 150 bp Illumina HiSeq3000 sequencing was performed at the GET platform (Gé-nopole Toulouse Midi-Pyrénées, Auzeville, France) following their standard protocol.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
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| Description |
This sample is from ectomycorrhizal root tips at 14d . It is the third of three biological replicates used in this experiment.
M14_39
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| Data processing |
Illumina software was used by the Genotoul sequencing facilities (Toulouse, France) to generate fastq raw data files
Raw reads were trimmed for low quality (quality score 0.05), Illumina adapters and sequences shorter than 15 nucleotides and aligned to the L. bicolor v2 reference transcripts available at the JGI database https://mycocosm.jgi.doe.gov/Lacbi2/Lacbi2.home.html using CLC Genomics Workbench v8. For read mapping the CLC genomic workbench parameters were the following: minimum length fraction 0.9, minimum similarity frac-tion 0.8, Mismatch cost = 2, insertion cost = 3, Deletion cost = 3 and the maximum number of hits for a read was set to 10. The unique and total mapped reads number for each transcript were determined and then normalized to RPKM (Reads Per Kilobase of exon model per Million mapped reads).
We calculated differential expression of genes with DESeq2
Genome_build: reference genome sequence of Laccaria bicolor (https://mycocosm.jgi.doe.gov/Lacbi2/Lacbi2.home.html )
Supplementary_files_format_and_content: tab-delimited text file including JGI-Lacbi2 protein ID, aligned reads (raw reads) and normalised expression values (rpkm).
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| Submission date |
Dec 08, 2021 |
| Last update date |
Dec 15, 2021 |
| 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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| Platform ID |
GPL31043 |
| Series (1) |
| GSE190443 |
Time Course of Laccaria bicolor S238N and Populus tremula x alba 717-1B4 in vitro ectomycorrhizal development |
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| Relations |
| BioSample |
SAMN23787719 |
| SRA |
SRX13351626 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5723883_M14_39.txt.gz |
190.1 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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