|
| Status |
Public on Dec 15, 2021 |
| Title |
late fruiting body stipe-1 |
| Sample type |
SRA |
| |
|
| Source name |
late fruiting body stipe
|
| Organism |
Laccaria bicolor |
| Characteristics |
tissue: Stipe
developmental stage: late
strain: S238N
|
| Growth protocol |
L. bicolor fruiting bodies were harvested from a nursery experiment of inoculated Douglas fir seedlings as described by [24]. Cap and stipe were separated from early, medium and late stage mushrooms (see Figure 3A-C) and immediately frozen in liquid nitrogen and stored at -80°C .
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA of basidiocarp stipes and caps was extracted using a CTAB (cetyltrime-thylammonium bromide) based protocol including a LiCl precipitation of total RNA. RNA concentration of all samples was determined spectrophotometrically and integrity was assessed using the Biorad Experion and RNA StdSens kit and chips.
Preparation of libraries from total RNA (TruSeq Stranded mRNA Kit Illumina) and 2 x 100 bp Illumina HiSeq2000 sequencing was performed at the GET platform (Génopole Toulouse Midi-Pyrénées, Auzeville, France) following their standard protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
This sample is from late stage L.bicolor fruiting body stipe . It is the first of three biological replicates used in this experiment.
LBFB3_stipe1
|
| 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).
|
| |
|
| Submission date |
Dec 08, 2021 |
| Last update date |
Dec 15, 2021 |
| 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 |
GPL19637 |
| Series (1) |
| GSE190444 |
Gene expression changes in different stages of Laccaria bicolor basidiocarps |
|
| Relations |
| BioSample |
SAMN23787738 |
| SRA |
SRX13351606 |
