|
| Status |
Public on May 22, 2020 |
| Title |
Time_0_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
mycelia
|
| Organism |
Laetiporus sulphureus |
| Characteristics |
strain: ATCC 52600
|
| Treatment protocol |
Mycelia were then filtered and washed with water and then transferred to liquid medium containing 1.0 g of in natura sugarcane bagasse and 100 mL of medium pH 7.0 composed of 6 g/L (NH4)2SO4, 1 g/L KH2PO4, 1 g/L KCl and 1 g/L MgSO4. Cultivation was performed under 180 rpm for 24 h at 30 °C. Mycelia and substrate mixtures were collected by filtration, washed with sterile water, manually dried in filter paper, and stored at -80 °C before RNA extraction.
|
| Growth protocol |
Pre-inoculum, consisting of 15 discs (8 mm diameter) of L. sulphureus ATCC 52600 pre-cultivated on agar plates, was inoculated into 100 mL of liquid medium and incubated under 180 rpm for 7 days at 30 °C. Mycelium from pre-inoculum was used as a reference before induction (T0)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The mycelium was ground with liquid nitrogen, and total RNA extraction was performed with mirVana™ Total Isolation Kit (Thermo Fisher), according to the manufacturer's instructions. The resulting solution was treated with DNAse (DNA-Free RNA Kit, Zymo Research), purified with RNeasy Kit (Qiagen) and quality was verified using RNAnano Bioanalyzer 2100 chip (Agilent).
Libraries were prepared using Illumina TruSeq mRNA kit according to the manufacturer's instructions and sequenced on the Illumina HiSeq 2500 platform.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
T0-1
|
| Data processing |
Paired-end reads (2x100pb) were filtered by quality and presence of adaptors using Trimmomatic v0.32
the evaluation and filtration of the rRNAs were performed using SortmeRNA
The filtered data were mapped into the L. sulphureus ATCC 52600 reference genome sequenced in this work using Tophat2 algorithm
Differential gene expression analysis was based on counting data and performed using the Bioconductor DESeq2 package using the R platform, by paired comparisons against the control condition.
Transcripts showing differential expression (log2-fold change ≥1 and ≤-1) relative to the non-induced condition (T0) were determined by applying p ≤ 0.05 as the threshold.
Genome_build: L. sulphureus ATCC 52600 reference genome sequenced in this work
Supplementary_files_format_and_content: Matrix tab-delimited file with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Matrix tab-delimited file include TPM values for each Sample
Supplementary_files_format_and_content: Matrix tab-delimited file include DESeq2 results
|
| |
|
| Submission date |
May 21, 2020 |
| Last update date |
May 22, 2020 |
| Contact name |
Gabriela F Persinoti |
| E-mail(s) |
gabriela.persinoti@lnbr.cnpem.br
|
| Phone |
551935175165
|
| Organization name |
Brazilian Center for Research in Energy and Materials CNPEM
|
| Department |
Brazilian Biorenewables National Laboratory LNBR
|
| Street address |
Rua Giuseppe Máximo Scalfaro, 10.000
|
| City |
Campinas |
| State/province |
São Paulo |
| ZIP/Postal code |
13083-970 |
| Country |
Brazil |
| |
|
| Platform ID |
GPL28568 |
| Series (1) |
| GSE151004 |
Multi-omic analysis provide insights into lignocellulosic biomass degradation by Laetiporus sulphureus ATCC 52600 |
|
| Relations |
| BioSample |
SAMN14992873 |
| SRA |
SRX8377590 |
