|
| Status |
Public on Jul 22, 2023 |
| Title |
POXKu70_24 |
| Sample type |
SRA |
| |
|
| Source name |
Mycelium
|
| Organism |
Penicillium oxalicum |
| Characteristics |
strain: MuKu70
|
| Growth protocol |
Mycelium of 1 gram Mutant Ku70 were cultured in 2% Avicel liquid medium for 24 hours
Fresh spores of the MuKu70 were statically incubated on potato-dextrose agar (PDA) plates at 28°C for 6 d, collected and resuspended in sterile water containing 0.1% Tween 80 with a final concentration of 1 × 108 per milliliter. Approximately 1.0 g of hyphae was transferred to 100 mL of basic medium with % (w/v) Avicel, and incubated in a shaker at 180 rpm and 28°C for 24 h.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA were extracted using TRIzol RNA Kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
The deletion mutant of the gene POXKu70 is a control strain for differential transcriptome analysis, It is transferred from glucose medium to medium containing Avicel and cultivated for 12h
|
| Data processing |
Remove reads with adapters;Remove reads in which unknown bases are more than 10%;Remove low quality reads (the percentage of low quality bases is over 50% in a read, we define the low quality base to be the base whose sequencing quality is no more than 10).
The clean reads mapped onto the genome of P. oxalicum wild type strain HP7-1 to functional annotation, susing the software BWA v0.7.10-r789 and Bowtie2 v2.1.0.
FPKM, representing gene expression levels, was calculated with the software RSEM v1.2.12
DEGs were screened with NOISeq or DESeq2 tools
Genome_build: GenBank database under accession number JRVD00000000
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample.
|
| |
|
| Submission date |
Aug 06, 2020 |
| Last update date |
Jul 22, 2023 |
| Contact name |
Li ChengXi |
| E-mail(s) |
[email protected]
|
| Organization name |
Bengbu Medical College
|
| Department |
Affiliated Sixth People’s Hospital
|
| Street address |
2600 Donghai Avenue, Bengbu, Anhui, China
|
| City |
bengbu |
| State/province |
Anhui |
| ZIP/Postal code |
233000 |
| Country |
China |
| |
|
| Platform ID |
GPL26664 |
| Series (1) |
| GSE155790 |
Large scale transcriptome analysis was used to identify the genes most related to the transcription of cellulase genes and/or xylanase genes expression |
|
| Relations |
| BioSample |
SAMN15747225 |
| SRA |
SRX8898410 |
