|
| Status |
Public on Jan 28, 2022 |
| Title |
mycelium, treated with HSAF for 60 min, J |
| Sample type |
SRA |
| |
|
| Source name |
mycelium
|
| Organism |
Neurospora crassa |
| Characteristics |
tissue: mycelium
strain: FGSC2489
genotype: wild type
age: post innoculate 48h
treatment: HSAF for 60 min
|
| Treatment protocol |
Treating mycelium with 40 μM HSAF for 0, 5, 30, 60min
|
| Growth protocol |
N. crassa cells were grown from freezer stocks on Vogel’s + sucrose + 2% agar slants for 1 d at 28 °C in the dark and 4 to 6 d at 28 °C in constant light.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The N. crassa sample was frozen with liquid nitrogen immediately. A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB, USA) following the manufacturer’s recommendations and index codes were added to attribute sequences to each sample.
Sequencing libraries were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
The qualified library was pooled based on pre-designed target data volume and then sequenced on Illumina sequencing platform.
Clean data with high quality was obtained by filtering Raw data, which removes adapter sequence and reads with low quality. These clean data were further mapped to pre-defined reference genome generating mapped data.
Assessment on insert size and sequencing randomness were processed on mapped data as library quality control. Basic analysis on mapped data included gene expression quantification, alternative splicing analysis, novel genes prediction and genes structure optimization.
Genome_build: GCF_000182925.2
Supplementary_files_format_and_content: all_gene_fpkm.txt (tab-delimited text file includes FPKM values for each sample)
Supplementary_files_format_and_content: all_gene_counts.txt (tab-delimited text file with raw gene counts for every gene and every sample)
|
| |
|
| Submission date |
Jan 26, 2022 |
| Last update date |
Feb 02, 2022 |
| Contact name |
Lina Qin |
| E-mail(s) |
[email protected]
|
| Organization name |
Fujian normal university
|
| Department |
College of Life Sciences
|
| Street address |
No.8 Xuefu South Road, Shangjie, Minhou
|
| City |
Fuzhou |
| ZIP/Postal code |
350003 |
| Country |
China |
| |
|
| Platform ID |
GPL23150 |
| Series (1) |
| GSE195441 |
Evaluating the mode of Antifungal action of Heat-Stable Antifungal Factor (HSAF) in Neurospora crassa |
|
| Relations |
| BioSample |
SAMN25276021 |
| SRA |
SRX13924310 |
