|
| Status |
Public on Apr 30, 2024 |
| Title |
PT286-PLM rep2 |
| Sample type |
SRA |
| |
|
| Source name |
PT286
|
| Organism |
Schizosaccharomyces pombe |
| Characteristics |
treatment: treated with phleomycin (5 ug/mL) for 8h
strain: PT286
|
| Treatment protocol |
For the stress experiments, cells were cultured in YES medium and harvested at 16h. Then changed medium to induce stress and harvested at 8h after addition of different DNA damage-inducing agents to the culture. Different DNA damage conditions were induced as follows. Camptothecin (APExBIO) was added to a fifinal concentration of 20 μM. Hydroxyurea (Sigma) was added to a fifinal concentration of 10 mM. Methyl methanesulfonate (Sigma) was added to a fifinal concentration of 0.02%. Phleomycin (APExBIO) was added to a fifinal concentration of 5 μg/mL.
|
| Growth protocol |
Strain PT286 was grown at 30℃ to mid-log phase in YES medium.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from harvested cells using TRIzol reagent (Invitrogen, USA) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Libraries were sequenced using PE150 (Pair End 150bp) on an Illumina HiSeq 6000 instrument (Novogene, China). Low quality reads (one end low quanlity base > 50%), N-containing reads (unidentified reads ratio > 0.002) and reads with adapters are removed from the raw data to generate clean reads for further analysis.
Clean reads were mapped onto the fission yeast genome released on Pombase using HISAT2
The expressions of mRNA and lncRNA were evaluated with Stringtie followed by the annotation references
Genome_build: reference sequence based on Pombase(https://www.pombase.org/)
|
| |
|
| Submission date |
Apr 30, 2021 |
| Last update date |
Apr 30, 2024 |
| Contact name |
Bingbing Ren |
| E-mail(s) |
[email protected]
|
| Phone |
17355505065
|
| Organization name |
University of Science and Technology of China
|
| Street address |
University of Science and Technology of China, 443 Huangshan Road, Hefei, Anhui
|
| City |
Hefei |
| State/province |
Anhui |
| ZIP/Postal code |
230027 |
| Country |
China |
| |
|
| Platform ID |
GPL28961 |
| Series (1) |
| GSE173677 |
LncRNA and mRNA expression profiles of Schizosaccharomyces pombe under normal conditions and DNA damage inducing conditions. |
|
| Relations |
| BioSample |
SAMN18942841 |
| SRA |
SRX10724376 |
