|
| Status |
Public on Jun 30, 2020 |
| Title |
ssu72Δ rep1 [WTCHG_337412_286171] |
| Sample type |
SRA |
| |
|
| Source name |
ssu72Δ
|
| Organism |
Schizosaccharomyces pombe |
| Characteristics |
strain background: ssu72 deletion
|
| Growth protocol |
S. pombe strains were grown in YES media(0.5% yeast extract, 3% glucose, 0.0225% supplements (Histidine, Adenine, Uracil, Leucin, Lysine) to exponential phase at 30°C. Meantime S. cerevisiae cells were grown YPD(1% yeast extract, 2% peptone, and 2% glucose). S. cerevisiae cells correspond to 10% of S. pombe cells were added to S. pombe cells.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs were extracted by a standard hot phenol method.
NEBNext ultra II directional RNA library prep kit for Illumina
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
WTCHG_337412_286171
|
| Data processing |
The libraries were sequenced by Illumina NextSeq 500.
Adaptor and low quality sequence were removed by Trimmomatic v0.39
Reads were aligned to the concatenated genome (S. pombe + S. cerevisiae) by Bowtie2 v2.3.5.1
Uniquely mapped reads were separated based on species by Samtools v1.9
Uniquely mapped to S. pombe reads were separated based on the strand by Samtools v1.9
The alignment files were converted to bedgraph format by Bedtools v2.26.0
Genome_build: ASM294v2.25 from pombase.org
Supplementary_files_format_and_content: bedgraph
|
| |
|
| Submission date |
Jan 31, 2020 |
| Last update date |
Jan 16, 2021 |
| Contact name |
Dong-hyuk Heo |
| E-mail(s) |
heo.donghyuk@gmail.com
|
| Organization name |
University of Oxford
|
| Department |
Department of Biochemistry
|
| Street address |
South Parks Road
|
| City |
Oxford |
| ZIP/Postal code |
OX1 3QU |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL20584 |
| Series (2) |
| GSE144591 |
RNA-seq analysis in ssu72 mutant cells [WT_ssu72] |
| GSE144603 |
Ssu72 is essential to suppress initiation of cryptic transcription in the 3' end of the RNA polymerase II transcribed regions. |
|
| Relations |
| BioSample |
SAMN13955570 |
| SRA |
SRX7655351 |
