|
| Status |
Public on Aug 22, 2022 |
| Title |
Med7C_DMSO_B (RNA-seq) |
| Sample type |
SRA |
| |
|
| Source name |
whole organism
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
genotype: MAT{alpha} Dade2::hisG his3D200 leu2D0 lys2D0 met15D0 trp1D63 ura3D0 pGPD1-OSTIR::HIS3 med7D::KanMX pSH1989 (ars cen LEU2 med7DC) pSH1990 (ars cen TRP1 med7DN-mini degron)
strain: SHY1428
treatment: DMSO
|
| Treatment protocol |
After reaching appropriate OD selected samples were treated with either DMSO or or 3-indolacetic acid (IAA), which was used to induce degradation of selected proteins. Newly synthesized RNA molecules were labeled for 5 minute with 4-thioU.
|
| Growth protocol |
30 degrees in a synthetic complete (SC) medium to mid-log phase.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Experiments were done as previously described (Donczew et al., 2021 [PMID: 34137374]). Detailed protocol is available in publication accompaning this submission.
Ovation Universal RNA-seq System kit (Tecan) was used for library construction.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Paired-end sequencing reads were aligned to S. cerevisiae reference genome (sacCer3) and S. pombe reference genome (ASM294v2.20) with Bowtie2 using optional arguments “-I 10 -X 700 --local --very-sensitive-local --no-unal --no-mixed --no-discordant”.
SAM files for S. cerevisiae data were used as an input for HTseq-count with default settings. The GFF file with S. cerevisiae genomic features was downloaded from the Ensembl website.
Signal per gene was normalized by the number of all S. pombe reads mapped for the sample and multiplied by 10000 (arbitrarily chosen number).
Genome_build: acCer3 (S. cerevisiae), ASM294v2.20 (S. pombe)
Supplementary_files_format_and_content: Processed CSV files contain normalized signal for all analyzed features (5797 mRNA coding genes).
|
| |
|
| Submission date |
Dec 13, 2021 |
| Last update date |
Aug 24, 2022 |
| Contact name |
Rafal Donczew |
| E-mail(s) |
Rafal-donczew@omrf.org
|
| Organization name |
Oklahoma Medical Research Foundation
|
| Department |
Cell Cycle and Cancer Biology
|
| Lab |
Hahn Lab
|
| Street address |
825 NE 13th St
|
| City |
Oklahoma City |
| State/province |
OK |
| ZIP/Postal code |
73104 |
| Country |
USA |
| |
|
| Platform ID |
GPL17342 |
| Series (2) |
| GSE190777 |
Mediator facilitates transcription initiation at most promoters via a Tail-independent mechanism [RNA-seq] |
| GSE190778 |
Mediator facilitates transcription initiation at most promoters via a Tail-independent mechanism |
|
| Relations |
| BioSample |
SAMN23997052 |
| SRA |
SRX13397104 |
