|
| Status |
Public on Aug 22, 2022 |
| Title |
Med15_C (ChEC-seq) |
| Sample type |
SRA |
| |
|
| Source name |
whole organism
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
genotype: MAT{alpha} Dade2::hisG his3D200 leu2D0 lys2D0 met15D0 trp1D63 ura3D0 MED15-MNase::TRP1
strain: SHY1229
|
| 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.
|
| Growth protocol |
30 degrees in a synthetic complete (SC) medium to mid-log phase.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChEC-seq was performed as previously described (Donczew et al., 2021 [PMID: 34137374]). Detailed protocol is available in publication accompaning this submission.
Sequencing libraries were constructed as previously described (Donczew et al., 2021 [PMID: 34137374]). Detailed protocol is available in publication accompaning this submission.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Library strategy: ChEC-seq
Paired-end sequencing reads were aligned to S. cerevisiae reference genome (sacCer3) and D. melanogaster reference genome (release 6.06) with Bowtie2 (Langmead and Salzberg, 2012) using optional arguments “-I 10 -X 700 --local --very-sensitive-local --no-unal --no-mixed --no-discordant”.
For each base pair in the genome, we counted the number of paired-end fragments aligned over it.
Signal per base pair was normalized by the number of all D. melanogaster reads mapped for the sample and multiplied by 10000 (arbitrarily chosen number).
Genome_build: sacCer3 (S. cerevisiae), release 6.06 (D. melanogaster)
Supplementary_files_format_and_content: Processed data is provided in a wig format and contains spike-in normalized signal per base pair.
|
| |
|
| 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) |
| GSE190774 |
Mediator facilitates transcription initiation at most promoters via a Tail-independent mechanism [ChEC-seq] |
| GSE190778 |
Mediator facilitates transcription initiation at most promoters via a Tail-independent mechanism |
|
| Relations |
| BioSample |
SAMN23980131 |
| SRA |
SRX13397184 |
