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| Status |
Public on Mar 14, 2024 |
| Title |
RDY73 cells, DMSO, repB |
| Sample type |
SRA |
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| Source name |
Saccharomyces cerevisiae
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| Organism |
Saccharomyces cerevisiae |
| Characteristics |
cell type: Saccharomyces cerevisiae
strain: RDY73
genotype: pGPD1-OsTIR1::HIS3 BDF2-3XV5-mAID-kanMX BDF1-3XV5-mAID-URA3
treatment: minus IAA, plus 4tU
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| Treatment protocol |
Saccharomyces cerevisiae cells were grown to an OD600 of ~0.45. Cultures were treated with 1 mM IAA freshly prepared in DMSO or DMSO alone, vigorously mixed, and incubated for 25 min. Immediately after IAA treatment, cultures were treated with 5 mM 4tU freshly prepared in DMSO or DMSO alone, vigorously mixed, and incubated for 4 min. Immediately after 4tU treatment, each culture was decanted into cold 100% methanol on dry ice. The resulting slurry was centrifuged at 3,000 g and 4°C to pellet the cells. Cells were resuspended in DNA/RNA shield (Zymo Research), flash frozen on dry ice, and stored at -80°C. The final OD600 of the cultures was ~0.7. All experiments were performed in biological triplicate.
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| Growth protocol |
Saccharomyces cerevisiae cells were grown in YPD medium (10 g/l yeast extract, 20 g/l peptone, 20 g/l glucose, 20 mg/ml adenine sulfate) at 30°C with shaking at 220 rpm.
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA purification and DNase I treatment were performed using a Quick-RNA Fungal/Bacterial Miniprep kit and DNase I set (Zymo Research) following the manufacturer s recommendations with minor modifications. Reagents (RNA lysis buffer, RNA wash buffer, RNA prep buffer, 100% ethanol, and nuclease-free water) were supplemented with DTT to maintain reducing conditions. Samples were protected from light when possible.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Demultiplexed, paired-end 150 bp reads were preprocessed using fastp (version 0.23.2) to extract UMIs and bbduk from the BBMap package (version 36.99) to trim adapter sequences and polyA tails. Forward reads were processed using SLAM-DUNK (version 0.4.3), i.e., reads were aligned against the S. cerevisiae genome (version R64-3-1) or the spike-in Schizosaccharomyces pombe genome (version ASM294v2) using NextGenMap (version 0.5.5) and SNPs were called using VarScan 2 (version 2.4.5). Total read counts were defined as all reads remaining after filtering in SLAM-DUNK. A conversion per read threshold of ≥ 1 or ≥ 2 T>C conversions was used to define T>C read counts based on subsequent analysis.
Assembly: S. cerevisiae strain S288C version R64-3-1 (RefSeq Assembly GCF_000146045.2); S. pombe strain 972h- version ASM294v2 (RefSeq Assembly GCF_000002945.1)
Supplementary files format and content: Raw read count tables are provided in tab-separated values format (.tsv). *_scer_onetcreadcount_tcount.tsv provides total read counts and T>C read counts with ≥ 1 T>C conversions for S. cerevisiae and *_scer_twotcreadcount_tcount.tsv provides total read counts and T>C read counts with ≥ 2 T>C conversions for S. cerevisiae. *_spom_onetcreadcount_tcount.tsv provides total read counts and T>C read counts with ≥ 1 T>C conversions for S. pombe and *_spom_twotcreadcount_tcount.tsv provides total read counts and T>C read counts with ≥ 2 T>C conversions for S. pombe.
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| Submission date |
Mar 07, 2024 |
| Last update date |
Mar 18, 2024 |
| Contact name |
John B Ridenour |
| E-mail(s) |
john-ridenour@omrf.org
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| Organization name |
Oklahoma Medical Research Foundation
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| Department |
Cell Cycle and Cancer Biology Research Program
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| Lab |
Donczew lab
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| Street address |
825 NE 13th St.
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| City |
Oklahoma City |
| State/province |
OK |
| ZIP/Postal code |
73104 |
| Country |
USA |
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| Platform ID |
GPL27812 |
| Series (1) |
| GSE261145 |
An end-to-end workflow to study newly synthesized mRNA following rapid protein depletion in Saccharomyces cerevisiae |
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| Relations |
| BioSample |
SAMN40301990 |
| SRA |
SRX23875873 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8136384_RDY73_DMSO_B_scer_onetcreadcount_tcount.tsv.gz |
242.0 Kb |
(ftp)(http) |
TSV |
| GSM8136384_RDY73_DMSO_B_scer_twotcreadcount_tcount.tsv.gz |
238.2 Kb |
(ftp)(http) |
TSV |
| GSM8136384_RDY73_DMSO_B_spom_onetcreadcount_tcount.tsv.gz |
215.6 Kb |
(ftp)(http) |
TSV |
| GSM8136384_RDY73_DMSO_B_spom_twotcreadcount_tcount.tsv.gz |
195.9 Kb |
(ftp)(http) |
TSV |
SRA Run Selector |
| Raw data are available in SRA |
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