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| Status |
Public on Sep 30, 2023 |
| Title |
3′-seq of Saccharomyces cerevisiae grown in eight different conditions |
| Organism |
Saccharomyces cerevisiae |
| Experiment type |
Other
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| Summary |
Saccharomyces cerevisiae strain BY4741 (MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0) was grown in YPD medium. For control conditions, cells were grown in mid-log phase at 30°C for 20 min or 2 hours. Stress conditions were heat shock (37°C for 20 min), diauxic shift (harvested at 2 hours after glucose depletion), DNA damage (harvested after 2 hours of treatment with 5 µg/ml 4-nitroquinoline 1-oxide (Sigma)). Moreover, four conditions of the yeast metabolic cycle were analyzed. S. cerevisiae strain CEN.PK (MATa URA3 TRP1 LEU2 HIS3 MAL2-8C SUC2) was used and cultivated as described elsewhere (Nocetti and Whitehouse, Genes Dev, 2016). The period of metabolic oscillation was approximately 3.2 h. Cells were harvested at 16, 32, 48, and 60 min from the start of each cycle for one oxidative, two reductive/building, and one reductive/charging phase points. Total RNA from each sample was extracted by the hot phenol method and used for library preparation. 3′-seq libraries were prepared as described previously (Lianoglou et al., Genes Dev, 2013). Each condition was sequenced in three biological replicates. The 27 individual libraries were pooled and subjected to sequencing with HiSeq with SR50 at the Integrated Genomics Operation (MSKCC).
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| Overall design |
Mapping cleavage and polyadenylation sites in Saccharomyces cerevisiae by analyzing pooled 3'-seq data from various conditions.
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| Contributor(s) |
Zhen G, Kwon B, Mayr C |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
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| Submission date |
Sep 19, 2022 |
| Last update date |
Sep 30, 2023 |
| Contact name |
Christine Mayr |
| E-mail(s) |
mayrc@mskcc.org
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| Organization name |
MSKCC
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| Department |
Cancer Biology and Genetics
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| Lab |
Christine Mayr
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| Street address |
417 E 68th Street
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| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10065 |
| Country |
USA |
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| Platforms (1) |
| GPL17342 |
Illumina HiSeq 2500 (Saccharomyces cerevisiae) |
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| Samples (27)
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| GSM6592520 |
Control2, biol rep1 |
| GSM6592521 |
Control2, biol rep2 |
| GSM6592522 |
Control2, biol rep3 |
| GSM6592523 |
Diauxic shift, biol rep 1 |
| GSM6592524 |
Diauxic shift, biol rep 2 |
| GSM6592525 |
Diauxic shift, biol rep 3 |
| GSM6592526 |
DNA damage, biol rep 1 |
| GSM6592527 |
DNA damage, biol rep 2 |
| GSM6592528 |
DNA damage, biol rep 3 |
| GSM6592529 |
Heat shock, biol rep 1 |
| GSM6592530 |
Heat shock, biol rep 2 |
| GSM6592531 |
Heat shock, biol rep 3 |
| GSM6592532 |
Metabolic cycle 1, biol rep 1 |
| GSM6592533 |
Metabolic cycle 1, biol rep 2 |
| GSM6592534 |
Metabolic cycle 1, biol rep 3 |
| GSM6592535 |
Metabolic cycle 2, biol rep 1 |
| GSM6592536 |
Metabolic cycle 2, biol rep 2 |
| GSM6592537 |
Metabolic cycle 2, biol rep 3 |
| GSM6592538 |
Metabolic cycle 3, biol rep 1 |
| GSM6592539 |
Metabolic cycle 3, biol rep 2 |
| GSM6592540 |
Metabolic cycle 3, biol rep 3 |
| GSM6592541 |
Metabolic cycle 4, biol rep 1 |
| GSM6592542 |
Metabolic cycle 4, biol rep 2 |
| GSM6592543 |
Metabolic cycle 4, biol rep 3 |
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| Relations |
| BioProject |
PRJNA882103 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE213720_c1.F.bedgraph.gz |
2.7 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE213720_c1.R.bedgraph.gz |
2.7 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE213720_c2.F.bedgraph.gz |
2.5 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE213720_c2.R.bedgraph.gz |
2.5 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE213720_diauxic.F.bedgraph.gz |
2.9 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE213720_diauxic.R.bedgraph.gz |
2.9 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE213720_dna_damage.F.bedgraph.gz |
2.9 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE213720_dna_damage.R.bedgraph.gz |
3.0 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE213720_hs.F.bedgraph.gz |
2.9 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE213720_hs.R.bedgraph.gz |
3.0 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE213720_ymc1.F.bedgraph.gz |
2.2 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE213720_ymc1.R.bedgraph.gz |
2.3 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE213720_ymc2.F.bedgraph.gz |
1.9 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE213720_ymc2.R.bedgraph.gz |
1.9 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE213720_ymc3.F.bedgraph.gz |
2.1 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE213720_ymc3.R.bedgraph.gz |
2.1 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE213720_ymc4.F.bedgraph.gz |
1.7 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE213720_ymc4.R.bedgraph.gz |
1.7 Mb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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