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| Status |
Public on Jan 28, 2023 |
| Title |
Xrn1 modulates the dynamic osmostress response at a transcriptional and translational level |
| Organism |
Saccharomyces cerevisiae |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
To study the role of the exonuclease Xrn1 in gene expression dynamics under osmotic stress conditions, we performed RNA-seq in Xrn1-depleted cells. By using an auxin-inducible degron, we were able to study immediate effects of Xrn1 depletion in gene expression dynamics. Therefore, we could overcome experimental limitations associated to stable deletion mutants.
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| Overall design |
RNA was obtained as described in (Ingolia, 2009), from BY25598 cells (Nishimura and Kanemaki, 2014) modified to express an Xrn1 protein tagged with an auxin inducible degron (AID). Libraries were obtained by the TrueSeq Stranded mRNA Sample kit (Illumina) from cells treated with auxin for 30 minutes (t30) and compared from libraries from untreated controls (t0). After 30 minutes of treatment, Xrn1 protein was reduced to less than 10%. Stressed samples were treated with 0.4 M NaCl for 10 and 30 min in cells treated with auxin (Xrn1-AID) or untreated with auxin (Xrn1-WT). Strains were grown to logaritmic phase and collected at approximately 0,5 OD.
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| Contributor(s) |
de Campos-Mata L, Jungfleisch J, Díez J, Böttcher R |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| Submission date |
Jan 29, 2020 |
| Last update date |
Jan 28, 2023 |
| Contact name |
Juana Díez |
| E-mail(s) |
juana.diez@upf.edu
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| Phone |
+34 933160862
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| Organization name |
Universitat Pompeu Fabra
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| Department |
Department of Experimental and Health Sciences
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| Lab |
Molecular Virology Group
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| Street address |
Carrer del Dr. Aiguader 88
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| City |
Barcelona |
| State/province |
Barcelona |
| ZIP/Postal code |
08003 |
| Country |
Spain |
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| Platforms (1) |
| GPL17342 |
Illumina HiSeq 2500 (Saccharomyces cerevisiae) |
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| Samples (17)
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| GSM4288304 |
Xrn1-AID 10 min NaCl, replicate 1 |
| GSM4288305 |
Xrn1-AID 10 min NaCl, replicate 2 |
| GSM4288306 |
Xrn1-AID 10 min NaCl, replicate 3 |
| GSM4288307 |
Xrn1-AID 30 min NaCl, replicate 1 |
| GSM4288308 |
Xrn1-AID 30 min NaCl, replicate 2 |
| GSM4288309 |
Xrn1-WT, no stress, replicate 1 |
| GSM4288310 |
Xrn1-WT, no stress, replicate 2 |
| GSM4288311 |
Xrn1-WT, no stress, replicate 3 |
| GSM4288312 |
Xrn1-WT 10 min NaCl, replicate 1 |
| GSM4288313 |
Xrn1-WT 10 min NaCl, replicate 2 |
| GSM4288314 |
Xrn1-WT 10 min NaCl, replicate 3 |
| GSM4288315 |
Xrn1-WT 30 min NaCl, replicate 1 |
| GSM4288316 |
Xrn1-WT 30 min NaCl, replicate 2 |
| GSM4288317 |
Xrn1-WT 30 min NaCl, replicate 3 |
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| Relations |
| BioProject |
PRJNA603665 |
| SRA |
SRP245818 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE144440_raw_counts_mRNA.tsv.gz |
227.5 Kb |
(ftp)(http) |
TSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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