|
| Status |
Public on Jan 28, 2023 |
| Title |
Xrn1-WT, no stress, replicate 3 |
| Sample type |
SRA |
| |
|
| Source name |
whole cell
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
genotype: BY25598; MATa ura3-1::ADH1-OsTIR1-9Myc(URA3) ade2-1 his3-11,15 leu2-3,112 trp1-1 can1-100 XRN1-AID (HIS)
pretreatment: none
treatment: none
|
| Treatment protocol |
Samples were treated with auxin (Xrn1-AID) or not (Xrn1-WT) before being osmostressed with NaCl (10 min NaCl; 30 min NaCl) or not (no stress).
|
| Growth protocol |
Xrn1-AID cells were grown to log-phase on YPD medium at 30ºC (no stress) and then subjected to auxin (500 µM) for 30 minutes (Xrn1-AID) or not subjected to auxin (Xrn1-WT). Stressed samples were incubated with 0.4 M NaCl diluted in YAPD media for 10 and 30 min for both Xrn1-AID and Xrn1-WT cells.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The samples were treated with Proteinase K (New England Biolabs) to get rid of the proteins, and then total RNA was extracted by a phenol-chloropropane method. After, remaining DNA was digested by Turbo DNase (Ambion) and RNA was extracted again with acid phenol-chloroform method. RNA concentration was measured by Nanodrop.
Libraries were prepared using the protocol described in TrueSeq Stranded mRNA Sample kit (Illumina). The libraries were sequenced by HiSeq 2500 System (Illumina) in reads of 50 base-pair length (1x50).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
3_0_WT
|
| Data processing |
RNA-sequencing reads were mapped to the sacCer3 genome build using TopHat2 (v2.1.0, settings: “--max-multihits 1 --library-type fr-firststrand --b2-very-sensitive --no-coverage-search”) and quantified using featureCounts (v1.5.1, “-Q 1 -s 2”)
Differential expression testing was performed using DESeq2 v1.22.2.
Genome_build: sacCer3
Supplementary_files_format_and_content: The file raw_counts_mRNA.tsv contains raw mRNA read counts from featureCounts. Each column represents one sample in lexicographical order.
|
| |
|
| Submission date |
Jan 29, 2020 |
| Last update date |
Jan 28, 2023 |
| Contact name |
Juana Díez |
| E-mail(s) |
juana.diez@upf.edu
|
| Phone |
+34 933160862
|
| Organization name |
Universitat Pompeu Fabra
|
| Department |
Department of Experimental and Health Sciences
|
| Lab |
Molecular Virology Group
|
| Street address |
Carrer del Dr. Aiguader 88
|
| City |
Barcelona |
| State/province |
Barcelona |
| ZIP/Postal code |
08003 |
| Country |
Spain |
| |
|
| Platform ID |
GPL17342 |
| Series (1) |
| GSE144440 |
Xrn1 modulates the dynamic osmostress response at a transcriptional and translational level |
|
| Relations |
| BioSample |
SAMN13939981 |
| SRA |
SRX7646087 |
