|
| Status |
Public on Sep 05, 2022 |
| Title |
ZPR1-AID + DMSO 3h rep3 |
| Sample type |
SRA |
| |
|
| Source name |
W303
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: W303
genotype: ZPR1-AID
treatment: 3h DMSO
time: 3
|
| Treatment protocol |
ZPR1 was depleted by treating cells with 5-Ph-IAA for either 0.5h, 1.5h or 3 h.
|
| Growth protocol |
Cells were grown to mid-log phase and snap frozen before submission to GENEWIZ for processing.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA samples were extracted by the NGS facility at GENEWIZ according to standard protocols.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
zpr1_aid_DMSO_3h_3
|
| Data processing |
Raw reads from Illumina HiSeq were checked for read quality using FastQC (v. 0.11.5) and aligned to the reference genome S288c (v. R64-3-1) using the RNA-seq aligner STAR (v.2.7.0)
Genewise counts obtained from STAR were passed to the Bioconductor package DESeq2 (v. 1.34.0) to identify differentially expressed genes after ZPR1 depletion relative to the DMSO vehicle control (Benjamini-Hochberg FDR < 0.05).
Assembly: S288c (v. R64-3-1)
Supplementary files format and content: csv file with raw read counts per gene for all samples
|
| |
|
| Submission date |
Aug 31, 2022 |
| Last update date |
Sep 05, 2022 |
| Contact name |
Vladimir Denic |
| E-mail(s) |
[email protected]
|
| Organization name |
Harvard University
|
| Street address |
52 Oxford St
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02138 |
| Country |
USA |
| |
|
| Platform ID |
GPL13821 |
| Series (1) |
| GSE212387 |
Transcriptome profiling time course of ZPR1-depleted S.cerevisiae cells |
|
| Relations |
| BioSample |
SAMN30613362 |
| SRA |
SRX17380102 |
