|
| Status |
Public on Apr 11, 2023 |
| Title |
SLR2 time-point 105 |
| Sample type |
SRA |
| |
|
| Source name |
slr1- knockout cells
|
| Organism |
Schizosaccharomyces pombe |
| Characteristics |
strain: yMAB001
|
| Treatment protocol |
5mM 4tU was added to cultures and a portion of cells were removed at various time points. Cells were washed and flash frozen until extraction
|
| Growth protocol |
S. pombe strains were streaked on YES plates and incubated at 32C. For biological replicates, single colonies were used to inoculate 10mL of liquid media
|
| Extracted molecule |
total RNA |
| Extraction protocol |
4tU containing RNA was purified by biotin-streptavidin pull down and purified RNA was prepared for seqeucnign using the Illumina TruSeq Stranded mRNA Sample Preparation Kit
RNA was extracted from cells with acid phenol
Illumina TruSeq Stranded mRNA Sample Preparation
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Reads were trimmed and clipped for Illumina adaptors using Trimmomatic v0.36
Reads were aligned to the S. pombe genome using STAR version 2.5.2a
HTSeq 0.6.1p2 was used to calculate coverage per gene
DRUID pipeline (Lugowski et al., Methods, 2018) was used to calculate half-lives and downstream analyses were completed using R
Downstream analyses were performed with R version 3.5.2, using in-house scripts.
Assembly: S. pombe genome acquired from https://www.pombase.org/data/
Supplementary files format and content: Tab separated values files contain read counts per gene for each sample
|
| |
|
| Submission date |
Apr 11, 2022 |
| Last update date |
Apr 12, 2023 |
| Contact name |
Olivia Rissland |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Colorado Denver
|
| Department |
BMG
|
| Lab |
Rissland Lab
|
| Street address |
12801 East 17th Ave
|
| City |
Aurora |
| State/province |
CO |
| ZIP/Postal code |
80045 |
| Country |
USA |
| |
|
| Platform ID |
GPL28961 |
| Series (1) |
| GSE200633 |
The LARP1 homolog Slr1p controls the stability and expression of proto-5’TOP mRNAs in fission yeast |
|
| Relations |
| BioSample |
SAMN27522786 |
| SRA |
SRX14818426 |
