|
| Status |
Public on Sep 30, 2022 |
| Title |
AEP1 (WT) + preQ1-L1, IP, rep3 (Expt1) |
| Sample type |
SRA |
| |
|
| Source name |
AEP1 (WT)
|
| Organism |
Schizosaccharomyces pombe |
| Characteristics |
strain: AEP1 (WT)
genotype: FY7385; h- leu1-32 ura4-D18 his3-D3
growth condition: growth in full medium (YES) at 30C
treatment: metabolic labeling with preQ1-L1 dervitave
experimental design: IP via strep-coated magnetic beads
|
| Growth protocol |
Strains AEP1 and AEP288 were grown in full medium (YES) with 0.1 µM preQ1-L1. Cultures were inoculated at an OD600 of 0.2 and grown to an optical density of 1.0
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from 50 OD of cells. Cells were harvested and after addition of 1 mL of phenol, glass beads and vigorous shaking for 5 min, samples were centrifuged at 20.000 g for 5 min to clear the cell debris. Equal volume of phenol/chloroform/isoamylalcohol was added to the aqueous phase and centrifuged at 20.000 g for 5 min. After mixing the upper phase with an equal volume of chloroform followed by centrifugation at 20.000 g for 5 min, the RNA was precipitated.
Library preparation of immunoprecipitated RNAs for deep sequencing was performed using the NEBNext Small RNA Library Prep Set for Illumina (Multiplex Compatible; New England Biolabs) according to the manufacturer's protocols.
|
| |
|
| Library strategy |
RIP-Seq |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina MiSeq |
| |
|
| Description |
Q-RIP-Seq_exp1.csv
|
| Data processing |
Adapter-trimming was performed using Skewer version 0.2.2 and alignment to S. pombe RNAs (mRNA, ncRNA and tRNA; main and mitochondrial) from Pombase (https://www.pombase.org/) was achieved using Salmon version 14.0 and HISAT2 version 2.1.1, as a splice-site sensitive alignment program.
Conversion of sam to bam files was performed using SAMtools. Peak calling of aligned sequences was performed using the Bioconductor package exomePeak2 (adjusted P-value < 0.1).
Assembly: S.pombe genome version ASM294v2.29
Supplementary files format and content: comma-separated values files include read counts, log2-fold change, pvalues and the padj for IP (WT) and input (qtr2∆)
|
| |
|
| Submission date |
Aug 03, 2022 |
| Last update date |
Sep 30, 2022 |
| Contact name |
Ann E. Ehrenhofer-Murray |
| Organization name |
Humboldt-Universität zu Berlin
|
| Department |
Institut für Biologie
|
| Street address |
Philippstr. 13
|
| City |
Berlin |
| ZIP/Postal code |
10099 |
| Country |
Germany |
| |
|
| Platform ID |
GPL16192 |
| Series (1) |
| GSE210404 |
Identification of queuosine-modified RNAs in S. pombe using metabolic labelling with preQ1-L1 (Q-RIP-Seq) |
|
| Relations |
| BioSample |
SAMN30121673 |
| SRA |
SRX16812542 |
