|
| Status |
Public on May 01, 2024 |
| Title |
WT_RiboSeq_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Yeast strain yJD1046
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
condition: plasmid born WT rRNA sequence
molecule subtype: Ribosome protected fragments isolated via densitiy gradients
|
| Growth protocol |
Yeast cells were grown in YPD media to OD = 0.8. Cells were harvested bySnap freezing, ground in a cryomill and lysates were cleared by centrifugation.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Lysates were digested with RNAse1 and 80S ribosomes extracted from a density gradient after Ultracentrifugation. Size excluded RNA fragments were ligated to DeepSeq adapters.
mRNA fragments ranging rom 24-28nt were size excluded and dephosphorylated. Adapters were ligated and the resulting fragments were circularized. cDNA was prepared with circRNA as input and PCR amplicification was performed for 4-8 cycles.
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
NextSeq 550 |
| |
|
| Data processing |
Reads were trimmed using the FastX-toolkit. 6 randomized Linkernucleotides at the 3'End and three at the 5'end were trimmed.
Quality of reads was assessed using FastQC (v0.11.7)
Processed reads were mapped against noncoding RNAs and afterward against annotated open reading frames elongated at both ends by 21nt using bowtie (v1.2.3) with settings "-v 1 -m 1 --norc --best --strata
Supplementary files format and content: counts
Library strategy: Ribo-seq
|
| |
|
| Submission date |
Dec 09, 2022 |
| Last update date |
May 01, 2024 |
| Contact name |
Robert Rauscher |
| E-mail(s) |
ag.polacek@gmail.com
|
| Organization name |
University of Bern
|
| Street address |
Freiestrasse 3
|
| City |
Bern |
| State/province |
Bern |
| ZIP/Postal code |
3012 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL26302 |
| Series (1) |
| GSE220642 |
RiboSeq and mSeq of two yeast strains |
|
| Relations |
| BioSample |
SAMN32132229 |
| SRA |
SRX18629697 |
