|
| Status |
Public on Dec 08, 2021 |
| Title |
rancRNA_18_polysome-associated mRNA_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
yeast strain trm10∆
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: trm10<delta>
electroporation: rancRNA_18
mrna fraction: polysome-associated
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Yeast spheroplasts were electroporated with or without RNA, recovered and harvested by centrifugation. Pellets were opened using a FastPrep. Lysates were cleared by centrifugation and loaded on a density gradient for Ultracentrifugation. Fractions containing polysomes were pooled and RNA was extracted via hot acid phenol extraction.
Poly-A-Enrichment via oligo-dT-beads.
PolyA enriched mRNAs were transformed into a cDNA library using the Illumina TruSeq stranded mRNA Kit. Library size was determined using Qbit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Description |
mSeq of poly-A enriched RNA
mRNA
|
| Data processing |
Quality control using fastqc tool.
Mapping performed using HISAT2; more than 95% mapping rate, -p 8.
Counting was performed using featureCounts.
Genome_build: Strain BY4742 (PRJNA260311, Oct-12-2014)
Supplementary_files_format_and_content: *.txt: Tab-delimited text file; counts table.
|
| |
|
| Submission date |
Aug 06, 2019 |
| Last update date |
Dec 08, 2021 |
| Contact name |
Norbert Polacek |
| E-mail(s) |
ag.polacek@gmail.com, norbert.polacek@dcb.unibe.ch
|
| Organization name |
University of Bern
|
| Department |
Chemistry and Biochemistry
|
| Street address |
Freiestrasse 3
|
| City |
Bern |
| ZIP/Postal code |
3012 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL23014 |
| Series (1) |
| GSE135475 |
mRNA seq of total and polysome associated mRNAs in three different conditions |
|
| Relations |
| BioSample |
SAMN12511316 |
| SRA |
SRX6662822 |
