|
| Status |
Public on Sep 05, 2023 |
| Title |
SN87_WT_37_Rep2_RPF |
| Sample type |
SRA |
| |
|
| Source name |
Yeast
|
| Organism |
Candida albicans |
| Characteristics |
strain: SN87 - wild type
growth temperature: 37 C
|
| Treatment protocol |
Cells were harvested by vacuum filtration using a 0.45 µm nitrocellulose filter and immediately flash frozen in liquid nitrogen.
|
| Growth protocol |
C. albicans cultures were grown to mid-exponential phase (optical density 600 [OD600], ~0.4) at 30°C, 37°C or 41°C, 200 revolutions per minute in yeast extract peptone dextrose (YPD).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The cells were lysed using a Freezer-Mill (SPEX SamplePrep) with the settings: 2 cycles of 2 min precooling, 2 min at 5 CPS and 1 min intermittent cooling. 10 A260 units of cleared lysates were digested with 250 U Ambion RNase I for 1 h at 22 °C and 1400 rpm agitation. The reaction was stopped by adding 15 μl SuperaseIn. Lysates were thawed in lysis buffer (20 mM Tris-HCl pH 7.4, 5 mM MgCl2, 100 mM NaCl, 1 % Triton, 2 mM DTT, 100 μg/ml CHX and clarified by two rounds of centrifugation (3 min; 4 °C; 3000 g and 5 min, 4 °C and 10000 g).
Ribosome-protected footprints were purified from monosome fractions by size selection and gel extraction. Following 3' dephosphorylation these fragments were subjected to adaptor ligation, RT, circularization and PCR amplification.
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Ribosome profiling reads were processed by clipping the adapter sequence and trimming the 4 randomized nucleotides of the linker using the FASTX-Toolkit version 0.0.13
Processed reads were uniquely mapped to non-dubious ORF (Allele A, C_albicans_SC5314_version_A22) extended by 18 nt into the UTRs
Assembly: C_albicans_SC5314_version_A22
Supplementary files format and content: tab-delimited text files include raw counts for each sample
|
| |
|
| Submission date |
Mar 25, 2022 |
| Last update date |
Sep 05, 2023 |
| Contact name |
Sebastian Andreas Leidel |
| E-mail(s) |
sebastian.leidel@unibe.ch
|
| Phone |
+41 31 631 42 96
|
| Organization name |
University of Bern
|
| Department |
Department of Chemistry and Biochemistry
|
| Lab |
Research group for RNA Biochemistry
|
| Street address |
Freiestrasse 3
|
| City |
Bern |
| State/province |
Bern |
| ZIP/Postal code |
3012 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL22403 |
| Series (1) |
| GSE199422 |
Ncs2* mediates in vivo virulence of pathogenic yeast through sulphur modification of cytoplasmic transfer RNA |
|
| Relations |
| BioSample |
SAMN26947747 |
| SRA |
SRX14614395 |
