|
| Status |
Public on Nov 26, 2019 |
| Title |
IDRm_30°C_pellet_Rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Yeast liquid culture
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: W303 Ade+
genotype: Ded1_IDRm-mCherry
incubation temperature: 30°C
fraction: insoluble fraction yeast RNA
|
| Treatment protocol |
The main cultures were split into three 200 ml cultures that were incubated for 10 minutes at 30°C, 40°C or 42°C. The cultures were subsequently harvested by filtration and immediately flash frozen in liquid nitrogen and then stored at -80°C
|
| Growth protocol |
Cells from each strain were inoculated in duplicates in 50 ml pre-cultures, which were grown at 30°C overnight and subsequently diluted to an OD600 of 0.05 in a 1 L main culture. The main culture was grown at 30°C to an OD600 of 0.5.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using the hot acid-phenol method (according to Becker et al. 2013)
Ribosomal RNA was depleted using illumina ribominus, RNA libraries were prepared for sequencing using standard protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
| |
|
| Description |
IDR_30C_1_pellet_262
|
| Data processing |
Basecalling was performed with bcl2fastq 2.19.1
Mapping of remaining reads was performed with STAR 2.5.2b (--quantMode GeneCounts --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outFilterType BySJout --outFilterMultimapNmax 1 --outSJfilterCountUniqueMin 8 3 3 3)
Genome_build: R64-2-1_20150113
Supplementary_files_format_and_content: Raw counts
|
| |
|
| Submission date |
Nov 26, 2019 |
| Last update date |
May 16, 2022 |
| Contact name |
Scientific Computing Facility |
| Organization name |
MPI-CBG
|
| Street address |
Pfotenhauerstrasse 108
|
| City |
Dresden |
| ZIP/Postal code |
01307 |
| Country |
Germany |
| |
|
| Platform ID |
GPL26302 |
| Series (1) |
| GSE141029 |
RNAseq of total, soluble and insoluble fraction of WT and mutant yeast cells after 10 minutes at 30, 40 or 42°C |
|
| Relations |
| BioSample |
SAMN13389418 |
| SRA |
SRX7217551 |
