|
| Status |
Public on Jun 16, 2020 |
| Title |
Chemostat A18 rep1 [chemo.A18.F11.d236014] |
| Sample type |
SRA |
| |
|
| Source name |
Chemostat A18
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain background: S288C
strain: A18
growth phase/cell type: Chemostat Cultured Cells
extract_protocol: KAPA
|
| Growth protocol |
Selected complex aneuploid strains were grown on YEPD + 2% glucose plate for 2 days at 25ºC. Strains were inoculated in phosphate-limited media (http://dunham.gs.washington.edu/chemostatv2.htm) and grown overnight. Once chemostat was set up and filled, phosphate-limited media in the chemostat was inoculated with 2 mL of overnight culture, and cells were allowed to grow for 30-36 hours although some strains required 48+ hours of growth. The dilution pumps were then turned on, and the dilution rate was 0.17 +/- 0.01 chemostat volumes per hour. The chemostat was sampled daily to measure effluent volume, hemocytometer counts, and OD(600nm) measurements. When the chemostat had reached a steady-state, defined by less than 5% change from the previous day’s measurements, samples were harvested
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
3-5 mL samples of culture were taken, spun down at 3000rpm for 5 minutes, washed with 1 mL DEPC water, and transferred to a 2 mL RNase-free screw-cap tube. Samples were spun again at 8000rpm for 3 minutes, and supernatant was aspirated. Cells were snap frozen with liquid nitrogen and stored at -80C. RNA samples were prepared with RNeasy mini kit from Qiagen and treated with DNase on-column treatment (RNase-free) from Qiagen.
Illumina Truseq or KAPA
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
processed data file: terhorst_l2tpm.txt.gz
chemo.A18.F11.d236014
|
| Data processing |
HiSeq2000 using v3 chemistry. Software: Control v2.2.58, RTA 1.18.64. BCL files were converted to fastq using bcl2qseq. Indexes were split using custom scripts allowing 1 mismatch.
Reads were aligned to a S. cerevisiae transcriptome with STAR version 2.5.3a and gene expression was quantified with RSEM version 1.3.0. Transcript per million (TPM) values were offset by +1 and transformed to log 2 space.
Genome_build: SacCer3 plus spike-ins with an ensembl annotation
Supplementary_files_format_and_content: text format file of log2 TPM with a +1 offset of protein coding genes
|
| |
|
| Submission date |
Mar 11, 2020 |
| Last update date |
Jun 16, 2020 |
| Contact name |
Charles Arthur Whittaker |
| E-mail(s) |
charliew@mit.edu
|
| Organization name |
Koch Institute
|
| Street address |
77 Mass Ave 76-189
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02152 |
| Country |
USA |
| |
|
| Platform ID |
GPL13821 |
| Series (1) |
| GSE146791 |
The environmental stress response causes ribosome loss in aneuploid yeast cells. |
|
| Relations |
| BioSample |
SAMN14354892 |
| SRA |
SRX7894926 |
