|
| Status |
Public on Jun 30, 2020 |
| Title |
CT22 |
| Sample type |
SRA |
| |
|
| Source name |
Saccharomyces cerevisiae
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
biological replicate: 2
translation state: allowed
translation additive: 2% glucose
media ph: 4
temperature: unshocked
|
| Growth protocol |
Cells were grown in liquid culture at 30 C with shaking until in mid-log (OD 0.3)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were harvested by brief spin (3000 g for 1 min) and then flash-freezing. Total RNA was extracted using the Direct-zol kit from Zymo, with additional DNA removal by treatment with Turbo Dnase
Illumina TruSeq with no poly-A selection
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
BR2_unstressed
|
| Data processing |
each sample was quantified with kallisto (version 0.43.0) using paired-end mode, 100 rounds of bootstrapping
output abundances were merged and tidied using R into final file 20-04-15_processed-bootstrapped-revisionseq-data.tsv
Genome_build: S288C transcriptome: kallisto index built from this transcriptome is file scer-r64-merged-transcripts.index. FASTA is included.
Supplementary_files_format_and_content: tab-separated value format; each row is a gene, each column is an experiment, both raw counts and transcripts per million are included for each sample
|
| |
|
| Submission date |
Jun 21, 2020 |
| Last update date |
Jun 30, 2020 |
| Contact name |
Catherine Genevieve Triandafillou |
| E-mail(s) |
ctriandafillou@uchicago.edu
|
| Organization name |
University of Chicago
|
| Street address |
929 E 57th St
|
| City |
Chicago |
| State/province |
IL |
| ZIP/Postal code |
60637 |
| Country |
USA |
| |
|
| Platform ID |
GPL27812 |
| Series (1) |
| GSE152916 |
Measuring the dependence of the yeast heat shock response on intracellular pH and translation during stress |
|
| Relations |
| BioSample |
SAMN15337264 |
| SRA |
SRX8590483 |
