|
| Status |
Public on Oct 30, 2023 |
| Title |
YDJ5924 SD-CSM+rad rep 3 |
| Sample type |
SRA |
| |
|
| Source name |
yeast cell
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
cell type: yeast cell
ploidy: F0 heterozygous diploid
treatment: SD-CSM + 10µM radicicol
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was extracted from snap-frozen yeast cells and subjected to polyA selection.
Libraries were constructed using the DNBSEQ Eukaryotic Strand-specific mRNA library protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
DNBSEQ-G400 |
| |
|
| Description |
x5924_SD_3A_refCounts_1
radAseData.csv
|
| Data processing |
Raw reads were trimmed of adaptors and filtered for quality by BGI.
Transcriptomic reads were pseudo-aligned to the genome using Kallisto.
Kallisto was used to generate transcripts per million (TPM) estimates.
Allele-specific expression was estimated using custom code in MATLAB based on Kallisto pseudo-alignments.
Assembly: Saccharomyces cerevisiae R64.1
Supplementary files format and content: radAseData.csv contains allele-specific expression data for the F0 heterozygous diploid YJM5924 with and with radicicol treatment.
Supplementary files format and content: tpmSummary.csv contains TPM estimates for the homozygous parental diploids with and with radicicol treatment.
|
| |
|
| Submission date |
Sep 11, 2023 |
| Last update date |
Oct 30, 2023 |
| Contact name |
Christopher M Jakobson |
| E-mail(s) |
cjakobso@stanford.edu
|
| Organization name |
Stanford University School of Medicine
|
| Department |
Chemical and Systems Biology
|
| Lab |
Jarosz Lab
|
| Street address |
318 Campus Dr, Clark Center W350
|
| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
| |
|
| Platform ID |
GPL30266 |
| Series (1) |
| GSE242925 |
Hsp90 shapes adaptation by controlling the fitness consequences of regulatory variation |
|
| Relations |
| BioSample |
SAMN37354954 |
| SRA |
SRX21752070 |
