|
| Status |
Public on Dec 13, 2018 |
| Title |
YJM-SD-3 |
| Sample type |
SRA |
| |
|
| Source name |
YJM975_S-CSM with 2% glucose
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: YJM975
growth medium: S-CSM with 2% glucose
cell type: whole yeast cells
|
| Treatment protocol |
Cells were snap-frozen and stored at -80°C.
|
| Growth protocol |
Samples of exponentially growing (OD600 ~ 0.5-1.0) 5 mL liquid cultures of homozygous diploid RM11a/α and YJM975a/α strains (in the media conditions indicated) were harvested in biological triplicate
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA extraction, mRNA isolation by polyA enrichment were performed at the Beijing Genomics Institute
cDNA library preparation was performed at the Beijing Genomics Institute
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
BGISEQ-500 |
| |
|
| Description |
YJM975SD3
V100006883_L*_HK500YEAoyiEAAFRBAPEI-507
|
| Data processing |
Trimming and quality filtering were performed at the Beijing Genomics Institute
Pseudo-alignment and estimated of normalized abundance was performed using kallisto [kallisto quant -t yeastIndex.idx -o sampleName -b 100 library1_1.fastq.gz library1_2.fastq.gz library2_1.fastq.gz library2_2.fastq.gz]
TPM estimates from kallisto are collated in the processed data file tpmOutput.csv
Genome_build: S. cerevisiae cDNA from Ensembl
Supplementary_files_format_and_content: .csv; columns represent biological replicates as indicated in headers
|
| |
|
| Submission date |
Dec 12, 2018 |
| Last update date |
Dec 14, 2018 |
| 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 |
GPL25927 |
| Series (1) |
| GSE123702 |
Molecular basis of complex heritability in natural genotype-to-phenotype relationships |
|
| Relations |
| BioSample |
SAMN10585485 |
| SRA |
SRX5126542 |
