|
Status |
Public on Dec 13, 2018 |
Title |
RM-SD-1 |
Sample type |
SRA |
|
|
Source name |
RM11_S-CSM with 2% glucose
|
Organism |
Saccharomyces cerevisiae |
Characteristics |
strain: RM11 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
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|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
BGISEQ-500 |
|
|
Description |
RM11SD1 V100006883_L*_HK500YEAoyiEAAGRBAPEI-508
|
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
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|
|
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 |
SAMN10585501 |
SRA |
SRX5126537 |