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Sample GSM3509857 Query DataSets for GSM3509857
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
 
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
 
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

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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