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| Status |
Public on Jul 01, 2017 |
| Title |
YJM145 |
| Sample type |
SRA |
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| Source name |
YJM145
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| Organism |
Saccharomyces cerevisiae |
| Characteristics |
location isolated: USA
source: Lung of an AIDS patient
ecological environment: Clinical
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| Growth protocol |
Each of the nine yeast strains was streaked to form single colonies from frozen glycerol stocks held at -80°C onto YPD plates (1% yeast extract, 2% peptone, 2% glucose, 2% agar). After 48 hours of growth at 30°C, a single colony was picked and inoculated into 5 ml of the synthetic oak exudate medium (1% sucrose, 0.5% fructose, 0.5% glucose, 0.1% yeast extract, and 0.15% peptone). Strains were grown for 24 hours at 30°C before dilution into fresh synthetic oak exudate medium to an OD660 of 0.1. Cultures were grown at 30°C until OD660 = 0.5 (mid-log phase), at which point cells were harvested by centrifugation.
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Extraction of mRNA was carried out using MicroPoly(A)Purist Kit (Ambion) and 200 ng of the resulting mRNA sample was fragmented (Fragmentation Buffer, NEB) before ethanol precipitation.
First strand cDNA synthesis was performed using random hexamer priming (Superscript II, Invitrogen), followed by second strand cDNA synthesis (Invitrogen) as recommended by the manufacturer. End repair, A-tailing, and ligation of the Illumina adapters necessary for sequencing were then carried out using the NEBnext mRNA sample preparation kit (NEB). Libraries were then size-selected by agarose gel electrophoresis followed by gel extraction such that libraries consisted of fragments containing inserts of approximately 250 bp in length. Polymerase-chain-reaction amplification was performed for 15 cycles using NEBnext mRNA sample preparation kit
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer II |
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| Data processing |
All raw read sequences generated by RNA-seq were first processed by cutadapt to trim any remaining adaptor sequences
The trimmed reads were then aligned to the genome of the corresponding strains by tophat under the default parameter set except that a maximal intron size of 10 kb was allowed because the largest annotated intron in S. cerevisiae is 9349 bp
Alignment results were fed to cufflinks for quantification of known transcripts in S. cerevisiae, S. paradoxus, and S. mikatae.
Some ORFs are further filtered when they have no reliable one-to-one orthologs between the three species, giving rise to a final list of expression level for 4325 ORFs in the 9 species
Genome_build: S.cerevisiae (SGD R64.1.1), S. paradoxus and S.mikatae from [Scannell DR, et al. (2011) The Awesome Power of Yeast Evolutionary Genetics: New Genome Sequences and Strain Resources for the Saccharomyces sensu stricto Genus. G3 (Bethesda) 1:11-25.]
Supplementary_files_format_and_content: Tab-delimited text files. Containing ORF names (represented by the S.cerevisiae ORF ID) and expression level (RPKM) in each strain.
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| Submission date |
May 11, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Jian-Rong Yang |
| Organization name |
Sun Yat-sen University
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| Street address |
No. 74, Zhongshan 2nd Road
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| City |
Guangzhou |
| ZIP/Postal code |
510080 |
| Country |
China |
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| Platform ID |
GPL9377 |
| Series (1) |
| GSE81320 |
Intra- and inter-specific variations of gene expression levels in yeast are largely neutral |
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| Relations |
| BioSample |
SAMN04961137 |
| SRA |
SRX1746461 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2150328_YJM145.txt.gz |
39.8 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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