|
| Status |
Public on Dec 23, 2021 |
| Title |
The evolution, evolvability, and engineering of gene regulatory DNA [RNA-seq] |
| Organisms |
Schizosaccharomyces pombe; Schizosaccharomyces japonicus; Schizosaccharomyces octosporus; Lachancea waltii; Saccharomyces bayanus; Saccharomyces cerevisiae; Yarrowia lipolytica; Candida albicans; Nakaseomyces glabratus; Naumovozyma castellii; Kluyveromyces lactis |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
Here, we used RNA-seq to quantify expression conservation across many Ascomycete yeasts.
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| |
|
| Overall design |
We used strand-specific RNA-seq (dUTP) to quantify mRNA expression in each species. There was one replicate per species, and all species were grown in BMW media to log phase. With the exception of N. castellii (25C), all others were grown at 30C. Expression conservation was calculated using the RPKM for each species using orthologous genes.
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| |
|
| Contributor(s) |
Fan L, Adiconis X, Levin JZ, Vaishnav E, Yassour M, de Boer CG |
| Citation(s) |
35264797 |
| Submission date |
Dec 24, 2020 |
| Last update date |
Mar 18, 2022 |
| Contact name |
Carl G de Boer |
| Organization name |
The Broad Institute
|
| Lab |
Aviv Regev
|
| Street address |
415 Main St
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02139 |
| Country |
USA |
| |
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| Platforms (11)
|
| GPL13821 |
Illumina HiSeq 2000 (Saccharomyces cerevisiae) |
| GPL13988 |
Illumina HiSeq 2000 (Schizosaccharomyces pombe) |
| GPL15645 |
Illumina HiSeq 2000 (Candida albicans) |
| GPL17209 |
Illumina HiSeq 2000 (Yarrowia lipolytica) |
| GPL21165 |
Illumina HiSeq 2000 (Naumovozyma castellii) |
| GPL22158 |
Illumina HiSeq 2000 (Kluyveromyces lactis) |
| GPL22622 |
Illumina HiSeq 2000 ([Candida] glabrata) |
| GPL29533 |
Illumina HiSeq 2000 (Lachancea waltii) |
| GPL29534 |
Illumina HiSeq 2000 (Saccharomyces bayanus) |
| GPL29535 |
Illumina HiSeq 2000 (Schizosaccharomyces japonicus) |
| GPL29536 |
Illumina HiSeq 2000 (Schizosaccharomyces octosporus) |
|
| Samples (11)
|
| GSM4988913 |
dUTP strand-specific RNA-seq log-phase cells of Candida albicans grown in BMW |
| GSM4988914 |
dUTP strand-specific RNA-seq log-phase cells of Candida glabrata grown in BMW |
| GSM4988915 |
dUTP strand-specific RNA-seq log-phase cells of Kluyveromyces lactis grown in BMW |
| GSM4988916 |
dUTP strand-specific RNA-seq log-phase cells of Kluyveromyces waltii grown in BMW |
| GSM4988917 |
dUTP strand-specific RNA-seq log-phase cells of Saccharomyces bayanus grown in BMW |
| GSM4988918 |
dUTP strand-specific RNA-seq log-phase cells of Naumovozyma castellii grown in BMW |
| GSM4988919 |
dUTP strand-specific RNA-seq log-phase cells of Saccharomyces cerevisiae grown in BMW |
| GSM4988920 |
dUTP strand-specific RNA-seq log-phase cells of Schizosaccharomyces japonicus grown in BMW |
| GSM4988921 |
dUTP strand-specific RNA-seq log-phase cells of Schizosaccharomyces octosporus grown in BMW |
| GSM4988922 |
dUTP strand-specific RNA-seq log-phase cells of Schizosaccharomyces pombe grown in BMW |
| GSM4988923 |
dUTP strand-specific RNA-seq log-phase cells of Yarrowia lipolytica grown in BMW |
|
| Relations |
| BioProject |
PRJNA687774 |
| SRA |
SRP299482 |
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