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Series GSE163866 Query DataSets for GSE163866
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.
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.
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
Platforms (11)
GPL13821 Illumina HiSeq 2000 (Saccharomyces cerevisiae)
GPL13988 Illumina HiSeq 2000 (Schizosaccharomyces pombe)
GPL15645 Illumina HiSeq 2000 (Candida albicans)
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
BioProject PRJNA687774
SRA SRP299482

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Supplementary file Size Download File type/resource
GSE163866_All_yeast_logPhase_dUTP_RNASeq_RPKM.txt.gz 168.0 Kb (ftp)(http) TXT
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Raw data are available in SRA
Processed data are available on Series record

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