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| Status |
Public on Oct 31, 2017 |
| Title |
Transcriptomic comparison of aerial and root cells of a wild yeast biofilm colony |
| Organism |
Saccharomyces cerevisiae |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Wild yeast and many clinical strains form complex, biofilm colonies, providing protection from desiccation, drugs and other stresses. Few transcriptomic studies have focused on sub-surface invasive “roots” due to the challenges of cell isolation from agar and subpopulation cross-contamination. Here we present, a first transcriptomic analysis via RNA sequencing of root and aerial cells, separated by a novel method. We identified 719 coding genes with upregulated root expression, mainly involved in ribosome structure/biogenesis, biosynthesis and translation and 529 loci/genes with upregulated aerial expression, mainly involved in meiosis/sporulation, stress defense and protein degradation; all indicating that aerial cells are resting and root cells are metabolically active cells. On the basis of 172 root-upregulated and 233 aerial-upregulated non-coding loci detected, anti-regulated gene/lncRNA pairs have been identified that may contribute to negative regulation of gene expression. Importantly, cells showing typical markers of “roots” correspond with cells embedded in extracellular matrix and cells showing typical markers of “aerial” parts with ECM-free cells.
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| Overall design |
Identification of differences in gene expression and potential regulation by lncRNA between aerial and root cell subpopulations of differentiated yeast biofilm colonies
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| Contributor(s) |
Marsikova J, Wilkinson D, Hlavacek O, Gilfillan G, Mizeranschi A, Hughes T, Begany M, Resetarova S, Vachova L, Palkova Z |
| Citation(s) |
29061122 |
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| Submission date |
Apr 26, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Derek Wilkinson |
| E-mail(s) |
wilkinsd@natur.cuni.cz
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| Organization name |
Charles University
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| Department |
Genetics and Microbiology
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| Lab |
Yeast Colony Group, Biocev
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| Street address |
Prumyslova 595
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| City |
Vestec |
| ZIP/Postal code |
252 42 |
| Country |
Czech Republic |
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| Platforms (1) |
| GPL17342 |
Illumina HiSeq 2500 (Saccharomyces cerevisiae) |
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| Samples (6)
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| Relations |
| BioProject |
PRJNA384376 |
| SRA |
SRP105277 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE98243_BRF_Aerial_Root_ReadCounts.txt.gz |
126.8 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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