|
| Status |
Public on Jul 22, 2020 |
| Title |
mDrop-seq: Massively parallel single-cell RNA-seq of Saccharomyces Cerevisiae and Candida Albicans |
| Organisms |
Saccharomyces cerevisiae; Candida albicans |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
We present microbial Drop-seq or mDrop-seq, a high-throughput scRNA-seq technique that is used on two yeast species, Saccharomyces cerevisiae, a popular model organism and Candida albicans, a common opportunistic pathogen. We benchmarked mDrop-seq for sensitivity and specificity and used it to profile 35,109 S. cerevisiae cells to detect variation in mRNA levels between them. As a proof of concept, we quantified expression differences in heat-shocked S. cerevisiae using mDrop-seq. We detected differential activation of stress response genes within a seemingly homogenous population of S. cerevisiae under heat-shock. We also applied mDrop-seq to C. albicans cells, a polymorphic and clinically relevant yeast species with thicker cell wall compared to S. cerevisiae. Single cell transcriptomes in 39,705 C. albicans cells was characterized using mDrop-seq under different conditions, including exposure to fluconazole, a common anti-fungal drug.
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| |
|
| Overall design |
scRNA-seq data of S. cerevisiae with and without heat shock treatment and C. albicans with and without fluconazole treatment.
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| |
|
| Contributor(s) |
Dohn R, Back R, Selewa A, Eckart H, Basu A |
| Citation(s) |
35062691 |
| |
| Submission date |
Jul 15, 2020 |
| Last update date |
Apr 07, 2022 |
| Contact name |
Ryan Patrick Dohn |
| E-mail(s) |
dohnr@uchicago.edu
|
| Phone |
8479618001
|
| Organization name |
University of Chicago
|
| Department |
Department of Medicine
|
| Lab |
Basu
|
| Street address |
5841 S. Maryland Ave.
|
| City |
Chicago |
| State/province |
IL |
| ZIP/Postal code |
60637 |
| Country |
USA |
| |
|
| Platforms (3) |
| GPL19756 |
Illumina NextSeq 500 (Saccharomyces cerevisiae) |
| GPL22403 |
Illumina NextSeq 500 (Candida albicans) |
| GPL28878 |
Illumina NextSeq 500 (Candida albicans; Saccharomyces cerevisiae) |
|
| Samples (23)
|
| GSM4672371 |
S. cerevisiae cells - 15 minute Lysis - rep 1 |
| GSM4672372 |
S. cerevisiae cells - 20 minute Lysis - rep 1 |
| GSM4672373 |
S. cerevisiae cells - 15 minute Lysis - rep 2 |
| GSM4672374 |
S. cerevisiae cells - 20 minute Lysis - rep 2 |
| GSM4672375 |
S. cerevisiae cells - Heat Shock - rep 1 |
| GSM4672376 |
S. cerevisiae cells - Heat Shock - rep 2 |
| GSM4672377 |
C. albicans cells - 15 minute lysis |
| GSM4672378 |
C. albicans cells - 20 minute lysis - rep 1 |
| GSM4672379 |
C. albicans cells - 25 minute lysis - rep 1 |
| GSM4672380 |
Species Mixing - 350 cells/ul - SC_CA |
| GSM4672381 |
Species Mixing - 700 cells/ul - SC |
| GSM4672382 |
S. cerevisiae Aligned to C. albicans Genome |
| GSM4672383 |
C. albicans Aligned to S. cerevisiae Genome |
| GSM4672384 |
S. cerevisiae Bulk RNA |
| GSM4672385 |
C. albicans Bulk RNA |
| GSM5379905 |
C. albicans cells - 15 minute Lysis - rep 2 |
| GSM5379906 |
C. albicans cells - 20 minute Lysis - rep 2 |
| GSM5379907 |
C. albicans cells - Fluconazole Control - rep 1 |
| GSM5379908 |
C. albicans cells - Fluconazole 1.5 Hour - rep 1 |
| GSM5379909 |
C. albicans cells - Fluconazole 3 Hour - rep 1 |
| GSM5379910 |
C. albicans cells - Fluconazole Control - rep 2 |
| GSM5379911 |
C. albicans cells - Fluconazole 1.5 Hour - rep 2 |
| GSM5379912 |
C. albicans cells - Fluconazole 3 Hour - rep 2 |
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| Relations |
| BioProject |
PRJNA646515 |
| SRA |
SRP272127 |
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