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Series GSE154515 Query DataSets for GSE154515
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.
Overall design scRNA-seq data of S. cerevisiae with and without heat shock treatment and C. albicans with and without fluconazole treatment.
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
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
BioProject PRJNA646515
SRA SRP272127

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Supplementary file Size Download File type/resource
GSE154515_RAW.tar 150.4 Mb (http)(custom) TAR (of TAR, TXT)
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Raw data are available in SRA
Processed data provided as supplementary file

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